Sensory Systems

Sensory Systems
Physiology & Computer Simulations
Contents
1
Introduction
1.1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.1.1
Keep it simple: Unicellular Creatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.1.2
Not so simple: Three-hundred-and-two Neurons . . . . . . . . . . . . . . . . . . . . . . .
1.1.3
General principles of Sensory Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.1.4
Transduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.1.5
Neurons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.1.6
Principles of Information Processing in the Nervous System . . . . . . . . . . . . . . . . .
1.2
NeuralSimulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.3
Simulating Action Potentials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.3.1
Action Potential
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.3.2
Cell Membrane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.3.3
Hodgkin Huxley equation
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.3.4
Modeling the Action Potential Generation: The Fitzhugh-Nagumo model . . . . . . . . . .
1.4
Simulating a Single Neuron with Positive Feedback
. . . . . . . . . . . . . . . . . . . . . . . . .
1.5
Simulating a Simple Neural System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.6
The Development and Theory of Neuromorphic Circuits . . . . . . . . . . . . . . . . . . . . . . .
1.6.1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.6.2
Current Events in Neuromorphic Engineering . . . . . . . . . . . . . . . . . . . . . . . .
1.6.3
Transistor Structure & Physics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.6.4
Basic static circuits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
10
1.6.5
Silicon neurons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11
1.6.6
Silicon Synapses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
12
The NEURON simulation environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
15
1.7.1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
15
1.7.2
Model creation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
16
1.7.3
Neuron with Python . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
17
1.7.4
Tutorials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
18
1.7.5
Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
18
1.7
1.8
2
References
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
18
Sensory Systems in Humans
20
2.1
20
Auditory System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
i
ii
CONTENTS
2.2
2.3
2.4
2.5
2.6
2.1.1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
20
2.1.2
Anatomy of the Auditory System
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
20
2.1.3
Auditory Signal Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
23
Visual System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
27
2.2.1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
27
2.2.2
Anatomy of the Visual System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
29
2.2.3
Signal Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
33
Vestibular System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
50
2.3.1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
50
2.3.2
Anatomy of the Vestibular System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
51
2.3.3
53
2.3.4
Alcohol and the Vestibular System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
55
Somatosensory System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
56
2.4.1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
56
2.4.2
Anatomy of the Somatosensory System . . . . . . . . . . . . . . . . . . . . . . . . . . . .
56
2.4.3
Proprioceptive Signal Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
58
Olfactory System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
58
2.5.1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
58
2.5.2
Sensory Organs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
59
2.5.3
Sensory Organ Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
59
2.5.4
60
2.5.5
60
2.5.6
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
61
Gustatory System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
61
2.6.1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
61
2.6.2
Sensory Organs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
62
2.6.3
Transduction of Taste . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
63
2.6.4
64
2.6.5
Taste and Other Senses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
64
2.6.6
Taste disorders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
64
Sensory Systems in Non-Primates
65
3.1
NonPrimates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
65
3.1.1
Zebra Finches: Neural Mechanism for Song Learning . . . . . . . . . . . . . . . . . . . .
65
3.1.2
Octopus
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
68
3.1.3
Fish . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
71
3.1.4
Flies
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
72
3.1.5
Butteries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
74
3.1.6
Johnstons organ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
74
3.1.7
Spiders Visual System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
78
3.1.8
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
84
CONTENTS
iii
Appendix
86
4.1
Authors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
86
4.2
Sources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
86
4.3
Appendix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
87
4.3.1
Spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
87
4.3.2
Colour Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
87
4.3.3
History of Sensory Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
87
Text and image sources, contributors, and licenses
89
5.1
Text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
89
5.2
Images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
89
5.3
Content license . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
94
Chapter 1
Introduction
1.1 Introduction
In order to survive - at least on the species level - we continually need to make decisions:
Should I cross the road?"
Should I run away from the creature in front of
me?"
Should I eat the thing in front of me?"
Or should I try to mate it?"
Physarum polycephalum (left)
To help us to make the right decision, and make that decision quickly, we have developed an elaborate system:
a sensory system to notice whats going on around us;
and a nervous system to handle all that information. And
this system is big. VERY big! Our nervous system contains about 1011 nerve cells (or neurons), and about 10-50
times as many supporting cells. These supporting cells,
called gliacells, include oligodendrocytes, Schwann cells,
and astrocytes. But do we really need all these cells?
And such unicellular organisms can be amazingly smart:

the plasmodium of the slime mould Physarum polycephalum is a large amoebalike cell consisting of a dendritic network of tube-like structures. This single cell
creature manages to connect sources nding the shortest
connections (Nakagaki et al. 2000), and can even build
ecient, robust and optimized network structures that resemble the Tokyo underground system (Tero et al. 2010).
In addition, it has somehow developed the ability to read
1.1.1 Keep it simple: Unicellular Crea- its tracks and tell if its been in a place before or not: this
tures
way it can save energy and not forage through locations
where eort has already been put (Reid et al. 2012).
The answer is: No!", we do not REALLY need that
On the one hand, the approach used by the paramecium
many cells in order to survive. Creatures existing of a
cannot be too bad, as they have been around for a long
single cell can be large, can respond to multiple stimuli,
time. On the other hand, a single cell mechanism cannot
and can also be remarkably smart!
be as exible and as accurate in its responses as a more reWe often think of cells as really small things. But Xeno- ned version of creatures, which use a dedicated, specialphyophores (see image) are unicellular organisms that are ized system just for the registration of the environment:
found throughout the worlds oceans and can get as large a Sensory System.
as 20 centimetres in diameter.
And even with this single cell, those organisms can respond to a number of stimuli. For example look at a
creature from the group Paramecium: the paramecium is
a group of unicellular ciliate protozoa formerly known as
slipper animalcules, from their slipper shape. (The corresponding word in German is Pantoeltierchen.) Despite the fact that these creatures consist of only one cell,
they are able to respond to dierent environmental stimuli, e.g. to light or to touch.
1.1.2 Not so simple: Three-hundred-andtwo Neurons

While humans have hundreds of millions of sensory nerve
cells, and about 1011 nerve cells, other creatures get away
with signicantly less. A famous one is Caenorhabditis
elegans, a nematode with a total of 302 neurons.
1
CHAPTER 1. INTRODUCTION
1.1.4 Transduction
The role of our senses is to transduce relevant information from the world surrounding us into a type of signal
that is understood by the next cells receiving that signal:
the Nervous System. (The sensory system is often regarded as part of the nervous system. Here I will try to
C. elegans is one of the simplest organisms with a ner- keep these two apart, with the expression Sensory System
vous system, and it was the rst multicellular organism to referring to the stimulus transduction, and the Nervous
have its genome completely sequenced. (The sequence System referring to the subsequent signal processing.)
was published in 1998.) And not only do we know its
complete genome, we also know the connectivity be- Note here that only relevant information is to be transtween all 302 of its neurons. In fact, the developmen- duced by the sensory system! The task of our senses
tal fate of every single somatic cell (959 in the adult is NOT to show us everything that is happening around
hermaphrodite; 1031 in the adult male) has been mapped us. Instead, their task is to lter out the important bits
out. We know, for example, that only 2 of the 302 neu- of the signals around us: electromagnetic signals, chemrons are responsible for chemotaxis (movement guided ical signals, and mechanical ones. Our Sensory Systems
by chemical cues, i.e. essentially smelling). Neverthe- transduce those environmental variables that are (probaless, there is still a lot of research conducted also on its bly) important to us. And the Nervous System propagates
smelling - in order to understand how its nervous system them in such a way that the responses that we take help
us to survive, and to pass on our genes.
works!
1.1.3
General principles of Sensory Systems
Based on the example of the visual system, the general

principle underlying our neuro-sensory system can be described as below:
690
Types of sensory transducers

1. Mechanical receptors
Balance system (vestibular system)
Hearing (auditory system)
Pressure:
Fast adaptation (Meissners corpuscle,
Pacinian corpuscle) ? movement
Slow adaptation (Merkel disks, Runi
endings) ? shape Comment: these signals
are transferred fast
Muscle spindles
All sensory systems are based on

a Signal, i.e. a physical stimulus, provides information about our surrounding.
the Collection of this signal, e.g. by using an ear or
the lens of an eye.
the Transduction of this stimulus into a nerve signal.
Golgi organs: in the tendons

Joint-receptors
2. Chemical receptors
Smell (olfactory system)
Taste
the Processing of this information by our nervous

system.
3. Light-receptors (visual system): here we have

light-dark receptors (rods), and three dierent color
receptors (cones)
And the generation of a resulting Action.
4. Thermo-receptors
While the underlying physiology restricts the maximum

frequency of our nerve-cells to about 1 kHz, more than
one-million times slower than modern computers, our
nervous system still manages to perform stunningly difcult tasks with apparent ease. The trick: there are lots
of nerve cells (about 1011 ), and they are massively connected (one nerve cell can have up to 150'000 connections
with other nerve cells).
Heat-sensors (maximum sensitivity at ~ 45C,

signal temperatures < 50C)
Cold-sensors (maximum sensitivity at ~ 25C,
signal temperatures > 5C)
Comment: The information processing of
these signals is similar to those of visual color
signals, and is based on dierential activity of
the two sensors; these signals are slow
1.1. INTRODUCTION
5. Electro-receptors: for example in the bill of the

platypus
6. Magneto-receptors
7. Pain receptors (nocioceptors): pain receptors are
also responsible for itching; these signals are passed
on slowly.
1.1.5
Neurons
Now what distinguishes neurons from other cells in the

human body, like liver cells or fat cells? Neurons are
unique, in that they:
can switch quickly between two states (which can
also be done by muscle cells).
A conductile stage, the axon: once the cell body

has decided to send out a signal, an action potential
propagates along the axon, away from the cell body.
An action potential is a quick change in the state of a
neuron, which lasts for about 1 msec. Note that this
denes a clear direction in the signal propagation,
from the cell body, to the:
output Stage: The output is provided by synapses,
i.e. the points where a neuron contacts the next neuron down the line, most often by the emission of
neurotransmitters (i.e. chemicals that aect other
neurons) which then provide an input to the next
neuron.
1.1.6 Principles of Information Processing

in the Nervous System
That they can propagate this change into a specied Parallel processing
direction and over longer distances (which cannot
An important principle in the processing of neural signals
also be done by muscle cells).
is parallelism. Signals from dierent locations have dif And that this state-change can be signalled eec- ferent meaning. This feature, sometimes also referred to
as line labeling, is used by the
tively to other connected neurons.
While there are more than 50 distinctly dierent types of
neurons, they all share the same structure:
a
h
Olfactory system - to signal sweet or sour

Visual system - to signal the location of a visual signal
Vestibular system - to signal dierent orientations
and movements
Auditory system - to signal frequency
Population Coding
f
d
e
c
a) Dendrites, b) Soma, c) Nucleus, d) Axon hillock, e) Sheathed

Axon, f) Myelin Cell, g) Node of Ranvier, h) Synapse
Sensory information is rarely based on the signal nerve.

It is typically coded by dierent patterns of activity in a
population of neurons. This principle can be found in all
our sensory systems.
Learning
An input stage, often called dendrites, as the inputarea often spreads out like the branches of a tree. Input can come from sensory cells or from other neurons; it can come from a single cell (e.g. a bipolar
cell in the retina receives input from a single cone),
or from up to 150000 other neurons (e.g. Purkinje
cells in the Cerebellum); and it can be positive (excitatory) or negative (inhibitory).
An integrative stage: the cell body does the household chores (generating the energy, cleaning up,
generating the required chemical substances, etc),
combines the incoming signals, and determines
when to pass a signal on down the line.
The structure of the connections between nerve cells is

not static. Instead it can be modied, to incorporate experiences that we have made. Thereby nature walks a thin
line:
- If we learn too slowly, we might not make it. One example is the Passenger Pidgeon, an American bird which
is extinct by now. In the last century (and the one before),
this bird was shot in large numbers. The mistake of the
bird was: when some of them were shot, the others turned
around, maybe to see whats up. So they were shot in turn
- until the birds were essentially gone. The lesson: if you
learn too slowly (i.e. to run away when all your mates are
killed), your species might not make it.
Vision
Hearing
Balance
Feeling
Smell
Taste
Technological Aspects
Implants
Models
In Animals
Insects & Spiders
Birds,Fish,...
1.3 Simulating Action Potentials

1.3.1 Action Potential
Passenger Pidgeon
The action potential is the stereotypical voltage change

that is used to propagate signals in the nervous system.
Action
potential
ation
Dep
Failed
initiations
Threshold
-70
Stimulus
1.2 NeuralSimulation
Sensory Systems
Resting state
Refractory
period
Female Monarch buttery
- On the other hand, we must not learn too fast, either.

For example, the monarch buttery migrates. But it takes
them so long to get from start to nish, that the migration cannot be done by one buttery alone. In other
words, no single buttery makes the whole journey. Nevertheless, the genetic disposition still tells the butteries
where to go, and when they are there. If they would learn
any faster - they could never store the necessary information in their genes. In contrast to other cells in the human
body, nerve cells are not re-generated in the human body.
tion
-55
olariz
za
Repolari
Voltage (mV)
+40
2
3
Time (ms)
Action potential Time dependence
With the mechanisms described below, an incoming

stimulus (of any sort) can lead to a change in the voltage
potential of a nerve cell. Up to a certain threshold, thats
all there is to it (Failed initiations in Fig. 4). But when
the Threshold of voltage-gated ion channels is reached,
it comes to a feed-back reaction that almost immediately completely opens the Na+-ion channels (Depolarization below): This reaches a point where the permeability for Na+ (which is in the resting state is about 1%
of the permeability of K+) is 20\*larger than that of K+.
Together, the voltage rises from about 60mV to about
+50mV. At that point internal reactions start to close (and
1.3. SIMULATING ACTION POTENTIALS

block) the Na+ channels, and open the K+ channels to restore the equilibrium state. During this Refractory period of about 1 m, no depolarization can elicit an action
potential. Only when the resting state is reached can new
action potentials be triggered.
EX =
58mV
z
log
[X]o
[X]i
With typical K+ concentration inside and outside of neurons, this yields EK+ = 75mV . If the ion channels
for K+, Na+ and Cl- are considered simultaneously, the
equilibrium situation is characterized by the GoldmanTo simulate an action potential, we rst have to dene equation
the dierent elements of the cell membrane, and how to
PK [K + ]o +PN a [N a+ ]o +PCl [Cl]i
Vm = RT
describe them analytically.
F ln PK [K + ] +PN a [N a+ ] +PCl [Cl]
i
where Pi denotes the permeability of Ion i, and I the

concentration. Using typical ion concentration, the cell
1.3.2 Cell Membrane
has in its resting state a negative polarity of about 60
The cell membrane is made up by a water-repelling, al- mV.
most impermeable double-layer of proteins, the cell membrane. The real power in processing signals does not Activation of Ion Channels
come from the cell membrane, but from ion channels that
are embedded into that membrane. Ion channels are pro- The nifty feature of the ion channels is the fact that their
teins which are embedded into the cell membrane, and permeability can be changed by
which can selectively be opened for certain types of ions.
(This selectivity is achieved by the geometrical arrange A mechanical stimulus (mechanically activated ion
ment of the amino acids which make up the ion channels.)
channels)
In addition to the Na+ and K+ ions mentioned above,
ions that are typically found in the nervous system are
A chemical stimulus (ligand activated ion channels)
the cations Ca2+, Mg2+, and the anions Cl- .
Or an by an external voltage (voltage gated ion channels)
States of ion channels
Ion channels can take on one of three states:
Open (For example, an open Na-channel lets Na+
ions pass, but blocks all other types of ions).
Closed, with the option to open up.
Closed, unconditionally.
Resting state
The typical default situation when nothing is happening - is characterized by K+ that are open, and the other
channels closed. In that case two forces determine the
cell voltage:
The (chemical) concentration dierence between
the intra-cellular and extra-cellular concentration of
K+, which is created by the continuous activity of
the ion pumps described above.
Occasionally ion channels directly connect two cells,

in which case they are called gap junction channels.
Important
Sensory systems are essentially based ion channels,
which are activated by a mechanical stimulus (pressure, sound, movement), a chemical stimulus (taste,
smell), or an electromagnetic stimulus (light), and
produce a neural signal, i.e. a voltage change in a
nerve cell.
Action potentials use voltage gated ion channels, to
change the state of the neuron quickly and reliably.
The communication between nerve cells predominantly uses ion channels that are activated by neurotransmitters, i.e. chemicals emitted at a synapse by
the preceding neuron. This provides the maximum
exibility in the processing of neural signals.
The (electrical) voltage dierence between the inModeling a voltage dependent ion channel Ohms
side and outside of the cell.
law relates the resistance of a resistor, R, to the current it
passes, I, and the voltage drop across the resistor, V:
The equilibrium is dened by the Nernst-equation:
V = IR
[X]o
EX = RT
zF ln [X]i
or
R ... gas-constant, T ... temperature, z ... ion-valence, F
... Faraday constant, [X]o/i ion concentration outside/ I = gV
inside. At 25 C, RT/F is 25 mV, which leads to a resting where g = 1/R is the conductance of the resistor. If you
now suppose that the conductance is directly proportional
voltage of
to the probability that the channel is in the open conformation, then this equation becomes
I = gmax n V
where gmax is the maximum conductance of the cannel,
and n is the probability that the channel is in the open
conformation.
Example: the K-channel
Voltage gated potassium channels (Kv) can be only open
or closed. Let be the rate the channel goes from closed
to open, and the rate the channel goes from open to
closed
(Kv )closed (Kv )open
Since n is the probability that the channel is open, the

probability that the channel is closed has to be (1-n), since
all channels are either open or closed. Changes in the
conformation of the channel can therefore be described
by the formula
dn
dt
= (1 n) n = ( + )n
The nal equations in the original Hodgkin-Huxley

Note that and are voltage dependent! With a tech- model, where the currents in of chloride ions and other
nique called voltage-clamping, Hodgkin and Huxley leakage currents were combined, were as follows:
determine these rates in 1952, and they came up with
3
4
Cm dV
dt = GN a m h(EN a V ) + GK n (EK V ) +
something like
Gm (Vrest V ) + Iinj (t)
( 0.01(V)+10)
(V ) =
V + 10
exp
1
10
( )
V
(V ) = 0.125 exp
80
If you only want to model a voltage-dependent potassium
channel, these would be the equations to start from. (For
voltage gated Na channels, the equations are a bit more
dicult, since those channels have three possible conformations: open, closed, and inactive.)
Spiking behavior of a Hodgkin-Huxley model.
where m, h, and n are time- and voltage dependent functions which describe the membrane-permeability. For
example, for the K channels n obeys the equations described above, which were determined experimentally
with voltage-clamping. These equations describe the
1.3.3 Hodgkin Huxley equation
shape and propagation of the action potential with high
accuracy! The model can be solved easily with open
source tools, e.g. the Python Dynamical Systems ToolPyDSTools. A simple solution le is available under
The feedback-loop of voltage-gated ion channels men- box
[1]
,
and
the output is shown below.
tioned above made it dicult to determine their exact
behaviour. In a rst approximation, the shape of the action potential can be explained by analyzing the electrical Links to full Hodgkin-Huxley model
circuit of a single axonal compartment of a neuron, con http://itb.biologie.hu-berlin.de/~{}stemmler/sec1.
sisting of the following components: 1) membrane capachtml#SECTION00020000000000000000
itance, 2) Na channel, 3) K channel, 4) leakage current:
1.4. SIMULATING A SINGLE NEURON WITH POSITIVE FEEDBACK

http://www.afodor.net/HHModel.htm
1.3.4
ple neural systems, and gives a good understanding of the

underlying information processing.
Modeling the Action Potential Generation:

The Fitzhugh-Nagumo
model
Let us rst look at the response of a single neuron, with
an input x(t), and with feedback onto itself. The weight
of the input is v, and the weight of the feedback w. The
response y(t) of the neuron is given by
y(t) = wy(t 1) + vx(t 1)
This shows how already very simple simulations can capture signal processing properties of real neurons.
Phaseplane plot of the Fitzhugh-Nagumo model, with (a=0.7,

b=0.8, c=3.0, I=0.4). Solutions for four dierent starting conditions are shown. The dashed lines indicate the nullclines, and
the o the xed point of the model. I=0.2 would be a stimulation below threshold, leading to a stationary state. And I=1.6
would hyperpolarize the neuron, also leading to a - dierent stationary state.
The Hodgkin-Huxley model has four dynamical variables: the voltage V, the probability that the K channel
is open, n(V), the probability that the Na channel is open
given that it was closed previously, m(V), and the probability that the Na channel is open given that it was inactive previously, h(V). A simplied model of action potential generation in neurons is the Fitzhugh-Nagumo (FN)
model. Unlike the Hodgkin-Huxley model, the FN model
has only two dynamic variables, by combining the variables V and m into a single variable v, and combining the
variables n and h into a single variable r
dv
1
= c(v v 3 + r + I)
dt
3
The following two examples
1
dr
= (v a + br)
dt
c
are taken from I is an external current injected into the
neuron. Since the FN model has only two dynamic variables, its full dynamics can be explored using phase plane
methods (Sample solution in Python here [2] )
1.4 Simulating a Single Neuron

with Positive Feedback
The following two examples are taken from [3] . This
book provides a fantastic introduction into modeling sim-
System output for a input pulse: a leaky integrator
# -*- coding: utf-8 -*- import numpy as np import

matplotlib.pylab as plt def oneUnitWithPosFB(): '''Simulates a single model neuron with positive feedback '''
# set input ag (1 for impulse, 2 for step) inFlag = 1
cut = -np.inf # set cut-o sat = np.inf # set saturation
tEnd = 100 # set last time step nTs = tEnd+1 # nd the
number of time steps v = 1 # set the input weight w =
0.95 # set the feedback weight x = np.zeros(nTs) # open
(dene) an input hold vector start = 11 # set a start time
for the input if inFlag == 1: # if the input should be a
pulse x[start] = 1 # then set the input at only one time
point elif inFlag == 2: # if the input instead should be a
step, then x[start:nTs] = np.ones(nTs-start) #keep it up
until the end y = np.zeros(nTs) # open (dene) an output
hold vector for t in range(2, nTs): # at every time step
(skipping the rst) y[t] = w*y[t-1] + v*x[t-1] # compute
the output y[t] = np.max([cut, y[t]]) # impose the cut-o
constraint y[t] = np.min([sat, y[t]]) # mpose the saturation constraint # plot results (no frills) plt.subplot(211)
tBase = np.arange(tEnd+1) plt.plot(tBase, x) plt.axis([0,
tEnd, 0, 1.1]) plt.xlabel('Time Step') plt.ylabel('Input')
plt.subplot(212) plt.plot(tBase, y) plt.xlabel('Time
Step') plt.ylabel('Output') plt.show() if __name__ ==
'__main__': oneUnitWithPosFB()
1.5 Simulating a Simple Neural

System
Even very simple neural systems can display a surprisingly versatile set of behaviors. An example is Wilsons
model of the locust-ight central pattern generator. Here
the system is described by
y (t) = W y (t 1) + v x(t 1)
W is the connection matrix describing the recurrent connections of the neurons, and describes the input to the
system.
Input x connects to units yi (i=1,2,3,4) with weights vi , and units

y_l (l = 1,2,3,4) connect to units y_k (k = 1,2,3,4) with weights
w_kl . For clarity, the self-connections of y2 and y3 are not
shown, and the individual forward and recurrent weights are not
labeled. Based on Tom Anastasios excellent book Tutorial on
Neural Systems Modeling.
w12=0.2; w13 = w14 = 0. # feedback weights to unit
one w21=0.95; w22=0.4; w23=0.5; w24=0 # ... to
unit two w31=0; w32=0.5; w33=0.4; w34=0.95 # ...
to unit three w41 = w42 = 0.; w43=0.2; w44=0.9 # ... to
unit four V=np.array([v1, v2, v3, v4]) # compose input
weight matrix (vector) W=np.array([[w11, w12, w13,
w14], [w21, w22, w23, w24], [w31, w32, w33, w34],
[w41, w42, w43, w44]]) # compose feedback weight
matrix tEnd = 100 # set end time tVec = np.arange(tEnd)
# set time vector nTs = tEnd # nd number of time
steps x = np.zeros(nTs) # zero input vector y = 11
# set time to start ying x[y] = 1 # set input to one
at y time y = np.zeros((4,nTs)) # zero output vector
for t in range(1,nTs): # for each time step y[:,t] =
W.dot(y[:,t-1]) + V*x[t-1]; # compute output # These
calculations are interesting, but not absolutely necessary
(eVal,eVec) = np.linalg.eig(W); # nd eigenvalues and
eigenvectors magEVal = np.abs(eVal) # nd magnitude
of eigenvalues angEVal = np.angle(eVal)*(180/np.pi)
# nd angles of eigenvalues printInfo('Eigenvectors:
--------------', eVec) printInfo('Eigenvalues: --------------', eVal) printInfo('Angle of Eigenvalues: ------',
angEVal) # plot results (units y2 and y3 only) plt.gure()
plt.rcParams['font.size'] = 14 # set the default fontsize
plt.rcParams['lines.linewidth']=1 plt.plot(tVec, x, 'k.', tVec, y[1,:],'k', tVec,y[2,:],'k--', linewidth=2.5)
plt.axis([0, tEnd, 0.6, 1.1]) plt.xlabel('Time
Step',fontsize=14) plt.ylabel('Input and Unit Responses,fontsize=14) plt.legend(('Input','Left Motoneuron','Right Motoneuron')) plt.show() if __name__ ==
'__main__': plt.close('all') WilsonCPG()
1.6 The Development and Theory

of Neuromorphic Circuits
1.6.1 Introduction
The response of units representing motoneurons in the inear version of Wilsons model of the locust-ight central pattern generator (CPG): A simple input pulse elicits a sustained antagonistic
oscillation in neurons 2 and 3.
import numpy as np import matplotlib.pylab as plt def

printInfo(text, value): print(text) print(np.round(value,
2)) def WilsonCPG(): '''implements a linear version of
Wilsons locust ight central pattern generator (CPG) '''
v1 = v3 = v4 = 0. # set input weights v2 = 1. w11=0.9;
Neurmomorphic engineering uses very-large-scaleintegration (VLSI) systems to build analog and digital
circuits, emulating neuro-biological architecture and behavior. Most modern circuitry primarily utilizes digital
circuit components because they are fast, precise, and
insensitive to noise. Unlike more biologically relevant
analog circuits, digital circuits require higher power
supplies and are not capable of parallel computing.
Biological neuron behaviors, such as membrane leakage
and threshold constraints, are functions of material
substrate parameters, and require analog systems to
model and ne tune beyond digital 0/1. This paper will
briey summarize such neuromorphic circuits, and the
theory behind their analog circuit components.
1.6. THE DEVELOPMENT AND THEORY OF NEUROMORPHIC CIRCUITS
1.6.2
Current Events in Neuromorphic source and drain are in a bulk n-well that is in a p-type
substrate; current ows from the source to the drain.
Engineering
Recently, the eld of neuromorphic engineering has experienced a period of rapid growth, receiving widespread
attention from the press and scientic community. In
2013, after drawing the attention of the EU commission,
the Human Brain Project was initiated, funding it 1.2 billion euros over ten years. This project proposes computationally simulating the human brain from the level
of molecules and neurons up through neuronal circuits.
Shortly after this announcement, the U.S. National Insitiute of Health announced the funding of the US\$100
million BRAIN Project, aimed to reconstruct the activity of large populations of neurons. Corporate labs at
Hewlett-Packard and IBM are also investigating in various neuromorphic projects.
When the carriers move due to a concentration gradient,

this is called diusion. If the carriers are swept due to
an electric eld, this is called drift. By convention, the
nFET drain is biased at a higher potential than the source,
whereas the source is biased higher in a pFET.
In a nFET, when a positive voltage is applied to the gate,

positive charge accumulates on the metal contact. This
draws electrons from the bulk to the silicon-oxide interface, creating a negatively charged channel between the
source and the drain. The larger the gate voltage, the
thicker the channel becomes which reduces the internal
resistance, and thus increases the current logarithmically.
For small gate voltages, typically below the threshold voltage, Vth = 0.7V , the channel is not yet fully conducting
and the increase in current from the drain to the source
increases linearly on a logarithmic scale. This regime,
when Vgs < Vth , is called the subthreshold region. Be1.6.3 Transistor Structure & Physics
yond this threshold voltage, Vgs > Vth , the channel is
fully
conducting between the source and drain, and the
Metal-oxide-silicon-eld-eect-transistors (MOSFETs)
are common components of modern integrated circuits. current is in the superthreshold regime.
MOSFETs are classied as unipolar devices because each
transistor utilizes only one carrier type; negative-type
MOFETs (nFETs) have electrons as carriers and positivetype MOSFETs (pFETs) have holes as carriers.
Oxide
Source
Gate
Drain
n+
n+
p L
Body
Cross section of an n-type MOSFET. Transistor showing gate (G),
body (B), source (S), and drain (D). Positive current ows from
the n+ drain well to the n+ source well. Source: Wikipedia
The general MOSFET has a metal gate (G), and two pn

junction diodes known as the source (S) and the drain
(D) as shown in Fig \ref{g: transistor}. There is an insulating oxide layer that separates the gate from the silicon bulk (B). The channel that carries the charge runs
directly below this oxide layer. The current is a function
of the gate dimensions.
The source and the drain are symmetric and dier only
in the biases applied to them. In a nFET device, the
wells that form the source and drain are n-type and sit
in a p-type substrate. The substrate is biased through the
bulk p-type well contact. The positive current ows below the gate in the channel from the drain to the source.
The source is called as such because it is the source of
the electrons. Conversely, in a pFET device, the p-type
Transistor current as a function of Vg for a xed value value of

Vds .
For current to ow from the drain to the source, there

must initially be an electric eld to sweep the carriers
across the channel. The strength of this electric eld is a
function of the applied potential dierence between the
source and the drain ( Vds ), and thus controls the drainsource current. For small values of Vds , the current linearly increases as a function of Vds for constant Vgs values. As Vds increases beyond 100mV , the current saturates.
pFETs behave similarly to nFET except that the carriers
are holes, and the contact biases are negated.
In digital applications, transistors either operate in their
saturation region (on) or are o. This large range in potential dierences between the on and o modes is why
digital circuits have such a high power demand. Contrarily, analog circuits take advantage of the linear region of
transistors to produce a continuous signals with a lower
10
power demand. However, because small changes in gate

or source-drain voltages can create a large change in current, analog systems are prone to noise.
The eld of neuromorphic engineering takes advantage of
the noisy nature of analog circuits to replicate stochastic
neuronal behavior [4] [5] . Unlike clocked digital circuits,
analog circuits are capable of creating action potentials
with temporal dynamics similar to biological time scales
(approx. 10sec ). The potentials are slowed down and
ring rates are controlled by lengthening time constants
through leaking biases and variable resistive transistors.
Analog circuits have been created that are capable of
emulating biological action potentials with varying temporal dynamics, thus allowing silicon circuits to mimic
neuronal spike-based learning behavior [6] . Whereas,
digital circuits can only contain binary synaptic weights
[0,1], analog circuits are capable of maintaining synaptic
weights within a continuous range of values, making analog circuits particularly advantageous for neuromorophic
circuits.
1.6.4
Basic static circuits
With an understanding of how transistors work and how

they are biased, basic static analog circuits can be rationalized through. Afterward, these basic static circuits will
be combined to create neuromorphic circuits. In the following circuit examples, the source, drain, and gate voltages are xed, and the current is the output. In practice, the bias gate voltage is xed to a subthreshold value
( 0 < Vg < 0.7V ), the drain is held in saturation (
Vd > 100mV ), and the source and bulk are tied to
ground ( Vs , Vb = 0V ). All non-idealities are ignored.
Basic static circuits. (A) Diode-connected transistor. (B) Current

mirror. (C) Source follower. (D) Inverter. (E) Current conveyor.
(F) Dierential Pair.
two transistors share a common gate node, M 2 will also

sink the same current. This forces the output transistor
to duplicate the input current. The output will mirror the
input current as long as:
Diode-Connected Transistor
A diode-connected nFET has its gate tied to the drain.
Since the oating drain controls the gate voltage, the
drain-gate voltages will self-regulate so the device will
always sink the input current, Ids . Beyond several microvolts, the transistor will run in saturation. Similarly,
a diode-connected pFET has its gate tied to the source.
Though this simple device seems to merely function as
a short circuit, it is commonly used in analog circuits for
copying and regulating current. Particularly in neuromorphic circuits, they are used to slow current sinks, to increase circuit time constants to biologically plausible time
regimes.
Current Mirror
A current mirror takes advantage of the diode-connected
transistors ability to sink current. When an input current
is forced through the diode connected transistor, M 1 , the
oating drain and gate are regulated to the appropriate
voltage that allows the input current to pass. Since the
1. Vs1 = Vs2
2.
WM 1
LM 1
WM 2
LM 2
The current mirror gain can be controlled by adjusting

these two parameters. When using transistors with different dimensions, otherwise known as a tilted mirror, the
gain is:
Gain =
(W
L )M 2
.
(W
L )M 1
A pFET current mirror is simply a ipped nFET mirror,

where the diode-connected pFET mirrors the input current, and forces the other pFET to source output current.
Current mirrors are commonly used to copy currents
without draining the input current. This is especially essential for feedback loops, such as the one use to accelerate action potentials, and summing input currents at a
synapse.

Source Follower
A source follower consists of an input transistor, M1 ,
stacked on top of a bias transistor, Mb . The xed subthreshold ( < 0.7V ) bias voltage controls the gate Mb ,
forcing it to sink a constant current, Ib . M1 is thus also
forced to sink the same current ( I1 = Ib ) regardless of
what the input voltage, Vin .
A source follower is called so because the output, Vout ,
will follow Vin with a slight oset described by:
11
The current conveyor is often used in place of current

mirrors for large serially repetitious arrays. This is because the current mirror current is controlled through the
gate, whose oxide capacitance will result in a delayed output. Though this lag is negligible for a single output current mirror, long mirroring arrays will accumulative signicant output delays. Such delays would greatly hinder
large parallel processes such as those that try to emulate
biological neural network computational strategies.
Vout = (Vin Vb ), where kappa is the subthreshold Dierential Pair

slope factor, typically less than one.
The dierential pair is a comparative circuit composed
This simple circuit is often used as a buer. Since no cur- of two source followers with a common bias that forces
rent can ow through the gate, this circuit will not draw the current of the weaker input to be silenced. The bias
current from the input, an important trait for low-power transistor will force I to remain constant, tying the comb
circuits. Source followers can also isolate circuits, pro- mon node, V , to a xed voltage. Both input transistors
s
tecting them from power surges or static. A pFET source will want to drain current proportional to their input voltfollower only diers from an nFET source follower in that ages, I and I , respectively. However, since the com1
2
the bias pFET has its bulk tied to Vout .
mon node must remain xed, the drains of the input tranIn neuromorphic circuits, source followers and the like sistors must raise in proportion to the gate voltages. The
are used as simple current integrators which behave like transistor with the lower input voltage will act as a choke
post-synaptic neurons collecting current from many pre- and allow less current through its drain. The losing transistor will see its source voltage increase and thus fall out
synaptic neurons.
of saturation.
The dierential pair, in the setting of a neuronal circuit,
can function as an activation threshold of an ion channel
will not open,
An inverter consists of a pFET, M1 , stacked on top of a below which the voltage-gated ion channel
[8]
preventing
the
neuron
from
spiking
.
nFET, M2 , with their gates tied to the input, Vin and the
output is tied to the common source node, Vout . When
a high signal is input, the pFET is o but the nFET is on, 1.6.5 Silicon neurons
eectively draining the output node, Vout , and inverting
the signal. Contrarily, when the input signal is low, the Winner-Take-All
nFET is o but the pFET is on, charging up the Vout
node.
The Winner-Take-All (WTA) circuit, originally designed
Inverter
This simple circuit is eective as a quick switch. The

inverter is also commonly used as a buer because an
output current can be produced without directly sourcing the input current, as no current is allowed through the
gate. When two inverters are used in series, they can be
used as a non-inverting amplier. This was used in the
original Integrate-and-Fire silicon neuron by Mead et al.,
1989 to create a fast depolarizing spike similar to that of
a biological action potential [7] . However, when the input
uctuates between high and low signals both transistors
are in superthreshold saturation draining current, making
this a very power hungry circuit.
Current Conveyor
The current conveyor is also commonly known as a
buered current mirror. Consisting of two transistors
with their gates tied to a node of the other, the Current
Conveyor self regulates so that the output current matches
the input current, in a manner similar to the Current Mirror.
by Lazzaro et al. [9] , is a continuous time, analog circuit.

It compares the outputs of an array of cells, and only allows the cell with the highest output current to be on, inhibiting all other competing cells.
Each cell comprises a current-controlled conveyor, and
receives input currents, and outputs into a common line
controlling a bias transistor. The cell with the largest input current, will also output the largest current, increasing
the voltage of the common node. This forces the weaker
cells to turn o. The WTA circuit can be extended to include a large network of competing cells. A soft WTA
also has its output current mirrored back to the input, effectively increasing the cell gain. This is necessary to reduce noise and random switching if the cell array has a
small dynamic range.
WTA networks are commonly used as a form of competitive learning in computational neural networks that involve distributed decision making. In particular, WTA
networks have been used to perform low level recognition and classication tasks that more closely resemble
cortical activity during visual selection tasks [10] .
12
Spiking neuron circuit. The amplier consists of two inverting

ampliers that create the characteristic fast upward swing of an
actional potential. The output spike, Vo , is initiated by the input
current, Ii and the width is modulated by Vp . Source: adopted
from Mead et al., 1989
A two-input CMOS winner-take-all circuit
Integrate & Fire Neuron

The most general schematic of an Integrate & Fire Neuron, is also known as an Axon-Hillock Neuron, is the most
commonly used spiking neuron model [7] . Common elements between most Axon-Hillock circuits include: a
node with a memory of the membrane potential Vc , an
amplier, a positive feedback loop Cf , and a mechanism
to reset the membrane potential to its resting state, Vp .
The input current, Ii , charges the Vc , which is stored
in a capacitor, C. This capacitor is analogous to the
lipid cellular membrane which prevents free ionic diusion, creating the membrane potential from the accumulated charge dierence on either side of the lipid membrane. The input is amplied to output a voltage spike.
A change in membrane potential is positively fed back
through Cf to Vc , producing a faster spike. This closely
resembles how a biological axon hillock, which is densely
packed with voltage-gated sodium channels, amplies the
summed potentials to produce an action potential. When
a voltage spike is produced, the reset bias, Vp , begins to
drain the Vc node. This is similar to sodium-potassium
channels which actively pump sodium and potassium ions
against the concentration gradient to maintain the resting
membrane potential.
The original Axon Hillock silicon neuron has been
adapted to include an activation threshold with the addition of a Dierential Pair comparing the input to a set
threshold bias [8] . This conductance-based silicon neuron utilizes dierential-pair integrator (DPI) with a leaky
transistor to compare the input, Iin to the threshold, Vthr
. The leak bias Vtau , refractory period bias Vrf r , adaptation bias Vahp , and positive feed back gain, all inde-
pendently control the spiking frequency. Research has

been focused on implementing spike frequency adaptation to set refractory periods and modulating thresholds
[11]
. Adaptation allows for the neuron to modulate its output ring rate as a function of its input. If there is a constant high frequency input, the neuron will be desensitized
to the input and the output will be steadily diminished
over time. The adaptive component of the conductancebased neuron circuit is modeled through the calcium ux
and stores the memory of past activity through the adaptive capacitor, Cahp . The advent of spike frequency
adaptation allowed for changes on the neuron level to control adaptive learning mechanisms on the synapse level.
This model of neuronal learning is modeled from biology
[12]
and will be further discussed in Silicon Synapses.
1.6.6 Silicon Synapses

The most basic silicon synapse, originally used by Mead
et al.,1989 <refname=mead1989/>, simply consists of a
pFET source follower that receives a low signal pulse input and outputs a unidirectional current, Io [13] .
The amplitude of the spike is controlled by the weight
bias, Vw , and the pulse width is directly correlated with
the input pulse width which is set by $V_{\tau}$. The
capacitor in the Lazzaro et al. (1993) synapse circuit was
added to increase the spike time constant to a biologically
plausible value. This slowed the rate at which the pulse
hyperpolarizes and depolarizes, and is a function of the
capacitance.
For multiple inputs depicting competitive excitatory and
inhibitive behavior, the log-domain integrator uses I1 and
I2 to regulate the output current magnitude, Io , as function of the input current, Ii , according to:
The DPI neuron circuit. (A) Circuit schematic. The input DPI
low-pass lter (yellow, ML1 ML3) models the neurons leak
conductance. A spike event generation amplier (red, MA1
MA6) implements current-based positive feedback (modeling
both sodium activation and inactivation conductances) and produces address-events at extremely low-power. The reset block
(blue, MR1 MR6) resets the neuron and keeps it in a reset
state for a refractory period, set by the Vref bias voltage. An
additional DPI lter integrates the spikes and produces a slow
after hyper-polarizing current Ig responsible for spike-frequency
adaptation (green, MG1 MG6). (B) Response of the DPI neuron circuit to a constant input current. The measured data was
tted with a function comprising an exponential et/K at the
onset of the stimulation, characteristic of all conductance-based
models, and an additional exponential e+t/Na (characteristic
of exponential I&F computational models; Brette and Gerstner,
2005) at the onset of the spike Source: Indiveri et al., 2010.
Io = Ii
13
(A)Current depression mechanism. (B) Adaptive threshold mechanism as a function of Vmem (blue). The neurons spiking
threshold (red) increases with every spike, increasing the spiking
time constant. Source: Indiveri et al., 2010
I1
I2 .
I1 controls the rate at which Ii is able to charge the output

(A) Basic synapse circuit. (B)Synapse circuit with longer time
transistor gate. I2 governs the rate in which the output Io
constant. Sources: adopted from Mead et al., 1989, and Lazzaro
is sunk. This competitive nature is necessary to mimic et al., 1993, respectively.
biological behavior of neurotransmitters that either promote or depress neuronal ring.
Synaptic models have also been developed with rst
order linear integrators using log-domain lters capable of modeling the exponential decay of excitatory
post-synaptic current (EPSC) [14] . This is necessary to
have biologically plausible spike contours and time constants. The gain is also independently controlled from the
synapse time constant which is necessary for spike-rate
and spike-timing dependent learning mechanisms.
spike along the way. They do not, however, contain

any memory of previous spikes, nor are they capable of
adapting their behavior according to temporal dynamics.
These abilities, however, are necessary if neuromorphic
circuits are to learn like biological neural networks.
According to Hebbs postulate, behaviors like learning

and memory are hypothesized to occur on the synaptic level [15] . It accredits the learning process to longThe aforementioned synapses simply relay currents from term neuronal adaptation in which pre- and post-synaptic
the pre-synaptic sources, varying the shape of the pulse contributions are strengthened or weakened by biochem-
14
spike-timing-dependent plasticity (STDP). Since the conception of this theory, biological neuron activity has
been shown to exhibit behavior closely modeling Hebbian learning. One such example is of synaptic NMDA
and AMPA receptor plastic modications that lead to calcium ux induced adaptation [16] .
Learning and long-term memory of information in biological neurons is accredited to NMDA channel induced
adaptation. These NMDA receptors are voltage dependent and control intracellular calcium ion ux. It has been
shown in animal studies that neuronal desensitization is
diminished when extracellular calcium was reduced [16] .
Basic synapse circuit. Source: adopted from Lazzaro et al., 1992
(A)Simple synapse consisting of AMPA and NMDA channels,

and calcium. (B) Circuit models of individual elements of the
synapse. (C) Circuit outputs in response to a presynaptic action
(AP) potential input ( APP RE ). Source: Rachmuth et al., 2011
A) EPSC (Excitatory Post Synaptic Current) measurement

from a Dierential-Pair Integrator (log-domain) synapse. B)
Schematic diagram of the circuit used. (Based on images from
Giacomo Indiveri)
y2
y1
...
yq
...
b2
b1
w11
x1
w12
w1q
x2
bq
wp2
wp1
...
wpq
xp
An articial neural network. There are p presynaptic neurons (

x ), and q postsynaptic neurons ( b ). xp is a single presynaptic
neuron that synapses upon postsynaptic neuron bq with the synaptic weight wpq resulting in the postsynaptic neuron to output yq .
Source: Wikipedia
ical modications. This theory is often summarized in

the saying, Neurons that re together, wire together.
Articial neural networks model learning through these
biochemical wiring modications with a single parameter, the synaptic weight, wpq . A synaptic weight is
a parameter state variable that quanties how a presynaptic neuron spike aects a postsynaptic neuron output. Two models of Hebbian synaptic weight plasticity include spike-rate-dependent plasticity (SRDP), and
Since calcium concentration exponentially decays, this

behavior easily implemented on hardware using subthreshold transistors. A circuit model demonstrating calcium dependent biological behavior is shown by Rachmuth et al. (2011) [17] . The calcium signal, ICa2+ , regulates AMPA and NMDA channel activity through the
Vmem node according to calcium-dependent STDP and
SRDP learning rules. The output of these learning rules is
the synaptic weight, w , which is proportional to the number of active AMPA and NMDA channels. The SRDP
model describes the weight in terms of two state variables,
, which controls the update rule, and , which controls
the learning rate.
dw = ([Ca2+ ]) (([Ca2+ ]) w), where w
is the synaptic weight, ([Ca2+ ]) is the update rule,
([Ca2+ ]) is the learning rate, and is a constant that
allows the weight to drift out of saturation in absence of
an input.
The NMDA channel controls the calcium inux, ICa .
The NMDA receptor voltage-dependency is modeled by
Vmem , and the channel mechanics are controlled with a
large capacitor to increase the calcium time constant, Ca
. The output ICa is copied via current mirrors into the
and circuits to perform downstream learning functions.
The circuit compares ICa to threshold biases, LT P
and LT D ), that respectively control long-term potentiation or long-term depression through a series of dierential pair circuits. The output of dierential pairs determines the update rule. This circuit has been demonstrated to exhibit various Hebbian learning rules as observed in the hippocampus, and anti-Hebbian learning
rules used in the cerebellum.
The circuit controls when synaptic learning can occur
1.7. THE NEURON SIMULATION ENVIRONMENT
15
by only allowing updates when ICa is above a dierential

pair set threshold, . The learning rate (LR) is modeled
according to:
C
, where is a function of [Ca2+ ] and

LR I [Ca
2+ ]
controls the learning rate, C is the capacitance of the
circuit, and is the threshold voltage of the comparator. This function demonstrates that must be biased to
maintain an elevated [Ca2+ ] in order to simulate SRDT.
A leakage current, ILEAK , was included to drain V to
REST during inactivity.
1.7 The NEURON simulation environment
1.7.1
Introduction
Neuron is a simulation environment with which you can

simulate the propagation of ions and action potentials in
biological and articial neurons as well as in networks of
neurons [18] . The user can specify a model geometry by
dening and connecting neuron cell parts, which can be
equipped with various mechanisms such as ion channels,
clamps and synapses. To interact with NEURON the user
can either use the graphical user interface (GUI) or one of
the programming languages hoc (a language with a C like
syntax) or Python as an interpreter. The GUI contains
a wide selection of the most-used features, an example
screenshot is shown in the Figure on the right. The programming languages on the other hand can be exploited
to add more specic mechanisms to the model and for
automation purposes Furthermore, custom mechanisms
can be created with the programming language NMODL,
which is an extension to MODL, a model description
language developed by the NBSR (National Biomedical
Simulation Resource). These new mechanisms can then
be compiled, and added to models through the GUI or
interpreters.
Neuron was initially developed by John W. Moore at

Duke university in collaboration with Michael Hines. It
is currently used in numerous institutes and universities
for educational and research purposes. There is an extensive amount of information available including the ocial website containing the documentation, the NEURON
forum and various tutorials and guides. Furthermore in
2006 the authoritative reference book for NEURON was
published called The NEURON Book [19] . To read the
following chapters and to work with NEURON, some
background knowledge on the physiology of neurons is
recommended. Some examples of information sources
about neurons are the WikiBook chapter, or the videos in
the introduction of the Advanced Nervous System Physiology chapter on Khan academy. We will not cover specic commands or details about how to perform the here
mentioned actions with NEURON since this document is
not intended to be a tutorial but only an overview of the
possibilities and model structure within NEURON. For
more practical information on the implementation with
NEURON I would recommend the tutorials which are
linked below and the documentation on the ocial webpage [18] .
16
Dendrite
Axon Terminal
Cell body
Node of
Ranvier
Schwann cell
Axon
Myelin sheath
Nucleus
A schematic representation of a neuron.
1.7.2
Model creation
Single Cell Geometry

First we will discuss the creation of a model geometry
that consists of a single biological neuron. A schematic
representation of a Neuron is shown in the Figure on the
right. In the following Listing an example code snippet is
shown in which a multi-compartment cell with one soma
and two dendrites is specied using hoc.
load_le(nrngui.hoc) // Create a soma object and an

array containing 2 dendrite objects ndend = 2 create
soma, dend[ndend] access soma // Initialize the soma
and the dendrites soma { nseg = 1 diam = 18.8 L = 18.8
Ra = 123.0 insert hh } dend[0] { nseg = 5 diam = 3.18
L = 701.9 Ra = 123 insert pas } dend[1] { nseg = 5
diam = 2.0 L = 549.1 Ra = 123 insert pas } // Connect
the dendrites to the soma connect dend[0](0), soma(0)
connect dend[1](0), soma(1) // Create an electrode in
the soma objectvar stim stim = new IClamp(0.5) // Set
stimulation parameters delay, duration and amplitude
stim.del = 100 stim.dur = 100 stim.amp = 0.1 // Set the
simulation end time tstop = 300
long as there are no loops. The neuron as specied in the

Listing above, is visualized in the Figure on the right.
Segments In order to model the propagation of action
potentials through the sections more accurately, the sections can be divided into smaller parts called segments.
A model in which the sections are split into multiple segments is called a multi-compartment model. Increasing the number of segments can be seen as increasing
the granularity of the spatial discretization, which leads
to more accurate results when for example the membrane
properties are not uniform along the section. By default,
a section consists of one segment.
Membrane Mechanisms The default settings of a section do not contain any ion channels, but the user can add
them [20] . There are two types of built-in ion channel
membrane mechanisms available, namely a passive ion
channel membrane model and a Hodgkin-Huxley model
membrane model which represents a combination of passive and voltage gated ion channels. If this is not sucient, users can dene their own membrane mechanisms
using the programming language NMODL.
A schematic representation of a synapse
Point Processes Besides membrane mechanisms

which are dened on membrane areas, there are also
local mechanisms known as Point processes that can
be added to the sections. Some examples are synapses,
as shown in the Figure on the right, and voltage- and
current clamps. Again, users are free to implement
their own mechanisms with the programming language
NMODL. One key dierence between point processes
and membrane mechanisms is that the user can specify
the location where the point process should be added
Sections The basic building blocks in NEURON are onto the section, because it is a local mechanism [20] .
called sections. Initially a section only represents a
cylindrical tube with individual properties such as the
length and the diameter. A section can be used to rep- Output and Visualizations
resent dierent neuron parts, such as a soma, a dendrite
or an axon, by equipping it with the corresponding mech- The computed quantities can be tracked over time and
anisms such as ion channels or synapse connections with plotted, to create for example a graph of voltage verother cells or articial stimuli. A neuron cell can then be sus time within a specic segment, as shown in the GUI
created by connecting the ends of the sections together screenshot above. It is also possible to make animations,
however you want, for example in a tree like structure, as to show for example how the voltage distribution within
1.7. THE NEURON SIMULATION ENVIRONMENT
17
the axon develops over time. Note that the quantities are
only computed at the centre of each segment and at the
boundaries of each section.
Creating a Cell Network
Besides modeling the ion concentrations within single
cells it is also possible to connect the cells and to simulate networks of neurons. To do so the user has to attach synapses, which are point processes, to the postsynaptic neurons and then create NetCon objects which
will act as the connection between the presynaptic neuron
and the postsynaptic neuron. There are dierent types of
synapses that the user can attach to neurons, such as AlphaSynapse, in which the synaptic conductance decays
according to an alpha function and ExpSyn in which the
synaptic conductance decays exponentially. Like with
other mechanisms it is also possible to create custom
synapses using NMODL. For the NetCon object it is possible to specify several parameters, such as the threshold
and the delay, which determine the required conditions
for the presynaptic neuron to cause a postsynaptic potential.
Articial Neurons
Besides the biological neurons that we have discussed up
until now, there is also another type of neuron that can be
simulated with NEURON known as an articial neuron. The dierence between the biological and articial
neurons in NEURON is that the articial neuron does not
have a spatial extent and that its kinetics are highly simplied. There are several integrators available to model the
behaviour of articial cells in NEURON, which distinguish themselves by the extent to which they are simplications of the dynamics of biological neurons [21] . To reduce the computation time for models of articial spiking
neuron cells and networks, the developers of NEURON
have chosen to support event-driven simulations. This
substantially reduced the computational burden of simulating spike-triggered synaptic transmissions. Although
modelling conductance based neuron cells requires a continuous system simulation, NEURON can still exploit the
benets of event-driven methods for networks that contain biological and articial neurons by fully supporting
hybrid simulations. This way any combination of articial and conductance based neuron cells can be simulated
while still achieving the reduced computation time that
results from event-driven simulation of articial cells [22] .
The user can also add other articial neuron classes with
the language NMODL.
The Python logo
language has been extended and maintained to be used

with NEURON up until now, but because this maintenance takes a lot of time and because it has turned out
to be an orphan language limited to NEURON users,
the developers of NEURON desire a more modern programming language as an interpreter for NEURON. Because Python has become widely used within the area
of scientic computing with many users creating packages containing reusable code, it is now more attractive as an interpreter than hoc[23] . There are three ways
to use NEURON with Python. The rst way is to run
NEURON with the terminal accepting interactive Python
commands. The second way is to run NEURON with
the interpreter hoc, and to access Python commands
through special commands in hoc. The third way is to
use NEURON as an extension module for Python, such
that a NEURON module can be imported into Python or
IPython scripts.
Installation
To use the rst and second mode, so to use NEURON
with Python embedded, it is sucient to complete the
straightforward installation. To use the third mode however, which is NEURON as an extension module for
Python, it is necessary to build NEURON from the source
code and install the NEURON shared library for Python
which is explained in this installation guide.
NEURON commands in Python
Because NEURON was originally developed with hoc

as an interpreter the user still has to explicitly call hoc
functions and classes from within Python. All functions
and classes that have existed for hoc are accessible in
Python through the module neuron, both when using
Python embedded in NEURON or when using NEURON
as an extension module. There are only some minor differences between the NEURON commands in hoc and
Python so there should not be many complications for
users when changing from one to another [23] . There are
a couple of advantages of using NEURON with Python
instead of hoc. One of the primary advantages is that
Python oers a lot more functionality because it is a
1.7.3 Neuron with Python
complete object-oriented language and because there is
an extensive suite of analysis tools available for science
Since 1984 NEURON has provided the hoc interpreter and engineering. Also, loading user-dened mechanisms
for the creation and execution of simulations. The hoc from NMODL scripts has become easier, which makes
18
NEURON more attractive for simulations of very specic

mechanisms [23] . More details on NEURON in combination with Python can be found here.
1.7.4
Tutorials
[2] T. Haslwanter (2012).

Fitzhugh-Nagumo Model
[Python"].
private communications.
http://work.
thaslwanter.at/CSS/Code/Fitzhugh_Nagumo.py.
[3] T. Anastasio (2010). Tutorial on Neural systems Modeling. http://www.sinauer.com/detail.php?id=3396.
[4] E Aydiner, AM Vural, B Ozcelik, K Kiymac, U Tan
(2003), A simple chaotic neuron model: stochastic behavior of neural networks
[5] WM Siebert (1965), Some implications of the stochastic
behavior of primary auditory neurons
[6] G Indiveri, F Stefanini, E Chicca (2010), Spike-based
learning with a generalized integrate and re silicon neuron
[7] CA Mead (1989), Analog VLSI and Neural Systems
[8] RJ Douglas, MA Mahowald (2003), Silicon Neuron
A schematic representation of the neural network that you will

learn to model in the rst tutorial. The blue dot represents a
synapse between the two neurons.
[9] J Lazzaro, S Ryckebusch, MA Mahowald, CA Mead

(1989), Winner-Take-All: Networks of O(N ) Complexity
[10] M Riesenhuber, T Poggio (1999), Hierarchical models of
object recognition in cortex
There are multiple tutorials available online for getting

started with NEURON and two of them are listed below. [11]
In the rst tutorial you will start with learning how to create a single compartment cell and nish with creating a [12]
network of neurons as shown in the Figure on the right,
containing custom cell mechanisms. Meanwhile you will
be guided through the NEURON features for templates,
automation, computation time optimization and extrac- [13]
tion of resulting data. The tutorial uses hoc commands
but the procedures are almost the same within Python.
[14]
The second tutorial shows how to create a cell with a passive cell membrane and a synaptic stimulus, and how to
visualize the results with the Python module matplotlib.
1.7.5
Further Reading
E Chicca, G Indiveri, R Douglas (2004), An event-based

VLSI network of Integrate-and-Fire Neurons
G Indiveri, E Chicca, R Douglas (2004), A VLSI recongurable network of integrate-and-re neurons with spikebased learning synapses
J Lazzaro, J Wawrzynek (1993), Low-Power Silicon Neurons, Axons, and Synapses
S Mitra, G Indiveri, RE Cummings (2010), Synthesis
of log-domain integrators for silicon synapses with global
parametric control
[15] DO Hebb (1949), The organization of behavior

[16] PA Koplas, RL Rosenberg, GS Oxford (1997), The role
of calcium in the densensitization of capsaisin responses in
rat dorsal root ganglion neurons
Besides what is mentioned in this introduction to NEU[17] G Rachmuth, HZ Shouval, MF Bear, CS Poon (2011),
RON, there are many more options available which are
A biophysically-based neuromorphic model of spike ratecontinuously extended and improved by the developers.
timing-dependent plasticity
An extensive explanation of NEURON can be found in
The NEURON book [19] , which is the ocial reference [18] Neuron, for empirically-based simulations of neurons
and networks of neurons, http://www.neuron.yale.edu/
book. Furthermore the ocial website contains a lot of
neuron/
information and links to other sources as well.
1.8 References
[19] Nicholas T. Carnevale, Michael L. Hines (2009), The

NEURON book
[20] NEURON Tutorial 1, http://www.anc.ed.ac.uk/school/
neuron/tutorial/tutA.html
Two additional sources are ``An adaptive silicon

synapse, by Chicca et al. [24] and ``Analog VLSI: [21] M.L. Hines and N.T. Carnevale (2002), The NEURON
Simulation Environment
Circuits and Principles, by Liu et al. [25] .
[1] T. Haslwanter (2012). Hodgkin-Huxley Simulations
private communications.
http://work.
[Python"].
thaslwanter.at/CSS/Code/HH_model.py.
[22] Romain Brette, Michelle Rudolph, Ted Carnevale,

Michael Hines, David Beeman, James M. Bower, Markus
Diesmann, Abigail Morrison, Philip H. Goodman, Frederick C. Harris, Jr., Milind Zirpe, Thomas Natschlger,
1.8. REFERENCES
Dejan Pecevski, Bard Ermentrout, Mikael Djurfeldt, Anders Lansner, Olivier Rochel, Thierry Vieville, Eilif
Muller, Andrew P. Davison, Sami El Boustani, Alain Destexhe (2002), Simulation of networks of spiking neurons:
A review of tools and strategies
[23] Hines ML, Davison AP, Muller E. NEURON and Python.
Frontiers in Neuroinformatics. 2009;3:1. doi:10.3389/
neuro.11.001.2009. (2009), NEURON and Python
[24] E Chicca, G Indiveri, R Douglas (2003), An adaptive silicon synapse
[25] SC Liu, J Kramer, T Delbrck, G Indiveri, R Douglas
(2002), Analog VLSI: Circuits and Principles
19
Chapter 2
Sensory Systems in Humans

2.1 Auditory System
but also in the sense of balance and body position.

Humans have a pair of ears placed symmetrically on both
sides of the head which makes it possible to localize sound
sources. The brain extracts and processes dierent forms
of data in order to localize sound, such as:
Sensory Systems
Vision
Hearing
Balance
Feeling
Smell
Taste
the shape of the sound spectrum at the tympanic

membrane (eardrum)
the dierence in sound intensity between the left and
the right ear
the dierence in time-of-arrival between the left and
the right ear
the dierence in time-of-arrival between reections

of the ear itself (this means in other words: the shape
of the pinna (pattern of folds and ridges) captures
sound-waves in a way that helps localizing the sound
source, especially on the vertical axis.
Implants
Models
In Animals
Insects & Spiders
Birds,Fish,...
2.1.1
Introduction
The sensory system for the sense of hearing is the auditory system. This wikibook covers the physiology of
the auditory system, and its application to the most successful neurosensory prosthesis - cochlear implants. The
physics and engineering of acoustics are covered in a separate wikibook, Acoustics. An excellent source of images
and animations is Journey into the world of hearing [1] .
The ability to hear is not found as widely in the animal
kingdom as other senses like touch, taste and smell. It is
restricted mainly to vertebrates and insects. Within these,
mammals and birds have the most highly developed sense
of hearing. The table below shows frequency ranges of
humans and some selected animals:
The organ that detects sound is the ear. It acts as receiver
in the process of collecting acoustic information and passing it through the nervous system into the brain. The ear
includes structures for both the sense of hearing and the
sense of balance. It does not only play an important role
as part of the auditory system in order to receive sound
Healthy, young humans are able to hear sounds over a

frequency range from 20 Hz to 20 kHz. We are most
sensitive to frequencies between 2000 to 4000 Hz which
is the frequency range of spoken words. The frequency
resolution is 0.2% which means that one can distinguish
between a tone of 1000 Hz and 1002 Hz. A sound at 1
kHz can be detected if it deects the tympanic membrane
(eardrum) by less than 1 Angstrom, which is less than the
diameter of a hydrogen atom. This extreme sensitivity of
the ear may explain why it contains the smallest bone that
exists inside a human body: the stapes (stirrup). It is 0.25
to 0.33 cm long and weighs between 1.9 and 4.3 mg.
2.1.2 Anatomy of the Auditory System

The aim of this section is to explain the anatomy of
the auditory system of humans. The chapter illustrates
the composition of auditory organs in the sequence that
acoustic information proceeds during sound perception.
Please note that the core information for Sensory Organ
Components can also be found on the Wikipedia page
Auditory system, excluding some changes like extensions and specications made in this article. (see also:
Wikipedia Auditory system)
20
2.1. AUDITORY SYSTEM
21
Stapes
(attached to
oval window)
Malleus
Semicircular
Canals
Incus
Vestibular
Nerve
Cochlear
Nerve
External
Auditory Canal
Tympanic
Membrane
Cochlea
Tympanic
Cavity
Eustachian Tube
Round
Window
Anatomy of the human ear (green: outer ear / red: middle ear /
purple: inner ear)
The folds of cartilage surrounding the ear canal (external auditory meatus, external acoustic meatus) are called
the pinna. It is the visible part of the ear. Sound waves
are reected and attenuated when they hit the pinna, and
these changes provide additional information that will
help the brain determine the direction from which the
sounds came. The sound waves enter the auditory canal,
a deceptively simple tube. The ear canal amplies sounds
that are between 3 and 12 kHz. At the far end of the ear
canal is the tympanic membrane (eardrum), which marks
the beginning of the middle ear.
Human (external) ear
The auditory system senses sound waves, that are changes

in air pressure, and converts these changes into electrical
signals. These signals can then be processed, analyzed
and interpreted by the brain. For the moment, lets focus
on the structure and components of the auditory system.
The auditory system consists mainly of two parts:
the ear and
the auditory nervous system (central auditory system)
The ear
The ear is the organ where the rst processing of sound
occurs and where the sensory receptors are located. It
consists of three parts:
Micro-CT image of the ossicular chain showing the relative position of each ossicle.
outer ear
middle ear
inner ear
Outer ear Function: Gathering sound energy and amplication of sound pressure.
Middle ear Function: Transmission of acoustic energy

from air to the cochlea.
Sound waves traveling through the ear canal will hit the
tympanic membrane (tympanum, eardrum). This wave
information travels across the air-lled tympanic cavity
(middle ear cavity) via a series of bones: the malleus
(hammer), incus (anvil) and stapes (stirrup). These ossicles act as a lever and a teletype, converting the lower-
22
pressure eardrum sound vibrations into higher-pressure
sound vibrations at another, smaller membrane called the
oval (or elliptical) window, which is one of two openings
into the cochlea of the inner ear. The second opening is
called round window. It allows the uid in the cochlea to
move.
The malleus articulates with the tympanic membrane via
the manubrium, whereas the stapes articulates with the
oval window via its footplate. Higher pressure is necessary because the inner ear beyond the oval window contains liquid rather than air. The sound is not amplied
uniformly across the ossicular chain. The stapedius reex of the middle ear muscles helps protect the inner ear
from damage.
CHAPTER 2. SENSORY SYSTEMS IN HUMANS
Inner hair cells

Tectorial membrane
Outer hair cells
Basilar ber
Spiral ganglion
Cochlear nerve
The middle ear still contains the sound information in Section through the spiral organ of Corti
wave form; it is converted to nerve impulses in the
cochlea.
they are named. These cilia are the mechanosensors for
hearing. The shorter ones are called stereocilia, and the
Inner ear Function: Transformation of mechanical longest one at the end of each haircell bundle kinocilwaves (sound) into electric signals (neural signals).
ium. The location of the kinocilium determine the onThe inner ear consists of the cochlea and several non- direction, i.e. the direction of deection inducing the
auditory structures. The cochlea is a snail-shaped part maximum hair cell excitation. Lightly resting atop the
of the inner ear. It has three uid-lled sections: scala longest cilia is the tectorial membrane, which moves back
tympani (lower gallery), scala media (middle gallery, and forth with each cycle of sound, tilting the cilia and alcochlear duct) and scala vestibuli (upper gallery). The lowing electric current into the hair cell.
cochlea supports a uid wave driven by pressure across
the basilar membrane separating two of the sections
(scala tympani and scala media). The basilar membrane
is about 3 cm long and between 0.5 to 0.04 mm wide.
Reissners membrane (vestibular membrane) separates
scala media and scala vestibuli.
Strikingly, one section, the scala media, contains an extracellular uid similar in composition to endolymph, which
is usually found inside of cells. The organ of Corti is located in this duct, and transforms mechanical waves to
electric signals in neurons. The other two sections, scala
tympani and scala vestibuli, are located within the bony
labyrinth which is lled with uid called perilymph. The
chemical dierence between the two uids endolymph
(in scala media) and perilymph (in scala tympani and
scala vestibuli) is important for the function of the inner
ear.
Organ of Corti The organ of Corti forms a ribbon of
sensory epithelium which runs lengthwise down the entire cochlea. The hair cells of the organ of Corti transform the uid waves into nerve signals. The journey of
a billion nerves begins with this rst step; from here further processing leads to a series of auditory reactions and
sensations.
The function of hair cells is not fully established up to

now. Currently, the knowledge of the function of hair
cells allows to replace the cells by cochlear implants in
case of hearing lost. However, more research into the
function of the hair cells may someday even make it possible for the cells to be repaired. The current model is that
cilia are attached to one another by tip links, structures
which link the tips of one cilium to another. Stretching
and compressing, the tip links then open an ion channel
and produce the receptor potential in the hair cell. Note
that a deection of 100 nanometers already elicits 90%
of the full receptor potential.
Neurons The nervous system distinguishes between
nerve bres carrying information towards the central nervous system and nerve bres carrying the information
away from it:
Aerent neurons (also sensory or receptor neurons)
carry nerve impulses from receptors (sense organs)
towards the central nervous system
Eerent neurons (also motor or eector neurons)
carry nerve impulses away from the central nervous
system to eectors such as muscles or glands (and
also the ciliated cells of the inner ear)
Aerent neurons innervate cochlear inner hair cells, at

synapses where the neurotransmitter glutamate commuHair cells Hair cells are columnar cells, each with a nicates signals from the hair cells to the dendrites of the
bundle of 100-200 specialized cilia at the top, for which primary auditory neurons.
Transition from ear to auditory nervous system

There are far fewer inner hair cells in the cochlea than
aerent nerve bers. The neural dendrites belong to neurons of the auditory nerve, which in turn joins the vestibular nerve to form the vestibulocochlear nerve, or cranial
nerve number VIII'
23
Eect of the head
Sound waves with a wavelength shorter than the head

produce a sound shadow on the ear further away from
the sound source. When the wavelength is shorter than
Eerent projections from the brain to the cochlea also the head, diraction of the sound leads to approximately
play a role in the perception of sound. Eerent synapses equal sound intensities on both ears.
occur on outer hair cells and on aerent (towards the
brain) dendrites under inner hair cells.
Auditory nervous system

The sound information, now re-encoded in form of electric signals, travels down the auditory nerve (acoustic
nerve, vestibulocochlear nerve, VIIIth cranial nerve),
through intermediate stations such as the cochlear nuclei
and superior olivary complex of the brainstem and the inferior colliculus of the midbrain, being further processed
at each waypoint. The information eventually reaches the
thalamus, and from there it is relayed to the cortex. In
the human brain, the primary auditory cortex is located
in the temporal lobe.
Primary auditory cortex The primary auditory cortex is the rst region of cerebral cortex to receive auditory Dierence in loudness and timing help us to localize the source
of a sound signal.
input.
Perception of sound is associated with the right posterior
superior temporal gyrus (STG). The superior temporal
gyrus contains several important structures of the brain,
including Brodmann areas 41 and 42, marking the location of the primary auditory cortex, the cortical region
responsible for the sensation of basic characteristics of
sound such as pitch and rhythm.
Sound reception at the pinna
The pinna collects sound waves in air aecting sound

coming from behind and the front dierently with its corrugated shape. The sound waves are reected and attenuated or amplied. These changes will later help sound
The auditory association area is located within the temlocalization.
poral lobe of the brain, in an area called the Wernickes
area, or area 22. This area, near the lateral cerebral sul- In the external auditory canal, sounds between 3 and 12
cus, is an important region for the processing of acoustic kHz - a range crucial for human communication - are amsignals so that they can be distinguished as speech, music, plied. It acts as resonator amplifying the incoming frequencies.
or noise.
Sound conduction to the cochlea
2.1.3
Auditory Signal Processing
Now that the anatomy of the auditory system has been

sketched out, this topic goes deeper into the physiological processes which take place while perceiving acoustic
information and converting this information into data that
can be handled by the brain. Hearing starts with pressure
waves hitting the auditory canal and is nally perceived
by the brain. This section details the process transforming vibrations into perception.
Sound that entered the pinna in form of waves travels

along the auditory canal until it reaches the beginning
of the middle ear marked by the tympanic membrane
(eardrum). Since the inner ear is lled with uid, the
middle ear is kind of an impedance matching device in
order to solve the problem of sound energy reection on
the transition from air to the uid. As an example, on
the transition from air to water 99.9% of the incoming
sound energy is reected. This can be calculated using:
24
Ir
Ii
(
=
Z2 Z1
Z2 +Z1
)2
with I the intensity of the reected sound, I the intensity of the incoming sound and Z the wave resistance
of the two media ( Z = 414 kg m2 s1 and Z =
1.48*106 kg m2 s1 ). Three factors that contribute the
impedance matching are:
the relative size dierence between tympanum and
oval window
the lever eect of the middle ear ossicles and
the shape of the tympanum.
scala media. This elongation of Reissners membrane

causes the endolymph to move within the scala media
and induces a displacement of the basilar membrane.
The separation of the sound frequencies in the cochlea
is due to the special properties of the basilar membrane.
The uid in the cochlea vibrates (due to in- and outmotion of the stapes footplate) setting the membrane in
motion like a traveling wave. The wave starts at the base
and progresses towards the apex of the cochlea. The
transversal waves in the basilar membrane propagate with
ctrans =
with the shear modulus and the density of the material.

Since width and tension of the basilar membrane change,
the speed of the waves propagating along the membrane
changes from about 100 m/s near the oval window to 10
m/s near the apex.
Mechanics of the amplication eect of the middle ear.
The longitudinal changes in air pressure of the soundwave cause the tympanic membrane to vibrate which,
in turn, makes the three chained ossicles malleus, incus and stirrup oscillate synchronously. These bones vibrate as a unit, elevating the energy from the tympanic
membrane to the oval window. In addition, the energy
of sound is further enhanced by the areal dierence between the membrane and the stapes footplate. The middle ear acts as an impedance transformer by changing the
sound energy collected by the tympanic membrane into
greater force and less excursion. This mechanism facilitates transmission of sound-waves in air into vibrations
of the uid in the cochlea. The transformation results
from the pistonlike in- and out-motion by the footplate
of the stapes which is located in the oval window. This
movement performed by the footplate sets the uid in the
cochlea into motion.
There is a point along the basilar membrane where the

amplitude of the wave decreases abruptly. At this point,
the sound wave in the cochlear uid produces the maximal displacement (peak amplitude) of the basilar membrane. The distance the wave travels before getting to that
characteristic point depends on the frequency of the incoming sound. Therefore each point of the basilar membrane corresponds to a specic value of the stimulating
frequency. A low-frequency sound travels a longer distance than a high-frequency sound before it reaches its
characteristic point. Frequencies are scaled along the
basilar membrane with high frequencies at the base and
low frequencies at the apex of the cochlea.
Through the stapedius muscle, the smallest muscle in the

human body, the middle ear has a gating function: contracting this muscle changes the impedance of the middle
ear, thus protecting the inner ear from damage through
loud sounds.
The position x of the maximal amplitude of the travelling wave
corresponds in a 1-to-1 way to a stimulus frequency.
Frequency analysis in the cochlea

The three uid-lled compartements of the cochlea
(scala vestibuli, scala media, scala tympani) are separated by the basilar membrane and the Reissners
membrane. The function of the cochlea is to separate
sounds according to their spectrum and transform it
into a neural code. When the footplate of the stapes
pushes into the perilymph of the scala vestibuli, as a
consequence the membrane of Reissner bends into the
Sensory transduction in the cochlea

Most everyday sounds are composed of multiple frequencies. The brain processes the distinct frequencies, not
the complete sounds. Due to its inhomogeneous properties, the basilar membrane is performing an approximation to a Fourier transform. The sound is thereby split
into its dierent frequencies, and each hair cell on the
25
membrane corresponds to a certain frequency. The loudness of the frequencies is encoded by the ring rate of
the corresponding aerent ber. This is due to the amplitude of the traveling wave on the basilar membrane,
which depends on the loudness of the incoming sound.
+
AP
The sensory cells of the auditory system, known as hair

cells, are located along the basilar membrane within the
organ of Corti. Each organ of Corti contains about
16000 such cells, innervated by about 30'000 aerent
nerve bers. There are two anatomically and functionally
distinct types of hair cells: the inner and the outer hair
cells. Along the basilar membrane these two types are
arranged in one row of inner cells and three to ve rows
of outer cells. Most of the aerent innervation comes
from the inner hair cells while most of the eerent innervation goes to the outer hair cells. The inner hair cells inuence the discharge rate of the individual auditory nerve
bers that connect to these hair cells. Therefore inner hair
cells transfer sound information to higher auditory nervous centers. The outer hair cells, in contrast, amplify the
movement of the basilar membrane by injecting energy
into the motion of the membrane and reducing frictional
losses but do not contribute in transmitting sound information. The motion of the basilar membrane deects the
stereocilias (hairs on the hair cells) and causes the intracellular potentials of the hair cells to decrease (depolarization) or increase (hyperpolarization), depending on the
direction of the deection. When the stereocilias are in
a resting position, there is a steady state current owing
through the channels of the cells. The movement of the
stereocilias therefore modulates the current ow around
that steady state current.
Lets look at the modes of action of the two dierent hair
cell types separately:
Inner hair cells:
Transduction mechanism in auditory or vestibular hair cell. Tilting the hair cell towards the kinocilium opens the potassium ion
channels. This changes the receptor potential in the hair cell.
The resulting emission of neurotransmitters can elicit an action
potential (AP) in the post-synaptic cell.
Auditory haircells are very similar to those of the vestibular system. Here an electron microscopy image of a frogs sacculus haircell.
The deection of the hair-cell stereocilia opens mechanically gated ion channels that allow small, positively
charged potassium ions (K+ ) to enter the cell and causing it to depolarize. Unlike many other electrically active
cells, the hair cell itself does not re an action potential.
Instead, the inux of positive ions from the endolymph
in scala media depolarizes the cell, resulting in a receptor potential. This receptor potential opens voltage gated
calcium channels; calcium ions (Ca2+ ) then enter the cell
and trigger the release of neurotransmitters at the basal
end of the cell. The neurotransmitters diuse across the
narrow space between the hair cell and a nerve terminal,
where they then bind to receptors and thus trigger action
potentials in the nerve. In this way, neurotransmitter increases the ring rate in the VIIIth cranial nerve and the
mechanical sound signal is converted into an electrical
nerve signal.
The repolarization in the hair cell is done in a special manner. The perilymph in Scala tympani has a very low concentration of positive ions. The electrochemical gradient
makes the positive ions ow through channels to the perilymph. (see also: Wikipedia Hair cell)
Outer hair cells:
In humans outer hair cells, the receptor potential trig-
26
gers active vibrations of the cell body. This mechanical

response to electrical signals is termed somatic electromotility and drives oscillations in the cells length, which
occur at the frequency of the incoming sound and provide
mechanical feedback amplication. Outer hair cells have
evolved only in mammals. Without functioning outer hair
cells the sensitivity decreases by approximately 50 dB
(due to greater frictional losses in the basilar membrane
which would damp the motion of the membrane). They
have also improved frequency selectivity (frequency discrimination), which is of particular benet for humans,
because it enables sophisticated speech and music. (see
also: Wikipedia Hair cell)
electrical signals (electrical spikes, action potentials) are

generated and transmitted along the cochlear branch of
the auditory nerve (VIIIth cranial nerve) to the cochlear
nucleus in the brainstem.
With no external stimulation, auditory nerve bres discharge action potentials in a random time sequence. This
random time ring is called spontaneous activity. The
spontaneous discharge rates of the bers vary from very
slow rates to rates of up to 100 per second. Fibers are
placed into three groups depending on whether they re
spontaneously at high, medium or low rates. Fibers with
high spontaneous rates (> 18 per second) tend to be more
sensitive to sound stimulation than other bers.
One stream is the ventral cochlear nucleus which is split

further into the posteroventral cochlear nucleus (PVCN)
and the anteroventral cochlear nucleus (AVCN). The ventral cochlear nucleus cells project to a collection of nuclei
called the superior olivary complex.
Auditory pathway of nerve impulses
Lateral lemniscus in red, as it connects the cochlear nucleus, superior olivary nucleus and the inferior colliculus. Seen from behind.
So in the inner hair cells the mechanical sound signal is

nally converted into electrical nerve signals. The inner
hair cells are connected to auditory nerve bres whose
nuclei form the spiral ganglion. In the spiral ganglion the
From there, the auditory information is divided into at

least two streams:
Ventral Cochlear Nucleus:
Superior olivary complex: Sound localization The

superior olivary complex - a small mass of gray substance
- is believed to be involved in the localization of sounds
in the azimuthal plane (i.e. their degree to the left or the
right). There are two major cues to sound localization:
Interaural level dierences (ILD) and interaural time differences (ITD). The ILD measures dierences in sound
intensity between the ears. This works for high frequencies (over 1.6 kHz), where the wavelength is shorter than
the distance between the ears, causing a head shadow which means that high frequency sounds hit the averted
ear with lower intensity. Lower frequency sounds don't
cast a shadow, since they wrap around the head. However, due to the wavelength being larger than the distance
between the ears, there is a phase dierence between
the sound waves entering the ears - the timing dierence
measured by the ITD. This works very precisely for frequencies below 800 Hz, where the ear distance is smaller
than half of the wavelength. Sound localization in the median plane (front, above, back, below) is helped through
the outer ear, which forms direction-selective lters.
There, the dierences in time and loudness of the sound
information in each ear are compared. Dierences in
sound intensity are processed in cells of the lateral superior olivary complexm and timing dierences (runtime
delays) in the medial superior olivary complex. Humans
can detect timing dierences between the left and right
ear down to 10 s, corresponding to a dierence in sound
location of about 1 deg. This comparison of sound information from both ears allows the determination of the
direction where the sound came from. The superior olive
is the rst node where signals from both ears come together and can be compared. As a next step, the superior
olivary complex sends information up to the inferior colliculus via a tract of axons called lateral lemniscus. The
function of the inferior colliculus is to integrate information before sending it to the thalamus and the auditory
cortex. It is interesting to know that the superior collicu-
2.2. VISUAL SYSTEM

lus close by shows an interaction of auditory and visual
stimuli.
Dorsal Cochlear Nucleus:
27
[1] NeurOreille and authors (2010). Journey into the world

of hearing. http://www.cochlea.org/en/spe.
2.2 Visual System
The dorsal cochlear nucleus (DCN) analyzes the quality Sensory Systems
of sound and projects directly via the lateral lemnisucs to
the inferior colliculus.
Vision
Hearing
From the inferior colliculus the auditory information Balance
from ventral as well as dorsal cochlear nucleus proceeds Feeling
to the auditory nucleus of the thalamus which is the me- Smell
dial geniculate nucleus. The medial geniculate nucleus Taste
further transfers information to the primary auditory cortex, the region of the human brain that is responsible for Technological Aspects
processing of auditory information, located on the temporal lobe. The primary auditory cortex is the rst relay
Implants
involved in the conscious perception of sound.
Models
In Animals
Primary auditory cortex and higher order auditory
areas
Insects & Spiders
Birds,Fish,...
Sound information that reaches the primary auditory cortex (Brodmann areas 41 and 42). The primary auditory
cortex is the rst relay involved in the conscious percep- 2.2.1 Introduction
tion of sound. It is known to be tonotopically organized
and performs the basics of hearing: pitch and volume. Generally speaking, visual systems rely on electromagDepending on the nature of the sound (speech, music, netic (EM) waves to give an organism more information
noise), is further passed to higher order auditory areas. about its surroundings. This information could be regardSounds that are words are processed by Wernickes area ing potential mates, dangers and sources of sustenance.
(Brodmann area 22). This area is involved in understand- Dierent organisms have dierent constituents that make
ing written and spoken language (verbal understanding). up what is referred to as a visual system.
The production of sound (verbal expression) is linked to
Brocas area (Brodmann areas 44 and 45). The muscles to The complexity of eyes range from something as simple
produce the required sound when speaking are contracted as an eye spot, which is nothing more than a collection
by the facial area of motor cortex which are regions of the of photosensitive cells, to a fully edged camera eye. If
cerebral cortex that are involved in planning, controlling an organism has dierent types of photosensitive cells,
or cells sensitive to dierent wavelength ranges, the orand executing voluntary motor functions.
ganism would theoretically be able to perceive colour or
at the very least colour dierences. Polarisation, another
property of EM radiation, can be detected by some organisms, with insects and cephalopods having the highest
accuracy.
Lateral surface of the brain with Brodmanns areas numbered.
Please note, in this text, the focus has been on using EM

waves to see. Granted, some organisms have evolved alternative ways of obtaining sight or at the very least supplementing what they see with extra-sensory information.
For example, whales or bats, which use echo-location.
This may be seeing in some sense of the denition of
the word, but it is not entirely correct. Additionally, vision and visual are words most often associated with EM
waves in the visual wavelength range, which is normally
dened as the same wavelength limits of human vision.
Since some organisms detect EM waves with frequencies
below and above that of humans a better denition must
28
be made. We therefore dene the visual wavelength range

as wavelengths of EM between 300nm and 800nm. This
may seem arbitrary to some, but selecting the wrong limits would render parts of some birds vision as non-vision.
Also, with this range of wavelengths, we have dened
for example the thermal-vision of certain organisms, like
for example snakes as non-vision. Therefore snakes using their pit organs, which is sensitive to EM between
5000nm and 30,000nm (IR), do not see, but somehow
feel from afar. Even if blind specimens have been documented targeting and attacking particular body parts.
Firstly a brief description of dierent types of visual system sensory organs will be elaborated on, followed by a
thorough explanation of the components in human vision,
the signal processing of the visual pathway in humans and
nished o with an example of the perceptional outcome
due to these stages.
yielding similarities for organisms that have similar

niches. There is one underlying aspect that is essentially
identical, regardless of species, or complexity of sensory
organ type, the universal usage of light-sensitive proteins
called opsins. Without focusing too much on the molecular basis though, the various constructions can be categorised into distinct groups:
Spot Eyes
Pit Eyes
Pinhole Eyes
Lens Eyes
Refractive Cornea Eyes
Sensory Organs
Reector Eyes
Vision, or the ability to see depends on visual system sensory organs or eyes. There are many dierent constructions of eyes, ranging in complexity depending on the
requirements of the organism. The dierent constructions have dierent capabilities, are sensitive to dierent
wave-lengths and have diering degrees of acuity, also
they require dierent processing to make sense of the input and dierent numbers to work optimally. The ability
to detect and decipher EM has proved to be a valuable asset to most forms of life, leading to an increased chance
of survival for organisms that utilise it. In environments
without sucient light, or complete lack of it, lifeforms
have no added advantage of vision, which ultimately has
resulted in atrophy of visual sensory organs with subsequent increased reliance on other senses (e.g. some cave
dwelling animals, bats etc.). Interestingly enough, it appears that visual sensory organs are tuned to the optical
window, which is dened as the EM wavelengths (between 300nm and 1100nm) that pass through the atmosphere reaching to the ground. This is shown in the gure
below. You may notice that there exists other windows,
an IR window, which explains to some extent the thermal"vision of snakes, and a radiofrequency (RF) window, of
which no known lifeforms are able to detect.
Compound Eyes
Gamma rays, X-rays and ultraviolet

light blocked by the upper atmosphere
(best observed from space).
Visible light
observable
from Earth,
with some
atmospheric
distortion.
100 %
Most of the
infrared spectrum
absorbed by
atmospheric
gases (best
observed
from space).
Radio waves observable

from Earth.
Long-wavelength
radio waves
blocked.
The least complicated conguration of eyes enable organisms to simply sense the ambient light, enabling the
organism to know whether there is light or not. It is normally simply a collection of photosensitive cells in a cluster in the same spot, thus sometimes referred to as spot
eyes, eye spot or stemma. By either adding more angular
structures or recessing the spot eyes, an organisms gains
access to directional information as well, which is a vital
requirement for image formation. These so called pit eyes
are by far the most common types of visual sensory organs, and can be found in over 95% of all known species.
Pinhole eye
Atmospheric
opacity
Taking this approach to the obvious extreme leads to the

pit becoming a cavernous structure, which increases the
sharpness of the image, alas at a loss in intensity. In other
words, there is a trade-o between intensity or brightness and sharpness. An example of this can be found
in the Nautilus, species belonging to the family NautilThrough time evolution has yielded many eye construc- idae, organisms considered to be living fossils. They are
tions, and some of them have evolved multiple times, the only known species that has this type of eye, referred
50 %
0%
0.1 nm
1 nm
10 nm
100 nm
1 m
10 m
100 m
Wavelength
1 mm
1 cm
10 cm
1m
10 m
100 m
1 km
2.2. VISUAL SYSTEM

to as the pinhole eye, and it is completely analogous to
the pinhole camera or the camera obscura. In addition,
like more advanced cameras, Nautili are able to adjust
the size of the aperture thereby increasing or decreasing
the resolution of the eye at a respective decrease or increase in image brightness. Like the camera, the way to
alleviate the intensity/resolution trade-o problem is to
include a lens, a structure that focuses the light unto a
central area, which most often has a higher density of
photo-sensors. By adjusting the shape of the lens and
moving it around, and controlling the size of the aperture or pupil, organisms can adapt to dierent conditions
and focus on particular regions of interest in any visual
scene. The last upgrade to the various eye constructions
already mentioned is the inclusion of a refractive cornea.
Eyes with this structure have delegated two thirds of the
total optic power of the eye to the high refractive index
liquid inside the cornea, enabling very high resolution vision. Most land animals, including humans have eyes of
this particular construct. Additionally, many variations
of lens structure, lens number, photosensor density, fovea
shape, fovea number, pupil shape etc. exists, always, to
increase the chances of survival for the organism in question. These variations lead to a varied outward appearance of eyes, even with a single eye construction category.
Demonstrating this point, a collection of photographs of
animals with the same eye category (refractive cornea
eyes) is shown below.
29
The last group of eyes, found in insects and crustaceans,
is called compound eyes. These eyes consist of a number
of functional sub-units called ommatidia, each consisting of a facet, or front surface, a transparent crystalline
cone and photo-sensitive cells for detection. In addition
each of the ommatidia are separated by pigment cells, ensuring the incoming light is as parallel as possible. The
combination of the outputs of each of these ommatidia
form a mosaic image, with a resolution proportional to
the number of ommatidia units. For example, if humans
had compound eyes, the eyes would have covered our entire faces to retain the same resolution. As a note, there
are many types of compound eyes, but delving to deep
into this topic is beyond the scope of this text.
Not only the type of eyes vary, but also the number of
eyes. As you are well aware of, humans usually have two
eyes, spiders on the other hand have a varying number
of eyes, with most species having 8. Normally the spiders also have varying sizes of the dierent pairs of eyes
and the diering sizes have dierent functions. For example, in jumping spiders 2 larger front facing eyes, give
the spider excellent visual acuity, which is used mainly to
target prey. 6 smaller eyes have much poorer resolution,
but helps the spider to avoid potential dangers. Two photographs of the eyes of a jumping spider and the eyes of
a wolf spider are shown to demonstrate the variability in
the eye topologies of arachnids.
Eye Topologies of Spiders
Refractive Cornea Eyes

An alternative to the lens approach called reector eyes
can be found in for example mollusks. Instead of the conventional way of focusing light to a single point in the
back of the eye using a lens or a system of lenses, these
organisms have mirror like structures inside the chamber of the eye that reects the light into a central portion,
much like a parabola dish. Although there are no known
examples of organisms with reector eyes capable of image formation, at least one species of sh, the spooksh
(Dolichopteryx longipes) uses them in combination with
normal lensed eyes.
Wolf Spider
Jumping Spider
2.2.2 Anatomy of the Visual System

We humans are visual creatures, therefore our eyes are
complicated with many components. In this chapter, an
attempt is made to describe these components, thus giving some insight into the properties and functionality of
human vision.
Getting inside of the eyeball - Pupil, iris and the lens
Light rays enter the eye structure through the black aperture or pupil in the front of the eye. The black appearance is due to the light being fully absorbed by the tissue
inside the eye. Only through this pupil can light enter
into the eye which means the amount of incoming light
is eectively determined by the size of the pupil. A pigmented sphincter surrounding the pupil functions as the
eyes aperture stop. It is the amount of pigment in this iris,
that give rise to the various eye colours found in humans.
Compound eye
In addition to this layer of pigment, the iris has 2 layers

of ciliary muscles. A circular muscle called the pupillary
sphincter in one layer, that contracts to make the pupil
smaller. The other layer has a smooth muscle called the
pupillary dilator, which contracts to dilate the pupil. The
30
combination of these muscles can thereby dilate/contract

the pupil depending on the requirements or conditions of
the person. The ciliary muscles are controlled by ciliary
zonules, bres that also change the shape of the lens and
hold it in place.
The lens is situated immediately behind the pupil. Its
shape and characteristics reveal a similar purpose to that
of camera lenses, but they function in slightly dierent
ways. The shape of the lens is adjusted by the pull of
the ciliary zonules, which consequently changes the focal length. Together with the cornea, the lens can change
the focus, which makes it a very important structure indeed, however only one third of the total optical power of
the eye is due to the lens itself. It is also the eyes main
lter. Lens bres make up most of the material for the
Structure of the Cornea
lense, which are long and thin cells void of most of the
cell machinery to promote transparency. Together with
water soluble proteins called crystallins, they increase the
ness.
refractive index of the lens. The bres also play part in
Descemets membrane and Endothelium: Are two
the structure and shape of the lens itself.
layers adjusted to the anterior chamber of the eye
lled with aqueous humor uid produced by the cilCornea
Anterior chamber
iary body. This uid moisturises the lens, cleans
(aqueous humour)
Uvea
Pupil
Posterior chamber
it and maintains the pressure in the eye ball. The
Iris
Suspensory
Ciliary
chamber, positioned between cornea and iris, conligament
body
of lens
tains a trabecular meshwork body through which the
Lens
Choroid
uid is drained out by Schlemm canal, through posSclera
terior chamber.
Vitreous
humour
Hyaloid
canal
Retinal
blood
vessels
Retina
Macula
Fovea
Optic nerve
Optic disc
Schematic diagram of the human eye
Beamforming in the eye Cornea and its protecting

agent - Sclera The cornea, responsible for the remaining 2/3 of the total optical power of the eye, covers the
iris, pupil and lens. It focuses the rays that pass through
the iris before they pass through the lens. The cornea is
only 0.5mm thick and consists of 5 layers:
The surface of the cornea lies under two protective membranes, called the sclera and Tenons capsule. Both of
these protective layers completely envelop the eyeball.
The sclera is built from collagen and elastic bres, which
protect the eye from external damages, this layer also
gives rise to the white of the eye. It is pierced by nerves
and vessels with the largest hole reserved for the optic
nerve. Moreover, it is covered by conjunctiva, which
is a clear mucous membrane on the surface of the eyeball. This membrane also lines the inside of the eyelid. It
works as a lubricant and, together with the lacrimal gland,
it produces tears, that lubricate and protect the eye. The
remaining protective layer, the eyelid, also functions to
spread this lubricant around.
Moving the eyes extra-ocular muscles The eyeball

is moved by a complicated muscle structure of extraocular muscles consisting of four rectus muscles inferior, medial, lateral and superior and two oblique inferior and superior. Positioning of these muscles is pre Epithelium: A layer of epithelial tissue covering the sented below, along with functions:
surface of the cornea.
As you can see, the extra-ocular muscles (2,3,4,5,6,8) are
Bowmans membrane: A thick protective layer com- attached to the sclera of the eyeball and originate in the
posed of strong collagen bres, that maintain the annulus of Zinn, a brous tendon surrounding the optic
nerve. A pulley system is created with the trochlea acting
overall shape of the cornea.
as a pulley and the superior oblique muscle as the rope,
Stroma: A layer composed of parallel collagen b- this is required to redirect the muscle force in the correct
rils. This layer makes up 90% of the corneas thick- way. The remaining extra-ocular muscles have a direct
2.2. VISUAL SYSTEM
31
Filtering of the light performed by the cornea, lens and pigment

epithelium
Extra-ocular muscles: Green - Lateral Rectus; Red - Medial Rectus; Cyan - Superior Rectus; Pink - Inferior Rectus; Dark Blue Superior Oblique; Yellow - Inferior Oblique.
the pigment ephithelium, the last stage of ltering before

the photo-reception, aects around 30% of the EM between 430nm and 500nm.
path to the eye and therefore do not form these pulley

systems. Using these extra-ocular muscles, the eye can A part of the eye, which marks the transition from nonrotate up, down, left, right and alternative movements are photosensitive region to photosensitive region, is called
the ora serrata. The photosensitive region is referred to
possible as a combination of these.
as the retina, which is the sensory structure in the back
Other movements are also very important for us to be able of the eye. The retina consists of multiple layers preto see. Vergence movements enable the proper function sented below with millions of photoreceptors called rods
of binocular vision. Unconscious fast movements called and cones, which capture the light rays and convert them
saccades, are essential for people to keep an object in into electrical impulses. Transmission of these impulses
focus. The saccade is a sort of jittery movement per- is nervously initiaed by the ganglion cells and conducted
formed when the eyes are scanning the visual eld, in or- through the optic nerve, the single route by which inforder to displace the point of xation slightly. When you mation leaves the eye.
follow a moving object with your gaze, your eyes perform what is referred to as smooth pursuit. Additional A conceptual illustration of the structure of the retina is
involuntary movements called nystagmus are caused by shown on the right. As we can see, there are ve main
signals from the vestibular system, together they make up cell types:
the vestibulo-ocular reexes.
photoreceptor cells
The brain stem controls all of the movements of the eyes,
with dierent areas responsible for dierent movements.
horizontal cells
Pons: Rapid horizontal movements, such as saccades or nystagmus
bipolar cells
Mesencephalon: Vertical and torsional movements
ganglion cells
Cerebellum: Fine tuning

Edinger-Westphal nucleus: Vergence movements
amecrine cells
Photoreceptor cells can be further subdivided into two

main types called rods and cones. Cones are much less
numerous than rods in most parts of the retina, but there
is an enormous aggregation of them in the macula, especially in its central part called the fovea. In this central region, each photo-sensitive cone is connected to one
ganglion-cell. In addition, the cones in this region are
slightly smaller than the average cone size, meaning you
get more cones per area. Because of this ratio, and the
high density of cones, this is where we have the highest
visual acuity.
Where the vision reception occurs The retina Before being transduced, incoming EM passes through the
cornea, lens and the macula. These structures also act as
lters to reduce unwanted EM, thereby protecting the eye
from harmful radiation. The ltering response of each
of these elements can be seen in the gure Filtering of
the light performed by cornea, lens and pigment epithelium. As one may observe, the cornea attenuates the
lower wavelengths, leaving the higher wavelengths nearly There are 3 types of human cones, each of the cones reuntouched. The lens blocks around 25% of the EM be- sponding to a specic range of wavelengths, because of
low 400nm and more than 50% below 430nm. Finally, three types of a pigment called photopsin. Each pigment
32

and L-cones for their sensitivity to short-, medium- and
long-wavelength respectively. It consists of protein called
opsin and a bound chromphore called the retinal. The
main building blocks of the cone cell are the synaptic terminal, the inner and outer segments, the interior nucleus
and the mitochondria.
The spectral sensitivities of the 3 types of cones:
1. S-cones absorb short-wave light, i.e. blue-violet
light. The maximum absorption wavelength for the
S-cones is 420nm
2. M-cones absorb blue-green to yellow light. In this
case The maximum absorption wavelength is 535nm
3. L-cones absorb yellow to red light. The maximum absorption wavelength is 565nm
Structure of retina including the main cell components: RPE: retinal pigment epithelium; OS: outer segment of the photoreceptor
cells; IS: inner segment of the photoreceptor cells; ONL: outer nuclear layer; OPL: outer plexiform layer; INL: inner nuclear layer
IPL: inner plexiform layer; GC: ganglion cell layer; P: pigment
epithelium cell; BM: Bruch-Membran; R: rods; C: cones; H: horizontal cell; B: bipolar cell; M: Mller cell; A:amacrine cell; G:
ganglion cell; AX: Axon; arrow: Membrane limitans externa.
Cone cell structure
The inner segment contains organelles and the cells nucleus and organelles. The pigment is located in the outer
segment, attached to the membrane as trans-membrane
proteins within the invaginations of the cell-membrane
that form the membranous disks, which are clearly visible in the gure displaying the basic structure of rod and
cone cells. The disks maximize the reception area of
the cells. The cone photoreceptors of many vertebrates
Density of rods and cones around the eye
contain spherical organelles called oil droplets, which
are thought to constitute intra-ocular lters which may
serve to increase contrast, reduce glare and lessen chrois sensitive to red, blue or green wavelength of light, so matic aberrations caused by the mitochondrial size gradiwe have blue, green and red cones, also called S-, M- ent from the periphery to the centres.
2.2. VISUAL SYSTEM
33
Rods have a structure similar to cones, however they contain the pigment rhodopsin instead, which allows them to
detect low-intensity light and makes them 100 times more
sensitive than cones. Rhodopsin is the only pigment found
in human rods, and it is found on the outer side of the
pigment epithelium, which similarly to cones maximizes
absorption area by employing a disk structure. Similarly
to cones, the synaptic terminal of the cell joins it with
a bipolar cell and the inner and outer segments are connected by cilium.
in the inner nuclear layer. Dendrites interconnect exclusively with cones and rods and we dierentiate between
one rod bipolar cell and nine or ten cone bipolar cells.
These cells branch with amacrine or ganglion cells in the
inner plexiform layer using an axon. Rod bipolar cells
connect to triad synapses or 18-70 rod cells. Their axons
spread around the inner plexiform layer synaptic terminals, which contain ribbon synapses and contact a pair of
cell processes in dyad synapses. They are connected to
ganglion cells with AII amacrine cell links.
The pigment rhodopsin absorbs the light between 400600nm, with a maximum absorption at around 500nm.
This wavelength corresponds to greenish-blue light which
means blue colours appear more intense in relation to red
colours at night.
Amecrine cells can be found in the inner nuclear layer and

in the ganglion cell layer of the retina. Occasionally they
are found in the inner plexiform layer, where they work as
signal modulators. They have been classied as narroweld, small-eld, medium-eld or wide-eld depending
on their size. However, many classications exist leading
to over 40 dierent types of amecrine cells.
420
498
534 564
100
Normalized absorbance
Ganglion cells are the nal transmitters of visual signal

from the retina to the brain. The most common ganglion
cells in the retina is the midget ganglion cell and the parasol ganglion cell. The signal after having passed through
50
all the retinal layers is passed on to these cells which are
the nal stage of the retinal processing chain. All the inS
R
M L
formation is collected here forwarded to the retinal nerve
0
bres and optic nerves. The spot where the ganglion ax500
400
600
700
Violet
Blue
Cyan
Green
Yellow
Red
ons fuse to create an optic nerve is called the optic disc.
Wavelength (nm)
This nerve is built mainly from the retinal ganglion axons
and Portort cells. The majority of the axons transmit data
The sensitivity of cones and rods across visible EM
to the lateral geniculate nucleus, which is a termination
EM waves with wavelengths outside the range of 400 nexus for most parts of the nerve and which forwards the
700 nm are not detected by either rods nor cones, which information to the visual cortex. Some ganglion cells also
react to light, but because this response is slower than that
ultimately means they are not visible to human beings.
of rods and cones, it is believed to be related to sensing
Horizontal cells occupy the inner nuclear layer of the ambient light levels and adjusting the biological clock.
retina. There are two types of horizontal cells and both
types hyper-polarise in response to light i.e. they become
more negative. Type A consists of a subtype called HII- 2.2.3 Signal Processing
H2 which interacts with predominantly S-cones. Type B
cells have a subtype called HI-H1, which features a den- As mentioned before the retina is the main component
drite tree and an axon. The former contacts mostly M- in the eye, because it contains all the light sensitive cells.
and L-cone cells and the latter rod cells. Contacts with Without it, the eye would be comparable to a digital camcones are made mainly by prohibitory synapses, while the era without the CCD (Charge Coupled Device) sensor.
cells themselves are joined into a network with gap junc- This part elaborates on how the retina perceives the light,
tions.
how the optical signal is transmitted to the brain and how
the brain processes the signal to form enough information
for decision making.
Creation of the initial signals - Photosensor Function Vision invariably starts with light hitting the photosensitive cells found in the retina. Light-absorbing visual
pigments, a variety of enzymes and transmitters in retinal rods and cones will initiate the conversion from visible
Cross-section of the human retina, with bipolar cells indicated in EM stimuli into electrical impulses, in a process known
as photoelectric transduction. Using rods as an examred.
ple, the incoming visible EM hits rhodopsin molecules,
Bipolar cells spread single dendrites in the outer plexi- transmembrane molecules found in the rods outer disk
form layer and the perikaryon, their cell bodies, are found structure. Each rhodopsin molecule consists of a cluster
34
of helices called opsin that envelop and surround 11-cis
retinal, which is the part of the molecule that will change
due to the energy from the incoming photons. In biological molecules, moieties, or parts of molecules that
will cause conformational changes due to this energy is
sometimes referred to as chromophores. 11-cis retinal
straightens in response to the incoming energy, turning
into retinal (all-trans retinal), which forces the opsin helices further apart, causing particular reactive sites to be
uncovered. This activated rhodopsin molecule is sometimes referred to as Metarhodopsin II. From this point
on, even if the visible light stimulation stops, the reaction will continue. The Metarhodopsin II can then react
with roughly 100 molecules of a G protein called transducing, which then results in a and ? after the GDP
is converted into GTP. The activated a -GTP then binds
to cGMP-phosphodiesterase(PDE), suppressing normal
ion-exchange functions, which results in a low cytosol
concentration of cation ions, and therefore a change in
the polarisation of the cell.
The natural photoelectric transduction reaction has an
amazing power of amplication. One single retinal
rhodopsin molecule activated by a single quantum of light
causes the hydrolysis of up to 106 cGMP molecules per
second.

4. Metarhodopsin II is unstable and splits, yielding
opsin and all-trans retinal.
5. The opsin activates the regulatory protein
transducin. This causes transducin to dissociate from its bound GDP, and bind GTP, then the
alpha subunit of transducin dissociates from the
beta and gamma subunits, with the GTP still bound
to the alpha subunit.
6. The alpha subunit-GTP
phosphodiesterase.
complex
activates
7. Phosphodiesterase breaks down cGMP to 5'-GMP.

This lowers the concentration of cGMP and therefore the sodium channels close.
8. Closure of the sodium channels causes hyperpolarization of the cell due to the ongoing potassium current.
9. Hyperpolarization of the cell causes voltage-gated
calcium channels to close.
10. As the calcium level in the photoreceptor cell drops,
the amount of the neurotransmitter glutamate that is
released by the cell also drops. This is because calcium is required for the glutamate-containing vesicles to fuse with cell membrane and release their
contents.
11. A decrease in the amount of glutamate released by
the photoreceptors causes depolarization of On center bipolar cells (rod and cone On bipolar cells) and
hyperpolarization of cone O bipolar cells.
Representation of molecular steps in photoactivation (modied

from Leskov et al., 2000). Depicted is an outer membrane disk
in a rod. Step 1: Incident photon (h) is absorbed and activates
a rhodopsin by conformational change in the disk membrane to
R*. Step 2: Next, R* makes repeated contacts with transducin
molecules, catalyzing its activation to G* by the release of bound
GDP in exchange for cytoplasmic GTP (Step 3). The and
subunit G* binds inhibitory subunits of the phosphodiesterase
(PDE) activating its and subunits. Step 4: Activated PDE hydrolyzes cGMP. Step 5: Guanylyl cyclase (GC) synthesizes cGMP,
the second messenger in the phototransduction cascade. Reduced
levels of cytosolic cGMP cause cyclic nucleotide gated channels
to close preventing further inux of Na+ and Ca2+.
Without visible EM stimulation, rod cells containing a

cocktail of ions, proteins and other molecules, have membrane potential dierences of around 40mV. Compared to other nerve cells, this is quite high (65mV). In
this state, the neurotransmitter glutamate is continuously
released from the axon terminals and absorbed by the
neighbouring bipolar cells. With incoming visble EM and
the previously mentioned cascade reaction, the potential
dierence drops to 70mV. This hyper-polarisation of
the cell causes a reduction in the amount of released glutamate, thereby aecting the activity of the bipolar cells,
and subsequently the following steps in the visual pathway.
Similar processes exist in the cone-cells and in photosensitive ganglion cells, but make use of dierent opsins.
Photopsin I through III (yellowish-green, green and bluePhoto Transduction
violet respectively) are found in the three dierent cone
1. A light photon interacts with the retinal in a cells and melanopsin (blue) can be found in the photosenphotoreceptor. The retinal undergoes isomerisation, sitive ganglion cells.
changing from the 11-cis to all-trans conguration.
Processing Signals in the Retina Dierent bipolar
cells react dierently to the changes in the released glu3. Opsin therefore undergoes a conformational change tamate. The so called ON and OFF bipolar cells are used
to metarhodopsin II.
to form the direct signal ow from cones to bipolar cells.
2. Retinal no longer ts into the opsin binding site.
2.2. VISUAL SYSTEM
35
ble EM stimulation on the centric zone could lead to AP
frequency increase and the stimulation on the periphery
zone will decrease the AP frequency. When the light
source is turned o the excitation occurs. So the name
of ON eld (central eld ON) refers to this kind of region. Of course the RF of the OFF ganglion cells act the
opposite way and is therefore called OFF eld (central
eld OFF). The RFs are organised by the horizontal cells.
The impulse on the periphery region will be impulsed and
transmitted to the central region, and there the so-called
stimulus contrast is formed. This function will make the
dark seem darker and the light brighter. If the whole RF
is exposed to light. the impulse of the central region will
predominate.
Signal Transmission to the Cortex As mentioned

previously, axons of the ganglion cells converge at the
optic disk of the retina, forming the optic nerve. These
bres are positioned inside the bundle in a specic order. Fibres from the macular zone of the retina are in
the central portion, and those from the temporal half of
the retina take up the periphery part. A partial decussation or crossing occurs when these bres are outside
the eye cavity. The bres from the nasal halves of each
retina cross to the opposite halves and extend to the brain.
Those from the temporal halves remain uncrossed. This
partial crossover is called the optic chiasma, and the optic nerves past this point are called optic tracts, mainly
to distinguish them from single-retinal nerves. The function of the partial crossover is to transmit the right-hand
visual eld produced by both eyes to the left-hand half
of the brain only and vice versa. Therefore the information from the right half of the body, and the right visual
eld, is all transmitted to the left-hand part of the brain
The ON bipolar cells will depolarise by visible EM stim- when reaches the posterior part of the fore-brain (dienulation and the corresponding ON ganglion cells will be cephalon).
activated. On the other hand the OFF bipolar cells are
hyper polarised by the visible EM stimulation, and the The information relay between the bers of optic tracts
and the nerve cells occurs in the lateral geniculate bodies,
OFF ganglion cells are inhibited. This is the basic pathway of the Direct signal ow. The Lateral signal ow the central part of the visual signal processing, located
in the thalamus of the brain. From here the information
will start from the rods, then go to the bipolar cells, the
amacrine cells, and the OFF bipolar cells inhibited by the is passed to the nerve cells in the occipital cortex of the
corresponding side of the brain. Connections from the
Rod-amacrine cells and the ON bipolar cells will stimulated via an electrical synapse, after all of the previous retina to the brain can be separated into a 'parvocellular
steps, the signal will arrive at the ON or OFF ganglion pathway' and a magnocellular pathway. The parvocelcells and the whole pathway of the Lateral signal ow is lular pathways signals color and ne detail, whereas the
magnocellular pathways detect fast moving stimuli.
established.
When the action potential (AP) in ON, ganglion cells will Signals from standard digital cameras correspond apbe triggered by the visible EM stimulus. The AP fre- proximately to those of the parvocellular pathway. To
quency will increase when the sensor potential increases. simulate the responses of parvocellular pathways, reIn other words, AP depends on the amplitude of the sen- searchers have been developing neuromorphic sensory
sors potential. The region of ganglion cells where the systems, which try to mimic spike-based computation
stimulatory and inhibitory eects inuence the AP fre- in neural systems. Thereby they use a scheme called
quency is called receptive eld (RF). Around the gan- address-event representation for the signal transmission
glion cells, the RF is usually composed of two regions: in the neuromorphic electronic systems (Liu and Delthe central zone and the ring-like peripheral zone. They bruck 2010 ).
are distinguishable during visible EM adaptation. A visi- Anatomically, the retinal Magno and Parvo ganglion cells
36

are thought of as being intimately connected. This connection, called corpus callosum is made of neurons, axons and dendrites. Because the dendrites make synaptic connections to the related points of the hemispheres,
electric simulation of every point on one hemisphere indicates simulation of the interconnected point on the other
hemisphere. The only exception to this rule is the primary
visual cortex.
The synapses are made by the optic tract in the respective
layers of the lateral geniculate body. Then these axons of
these third-order nerve cells are passed up to the calcarine
ssure in each occipital lobe of the cerebral cortex. Because bands of the white bres and axons pair from the
nerve cells in the retina go through it, it is called the striate
cortex, which incidentally is our primary visual cortex,
sometimes known as V1. At this point, impulses from
the separate eyes converge to common cortical neurons,
which then enables complete input from both eyes in one
region to be used for perception and comprehension. Pattern recognition is a very important function of this particular part of the brain, with lesions causing problems
with visual recognition or blindsight.
The pathway to the central cortex
Connections from the retina to the brain can be separated into

a parvocellular pathway and a magnocellular pathway. The
parvocellular pathway originates in midget cells in the retina, and
signals color and ne detail; magnocellular pathway starts with
parasol cells, and detects fast moving stimuli.
respectively project to 2 ventral magnocellular layers and

4 dorsal parvocellular layers of the Lateral Geniculate
Nucleus (LGN). Each of the six LGN layers receives inputs from either the ipsilateral or contralateral eye, i.e.,
the ganglion cells of the left eye cross over and project
to layer 1, 4 and 6 of the right LGN, and the right eye
ganglion cells project (uncrossed) to its layer 2, 3 and 5.
From here the information from the right and left eye is
separated.
Although human vision is combined by two halves of the
retina and the signal is processed by the opposite cerebral
hemispheres, the visual eld is considered as a smooth
and complete unit. Hence the two visual cortical areas
Based on the ordered manner in which the optic tract bres pass information to the lateral geniculate bodies and
after that pass in to the striate area, if one single point
stimulation on the retina was found, the response which
produced electrically in both lateral geniculate body and
the striate cortex will be found at a small region on the
particular retinal spot. This is an obvious point-to-point
way of signal processing. And if the whole retina is stimulated, the responses will occur on both lateral geniculate
bodies and the striate cortex gray matter area. It is possible to map this brain region to the retinal elds, or more
usually the visual elds.
Any further steps in this pathway is beyond the scope of
this book. Rest assured that, many further levels and centres exist, focusing on particular specic tasks, like for example colour, orientations, spatial frequencies, emotions
etc.
Information Processing in the Visual System

Equipped with a rmer understanding of some of the
more important concepts of the signal processing in the
visual system, comprehension or perception of the processed sensory information is the last important piece in
the puzzle. Visual perception is the process of translating
information received by the eyes into an understanding of
the external state of things. It makes us aware of the world
around us and allows us to understand it better. Based
on visual perception we learn patterns which we then apply later in life and we make decisions based on this and
the obtained information. In other words, our survival
depends on perception. The eld of Visual Perception
has been divided into dierent subelds, due to the fact
that processing is too complex and requires of dierent
2.2. VISUAL SYSTEM
37
specialized mechanisms to perceive what is seen. These biological machinery the visual system of the brain. It
subelds include: Color Perception, Motion Perception, processes everything we see in a hierarchical way, startDepth Perception, and Face Recognition, etc.
ing from simpler features of the image to more complex
ones all the way to classication of objects into categories. Hence the visual system is said to have a deep
hierarchy. The deep hierarchy of the primate visual system has inspired computer scientists to create models of
articial neural networks that would also feature several
layers where each of them creates higher generalizations
of the input data.
Approximately half of the human neocortex is dedicated
to vision. The processing of visual information happens
over at least 10 functional levels. The neurons in the early
visual areas extract simple image features over small local regions of visual space. As the information gets transmitted to higher visual areas, neurons respond to increasingly complex features. With higher levels of information
processing the representations become more invariant
less sensitive to the exact feature size, rotation or position.
In addition, the receptive eld size of neurons in higher
visual areas increases, indicating that they are tuned to
more global image features. This hierarchical structure
allows for ecient computing dierent higher visual areas can use the same information computed in the lower
areas. The generic scene description that is made in the
early visual areas is used by other parts of the brain to
complete various dierent tasks, such as object recognition and categorization, grasping, manipulation, movement planning etc.
Deep hierarchies in the visual system
Deep Hierarchies in the Primate Visual Cortex Despite the ever-increasing computational power of electronic systems, there are still many tasks where animals
and humans are vastly superior to computers one of
them being the perception and contextualization of information. The classical computer, either the one in your
phone or a supercomputer taking up the whole room, is
in essence a number-cruncher. It can perform an incredible amount of calculations in a miniscule amount of time.
What it lacks is creating abstractions of the information
it is working with. If you attach a camera to your computer, the picture it perceives is just a grid of pixels,
a 2-dimensional array of numbers. A human would immediately recognize the geometry of the scene, the objects in the picture, and maybe even the context of whats
going on. This ability of ours is provided by dedicated
Sub-cortical vision The neural processing of visual information starts already before any of the cortical structures. Photoreceptors on the retina detect light and send
signals to retinal ganglion cells. The receptive eld size
of a photoreceptor is one 100th of a degree (a one degree
large receptive eld is roughly the size of your thumb,
when you have your arm stretched in front of you). The
number of inputs to a ganglion cell and therefore its receptive eld size depends on the location in the center
of the retina it receives signals from as few as ve receptors, while in the periphery a single cell can have several
thousand inputs. This implies that the highest spatial resolution is in the center of the retina, also called the fovea.
Due to this property primates posses a gaze control mechanism that directs the eyesight so that the features of interest project onto the fovea.
Ganglion cells are selectively tuned to detect various features of the image, such as luminance contrast, color contrast, and direction and speed of movement. All of these
features are the primary information used further up the
processing pipeline. If there are visual stimuli that are not
detectable by ganglion cells, then they are also not available for any cortical visual area.
Ganglion cells project to a region in thalamus called lateral geniculate nucleus (LGN), which in turn relays the
signals to the cortex. There is no signicant computation
38
known to happen in LGN there is almost a one-to-one
correspondence between retinal ganglion and LGN cells.
However, only 5% of the inputs to LGN come from the
retina all the other inputs are cortical feedback projections. Although the visual system is often regarded as a
feed-forward system, the recurrent feedback connections
as well as lateral connections are a common feature seen
throughout the visual cortex. The role of the feedback is
not yet fully understood but it is proposed to be attributed
to processes like attention, expectation, imagination and
lling-in the missing information.
Main areas of the visual system
Cortical vision The visual cortex can be divided into

three large parts the occipital part which receives input from LGN and then sends outputs to dorsal and ventral streams. Occipital part includes the areas V1-V4 and
MT, which process dierent aspects of visual information and gives rise to a generic scene representation. The
dorsal pathway is involved in the analysis of space and in
action planning. The ventral pathway is involved in object recognition and categorization.
V1 is the rst cortical area that processes visual information. It is sensitive to edges, gratings, line-endings,
motion, color and disparity (angular dierence between
the projections of a point onto the left and right retinas).
The most straight forward example of the hierarchical
bottom-up processing is the linear combination of the inputs from several ganglion cells with center-surround receptive elds to create a representation of a bar. This is
done by the simple cells of V1 and was rst described
by the prominent neuroscientists Hubel and Wiesel. This
type of information integration implies that the simple
cells are sensitive to the exact location of the bar and have
a relatively small receptive eld. The complex cells of V1
receive inputs from the simple cells, and while also responding to linear oriented patterns they are not sensitive
to the exact position of the bar and have a larger receptive eld. The computation present in this step could be
a MAX-like operation which produces responses similar
in amplitude to the larger of the responses pertaining to

the individual stimuli. Some simple and complex cells
can also detect the end of a bar, and a fraction of V1 cells
are also sensitive to local motion within their respective
receptive elds.
Area V2 features more sophisticated contour representation including texture-dened contours, illusory contours
and contours with border ownership. V2 also builds upon
the absolute disparity detection in V1 and features cells
that are sensitive to relative disparity which is the difference between the absolute disparities of two points in
space. Area V4 receives inputs from V2 and area V3, but
very little is known about the computation taking place in
V3. Area V4 features neurons that are sensitive to contours with dierent curvature and vertices with particular angles. Another important feature is the coding for
luminance-invariant hue. This is in contrast to V1 where
neurons respond to color opponency along the two principle axis (red-green and yellow-blue) rather than the actual
color. V4 further outputs to the ventral stream, to inferior temporal cortex (IT) which has been shown through
lesion studies to be essential for object discrimination.
Stimulus reduction in area TE
Inferior temporal cortex: object discrimination Inferior temporal cortex (IT) is divided into two areas:
TEO and TE. Area TEO integrates information about the
shapes and relative positions of multiple contour elements
and features mostly cells which respond to simple combinations of features. The receptive eld size of TEO neurons is about 3-5 degrees. Area TE features cells with
signicantly larger receptive elds (10-20 degrees) which
respond to faces, hands and complex feature congurations. Cells in TE respond to visual features that are a
simpler generalization of the object of interest but more
complex than simple bars or spots. This was shown using
a stimulus-reduction method by Tanaka et al. where rst
a response to an object is measured and then the object is
replaced by simpler representations until the critical feature that the TE neurons are responding to is narrowed
down.
It appears that the neurons in IT pull together various
features of medium complexity from lower levels in the
ventral stream to build models of object parts. The neurons in TE that are selective to specic objects have to
full two seemingly contradictory requirements selectivity and invariance. They have to distinguish between
dierent objects by the means of sensitivity to features
in the retinal images. However, the same object can be
viewed from dierent angles and distances at dierent
light conditions yielding highly dissimilar retinal images
of the same object. To treat all these images as equivalent, invariant features must be derived that are robust
2.2. VISUAL SYSTEM

against certain transformations, such as changes in position, illumination, size on the retina etc. Neurons in
area TE show invariance to position and size as well as to
partial occlusion, position-in-depth and illumination direction. Rotation in depth has been shown to have the
weakest invariance, with the exception if the object is a
human face.
Object categories are not yet explicitly present in area TE
a neuron might typically respond to several but not all
exemplars of the same category (e.g., images of trees) and
it might also respond to exemplars of dierent categories
(e.g., trees and non-trees). Object recognition and classication most probably involves sampling from a larger
population of TE neurons as well as receiving inputs from
additional brain areas, e.g., those that are responsible for
understanding the context of the scene. Recent readout
experiments have demonstrated that statistical classiers
(e.g. support vector machines) can be trained to classify
objects based on the responses of a small number of TE
neurons. Therefore, a population of TE neurons in principle can reliably signal object categories by their combined
activity. Interestingly, there are also reports on highly selective neurons in medial temporal lobe that respond to
very specic cues, e.g., to the tower of Pisa in dierent
images or to a particular persons face.
39
inception in the 1980s deep learning didnt get much attention until the mid-2000s with the abundance of digital
data and the invention of faster training algorithms. Deep
neural networks have proved themselves to be very eective in tasks that not so long ago seemed possible only
for humans to perform, such as recognizing the faces of
particular people in photos, understanding human speech
(to some extent) and translating text from foreign languages. Furthermore, they have proven to be of great
assistance in industry and science to search for potential
drug candidates, map real neural networks in the brain
and predict the functions of proteins. It must be noted
that deep learning is only very loosely inspired from the
brain and is much more of an achievement of the eld
of computer science / machine learning than of neuroscience. The basic parallels are that the deep neural networks are composed of units that integrate information
inputs in a non-linear manner (neurons) and send signals
to each other (synapses) and that there are dierent levels
of increasingly abstract representations of the data. The
learning algorithms and mathematical descriptions of the
neurons used in deep learning are very dierent from
the actual processes taking place in the brain. Therefore,
the research in deep learning, while giving a huge push to
a more sophisticated articial intelligence, can give only
limited insights about the brain.
Learning in the Visual System Learning can alter the

visual feature selectivity of neurons, with the eect of References
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cells in V1 inspired the creation of one of the rst deep
Li, Nuo; DiCarlo, James J. (23 September 2010).
learning architectures, the neocognitron a multilayered
Unsupervised Natural Visual Experience Rapidly
articial neural network model. It was used for dierReshapes Size-Invariant Object Representation in
ent pattern recognition tasks, including the recognition
Inferior Temporal Cortex. Neuron 67 (6): 1062
of handwritten characters. However, it took a lot of time
1075. doi:10.1016/j.neuron.2010.08.029.
to train the network (in the order of days) and since its
40
Raiguel, S.; Vogels, R.; Mysore, S. G.; Orban, G.

A. (14 June 2006). Learning to See the Dierence
Specically Alters the Most Informative V4 Neurons. Journal of Neuroscience 26 (24): 65896602.
doi:10.1523/JNEUROSCI.0457-06.2006.
Schoups, A; Vogels, R; Qian, N; Orban, G (2 August 2001). Practising orientation identication
improves orientation coding in V1 neurons.. Nature 412 (6846): 549-53. PMID 11484056.
A recent and accessible overview of the status quo of
the deep learning research
Jones, Nicola (8 January 2014). Computer science:
The learning machines. Nature 505 (7482): 146
148. doi:10.1038/505146a.
Motion Perception
Example of a Beta movement.
Motion Perception is the process of inferring speed and

direction of moving objects. Area V5 in humans and area
MT (Middle Temporal) in primates are responsible for
cortical perception of Motion. Area V5 is part of the
extrastriate cortex, which is the region in the occipital region of the brain next to the primary visual cortex. The
function of Area V5 is to detect speed and direction of
visual stimuli, and integrate local visual motion signals
into global motion. Area V1 or Primary Visual cortex is
located in the occipital lobe of the brain in both hemispheres. It processes the rst stage of cortical processing
of visual information. This area contains a complete map
of the visual eld covered by the eyes. The dierence
between area V5 and area V1 (Primary Visual Cortex) is
that area V5 can integrate motion of local signals or individual parts of an object into a global motion of an entire
object. Area V1, on the other hand, responds to local motion that occurs within the receptive eld. The estimates
from these many neurons are integrated in Area V5.
Second order motion refers to the motion that occurs when

a moving contour is dened by contrast, texture, icker
or some other quality that does not result in an increase
in luminance or motion energy of the image. Evidence
suggests that early processing of First order motion and
Second order motion is carried out by separate pathways.
Second order mechanisms have poorer temporal resolution and are low-pass in terms of the range of spatial frequencies to which they respond. Second-order motion
produces a weaker motion aftereect. First and secondorder signals are combined in are V5.
Movement is dened as changes in retinal illumination

over space and time. Motion signals are classied into
First order motions and Second order motions. These
motion types are briey described in the following paragraphs.
First-order motion perception refers to the motion perceived when two or more visual stimuli switch on and
o over time and produce dierent motion perceptions.
First order motion is also termed apparent motion, and
it is used in television and lm. An example of this is
the Beta movement, which is an illusion in which xed
images seem to move, even though they do not move in
reality. These images give the appearance of motion, because they change and move faster than what the eye can
detect. This optical illusion happens because the human
optic nerve responds to changes of light at ten cycles per
second, so any change faster than this rate will be registered as a continuum motion, and not as separate images.
In this chapter, we will analyze the concepts of Motion

Perception and Motion Analysis, and explain the reason
why these terms should not be used interchangeably. We
will analyze the mechanisms by which motion is perceived such as Motion Sensors and Feature Tracking.
There exist three main theoretical models that attempt to
describe the function of neuronal sensors of motion. Experimental tests have been conducted to conrm whether
these models are accurate. Unfortunately, the results of
these tests are inconclusive, and it can be said that no
single one of these models describes the functioning of
Motion Sensors entirely. However, each of these models
simulates certain features of Motion Sensors. Some properties of these sensors are described. Finally, this chapter
shows some motion illusions, which demonstrate that our
sense of motion can be mislead by static external factors
that stimulate motion sensors in the same way as motion.
Motion Analysis and Motion Perception The concepts of Motion Analysis and Motion Perception are often confused as interchangeable. Motion Perception and
Motion Analysis are important to each other, but they are
not the same.
Motion Analysis refers to the mechanisms in which motion signals are processed. In a similar way in which
2.2. VISUAL SYSTEM
41
Motion Perception does not necessarily depend on signals generated by motion of images in the retina, Motion Analysis may or may not lead to motion perception.
An example of this phenomenon is Vection, which occurs when a person perceives that she is moving when she
is stationary, but the object that she observes is moving.
Vection shows that motion of an object can be analyzed,
even though it is not perceived as motion coming from
the object. This denition of Motion analysis suggests
that motion is a fundamental image property. In the visual eld, it is analyzed at every point. The results from
this analysis are used to derive perceptual information.
Motion Perception refers to the process of acquiring perceptual knowledge about motion of objects and surfaces
in an image. Motion is perceived either by delicate local
sensors in the retina or by feature tracking. Local motion
sensors are specialized neurons sensitive to motion, and
analogous to specialized sensors for color. Feature tracking is an indirect way to perceive motion, and it consists
of inferring motion from changes in retinal position of
objects over time. It is also referred to as third order motion analysis. Feature tracking works by focusing attention to a particular object and observing how its position
has changed over time.
Two dierent mechanisms for motion detection. Left) A Reichardt detector consists of two mirror-symmetrical subunits. In
each subunit, the luminance values as measured in two adjacent
points become multiplied (M) with each other after one of them
is delayed by a low-pass lter with time-constant . The resulting output signals of the multipliers become nally subtracted.
Right) In the gradient detector, the temporal luminance gradient
as measured after one photoreceptor (I/t, Left) is divided by
the spatial luminance gradient (I/x). Here, the spatial gradient
is approximated by the dierence between the luminance values
in two adjacent points.
Motion Sensors Detection of motion is the rst stage

of visual processing, and it happens thanks to specialized
neural processes, which respond to information regarding
local changes of intensity of images over time. Motion
is sensed independently of other image properties at all
locations in the image. It has been proven that motion
sensors exist, and they operate locally at all points in the
image. Motion sensors are dedicated neuronal sensors
located in the retina that are capable of detecting a motion produced by two brief and small light ashes that are
so close together that they could not be detected by feature tracking. There exist three main models that attempt
to describe the way that these specialized sensors work.
These models are independent of one another, and they
try to model specic characteristics of Motion Perception. Although there is not sucient evidence to support
that any of these models represent the way the visual system (motion sensors particularly) perceives motion, they
still correctly model certain functions of these sensors.
tiotemporal correlation of luminance signals at neighboring points. It uses the fact that two receptive elds at different points on the trajectory of a moving object receive
a time shifted version of the same signal a luminance
pattern moves along an axis and the signal at one point
in the axis is a time shifted version of a previous signal
in the axis. The Reichardt Detector model has two spatially separate neighboring detectors. The output signals
of the detectors are multiplied (correlated) in the following way: a signal multiplied by a second signal that is
the time-shifted version of the original. The same procedure is repeated but in the reverse direction of motion
(the signal that was time-shifted becomes the rst signal
and vice versa). Then, the dierence between these two
multiplications is taken, and the outcome gives the speed
of motion. The response of the detector depends upon
the stimulus phase, contrast and speed. Many detectors
tuned at dierent speeds are necessary to encode the true
speed of the pattern. The most compelling experimental
evidence for this kind of detector comes from studies of
direction discrimination of barely visible targets.
The Reichardt Detector
Motion-Energy Filtering
The Reichardt Detector is used to model how motion sensors respond to First order motion signals. When an objects moves from point A in the visual eld to point B,
two signals are generated: one before the movement began and another one after the movement has completed.
This model perceives this motion by detecting changes
in luminance at one point on the retina and correlating it
with a change in luminance at another point nearby after a short delay. The Reichardt Detector operates based
on the principle of correlation (statistical relation that involves dependency). It interprets a motion signal by spa-
Motion Energy Filter is a model of Motion Sensors based

on the principle of phase invariant lters. This model
builds spatio-temporal lters oriented in space-time to
match the structure of moving patterns. It consists of separable lters, for which spatial proles remain the same
shape over time but are scaled by the value of the temporal lters. Motion Energy Filters match the structure
of moving patterns by adding together separable lters.
For each direction of motion, two space-time lters are
generated: one, which is symmetric (bar-like), and one
which is asymmetric (edge-like). The sum of the squares
42
of these lters is called the motion energy. The dierence in the signal for the two directions is called the opponent energy. This result is then divided by the squared
output of another lter, which is tuned to static contrast.
This division is performed to take into account the effect of contrast in the motion. Motion Energy Filters can
model a number of motion phenomenon, but it produces
a phase independent measurement, which increases with
speed but does not give a reliable value of speed.
blank intervals. They can also separate these two stages

(movements and blank intervals). Motion sensors, on the
other hand, would just integrate the blanks with the moving stimulus and see a continuous movement. Feature
trackers operate on the locations of identied features.
For that reason, they have a minimum distance threshold that matches the precision with which locations of
features can be discriminated. Feature trackers do not
show motion aftereects, which are visual illusions that
are caused as a result of visual adaptation. Motion afterSpatiotemporal Gradients
eects occur when, after observing a moving stimulus, a
stationary object appears to be moving in the opposite direction of the previously observed moving stimulus. It is
I(x,t)
dx
Dt I
t
impossible for this mechanism to monitor multiple mov=
= I(x,t) =
dt
Dx I
tions in dierent parts of the visual eld and at the same
x
time. On the other hand, multiple motions are not a probThis model of Motion sensors was originally developed in lem for motion sensors, because they operate in parallel
the eld of computer vision, and it is based on the prin- across the entire visual eld.
ciple that the ratio of the temporal derivative of image
brightness to the spatial derivative of image brightness Experiments have been conducted using the informagives the speed of motion. It is important to note that tion above to reach interesting conclusions about feature
at the peaks and troughs of the image, this model will trackers. Experiments with brief stimuli have shown that
not compute an adequate answer, because the derivative color patterns and contrast patterns at high contrasts are
in the denominator would be zero. In order to solve this not perceived by feature trackers but by motion sensors.
problem, the rst-order and higher-order spatial deriva- Experiments with blank intervals have conrmed that featives with respect to space and time can also be analyzed. ture tracking can occur with blank intervals in the display.
Spatiotemporal Gradients is a good model for determin- It is only at high contrast that motion sensors perceive
the motion of chromatic stimuli and contrast patterns. At
ing the speed of motion at all points in the image.
low contrasts feature trackers analyze the motion of both
chromatic patterns and contrast envelopes and at high
Motion Sensors are Orientation-Selective One contrasts motion sensors analyze contrast envelopes. Exof the properties of Motion Sensors is orientation- periments in which subjects make multiple motion judgselectivity, which constrains motion analysis to a single ments suggest that feature tracking is a process that ocdimension. Motion sensors can only record motion in curs under conscious control and that it is the only way
one dimension along an axis orthogonal to the sensors we have to analyze the motion of contrast envelopes in
preferred orientation. A stimulus that contains features low-contrast displays. These results are consistent with
of a single orientation can only be seen to move in a the view that the motion of contrast envelopes and color
direction orthogonal to the stimulus orientation. One- patterns depends on feature tracking except when colors
dimensional motion signals give ambiguous information are well above threshold or mean contrast is high. The
about the motion of two-dimensional objects. A second main conclusion of these experiments is that it is probstage of motion analysis is necessary in order to resolve ably feature tracking that allows perception of contrast
the true direction of motion of a 2-D object or pattern. envelopes and color patterns.
1-D motion signals from sensors tuned to dierent
orientations are combined to produce an unambiguous
2-D motion signal. Analysis of 2-D motion depends on Motion Illusions As a consequence of the process in
signals from local broadly oriented sensors as well as on which Motion detection works, some static images might
seem to us like they are moving. These images give an
signals from narrowly oriented sensors.
insight into the assumptions that the visual system makes,
and are called visual illusions.
Feature Tracking Another way in which we perceive A famous Motion Illusion related to rst order motion
motion is through Feature Tracking. Feature Tracking signals is the Phi phenomenon, which is an optical illuconsists of analyzing whether or not the local features of sion that makes us perceive movement instead of a sean object have changed positions, and inferring move- quence of images. This motion illusion allows us to watch
ment from this change. In this section, some features movies as a continuum and not as separate images. The
about Feature trackers are mentioned.
phi phenomenon allows a group of frozen images that are
Feature trackers fail when a moving stimulus occurs very
rapidly. Feature trackers have the advantage over Motion sensors that they can perceive movement of an object even if the movement is separated by intermittent
changed at a constant speed to be seen as a constant movement. The Phi phenomenon should not be confused with
the Beta Movement, because the former is an apparent
movement caused by luminous impulses in a sequence,
2.2. VISUAL SYSTEM
43
while the later one is an apparent movement caused by Conclusions In this chapter, we introduced Motion
luminous stationary impulses.
Perception and the mechanisms by which our visual sysMotion Illusions happen when Motion Perception, Mo- tem detects motion. Motion Illusions showed how Motion Analysis and the interpretation of these signals are tion signals can be misleading, and consequently lead to
misleading, and our visual system creates illusions about incorrect conclusions about motion. It is important to remotion. These illusions can be classied according to member that Motion Perception and Motion Analysis are
which process allows them to happen. Illusions are classi- not the same. Motion Sensors and Feature trackers comed as illusions related to motion sensing, 2D integration, plement each other to make the visual system perceive
motion.
and 3D interpretation
The most popular illusions concerning motion sensing are Motion Perception is complex, and it is still an open area
four-stroke motion, RDKs and second order motion sig- of research. This chapter describes models about the way
nals illusions. The most popular motion illusions con- that Motion Sensors function, and hypotheses about Feacerning 2D integration are Motion Capture, Plaid Mo- ture trackers characteristics; however, more experiments
tion and Direct Repulsion. Similarly, the ones concerning are necessary to learn about the characteristics of these
3D interpretation are Transformational Motion, Kinetic mechanisms and be able to construct models that resemDepth, Shadow Motion, Biological Motion, Stereokinetic ble the actual processes of the visual system more accumotion, Implicit Figure Motion and 2 Stroke Motion. rately.
There are far more Motion Illusions, and they all show
something interesting regarding human Motion Detection, Perception and Analysis mechanisms. For more
information, visit the following link: http://www.lifesci.
sussex.ac.uk/home/George_Mather/Motion/
The variety of mechanisms of motion analysis and motion

perception described in this chapter, as well as the sophistication of the articial models designed to describe them
demonstrate that there is much complexity in the way in
which the cortex processes signals from the outside environment. Thousands of specialized neurons integrate and
interpret pieces of local signals to form global images of
moving objects in our brain. Understanding that so many
actors and processes in our bodies must work in concert
to perceive motion makes our ability to it all the more remarkable that we as humans are able to do it with such
ease.
Open Problems Although we still do not understand

most of the specics regarding Motion Perception, understanding the mechanisms by which motion is perceived
as well as motion illusion can give the reader a good
overview of the state of the art in the subject. Some of
the open problems regarding Motion Perception are the
Color Perception
mechanisms of formation of 3D images in global motion
and the Aperture Problem.
Introduction Humans (together with primates like
Global motion signals from the retina are integrated to monkeys and gorillas) have the best color perception
arrive at a 2 dimensional global motion signal; however, among mammals [1] . Hence, it is not a coincidence that
it is unclear how 3D global motion is formed. The Aper- color plays an important role in a wide variety of aspects.
ture Problem occurs because each receptive eld in the vi- For example, color is useful for discriminating and difsual system covers only a small piece of the visual world, ferentiating objects, surfaces, natural scenery, and even
which leads to ambiguities in perception. The aperture faces [2] ,[3] . Color is also an important tool for nonverbal
problem refers to the problem of a moving contour that, communication, including that of emotion [4] .
when observed locally, is consistent with dierent possibilities of motion. This ambiguity is geometric in origin For many decades, it has been a challenge to nd the links
- motion parallel to the contour cannot be detected, as between the physical properties of color and its percepchanges to this component of the motion do not change tual qualities. Usually, these are studied under two dierthe images observed through the aperture. The only com- ent approaches: the behavioral response caused by color
and the actual physiological
ponent that can be measured is the velocity orthogonal to (also called psychophysics)
[5]
.
response
caused
by
it
the contour orientation; for that reason, the velocity of
the movement could be anything from the family of mo- Here we will only focus on the latter. The study of the
tions along a line in velocity space. This aperture prob- physiological basis of color vision, about which practilem is not only observed in straight contours, but also cally nothing was known before the second half of the
in smoothly curved ones, since they are approximately twentieth century, has advanced slowly and steadily since
straight when observed locally. Although the mechanisms 1950. Important progress has been made in many arto solve the Aperture Problem are still unknown, there ex- eas, especially at the receptor level. Thanks to molecuist some hypothesis on how it could be solved. For exam- lar biology methods, it has been possible to reveal preple, it could be possible to resolve this problem by com- viously unknown details concerning the genetic basis for
bining information across space or from dierent con- the cone pigments. Furthermore, more and more cortical regions have been shown to be inuenced by visual
tours of the same object.
44
stimuli, although the correlation of color perception with green-red nomenclature is somewhat misleading, since
wavelength-dependent physiology activity beyond the re- all types of cones are sensitive to a large range of waveceptors is not so easy to discern [6] .
lengths.
In this chapter, we aim to explain the basics of the dierent processes of color perception along the visual path,
from the retina in the eye to the visual cortex in the brain.
For anatomical details, please refer to Sec. Anatomy of
the Visual System of this Wikibook.
Color Perception at the Retina All colors that can be
discriminated by humans can be produced by the mixture
of just three primary (basic) colors. Inspired by this idea
of color mixing, it has been proposed that color is subserved by three classes of sensors, each having a maximal
sensitivity to a dierent part of the visible spectrum [1] . It
was rst explicitly proposed in 1853 that there are three
degrees of freedom in normal color matching [7] . This
was later conrmed in 1886 [8] (with remarkably close
results to recent studies [9] , [10] ).
These proposed color sensors are actually the so called
cones (Note: In this chapter, we will only deal with cones.
Rods contribute to vision only at low light levels. Although they are known to have an eect on color perception, their inuence is very small and can be ignored
here.) [11] . Cones are of the two types of photoreceptor
cells found in the retina, with a signicant concentration
of them in the fovea. The Table below lists the three types
of cone cells. These are distinguished by dierent types
of rhodopsin pigment. Their corresponding absorption
curves are shown in the Figure below.
An important feature about the three cone types is their

relative distribution in the retina. It turns out that the Scones present a relatively low concentration through the
retina, being completely absent in the most central area of
the fovea. Actually, they are too widely spaced to play an
important role in spatial vision, although they are capable
of mediating weak border perception [12] . The fovea is
dominated by L- and M-cones. The proportion of the
two latter is usually measured as a ratio. Dierent values
have been reported for the L/M ratio, ranging from 0.67
[13]
up to 2 [14] , the latter being the most accepted. Why
L-cones almost always outnumber the M-cones remains
unclear. Surprisingly, the relative cone ratio has almost
no signicant impact on color vision. This clearly shows
that the brain is plastic, capable of making sense out of
whatever cone signals it receives [15] , [16] .
It is also important to note the overlapping of the L- and
M-cone absorption spectra. While the S-cone absorption
spectrum is clearly separated, the L- and M-cone peaks
are only about 30 nm apart, their spectral curves significantly overlapping as well. This results in a high correlation in the photon catches of these two cone classes.
This is explained by the fact that in order to achieve the
highest possible acuity at the center of the fovea, the visual system treats L- and M-cones equally, not taking into
account their absorption spectra. Therefore, any kind of
dierence leads to a deterioration of the luminance signal
[17]
. In other words, the small separation between L- and
M-cone spectra might be interpreted as a compromise between the needs for high-contrast color vision and high
acuity luminance vision. This is congruent with the lack
of S-cones in the central part of the fovea, where visual
acuity is highest. Furthermore, the close spacing of Land M-cone absorption spectra might also be explained
by their genetic origin. Both cone types are assumed to
have evolved recently (about 35 million years ago) from
a common ancestor, while the S-cones presumably split
o from the ancestral receptor much earlier[11] .
Absorption curves for the dierent cones. Blue, green, and red
represent the absorption of the S (420 nm), M (530 nm), and L
(560 nm) cones, respectively.
The spectral absorption functions of the three dierent

types of cone cells are the hallmark of human color vision. This theory solved a long-known problem: although
we can see millions of dierent colors (humans can distinguish between 7 to 10 million dierent colors[5] , our
retinas simply do not have enough space to accommodate
an individual detector for every color at every retinal location.
Although no consensus has been reached for naming the

dierent cone types, the most widely utilized designations refer either to their action spectra peak or to the
color to which they are sensitive themselves (red, green,
blue)[6] . In this text, we will use the S-M-L designation
(for short, medium, and long wavelength), since these
names are more appropriately descriptive. The blue-
From the Retina to the Brain The signals that are

transmitted from the retina to higher levels are not simple point-wise representations of the receptor signals, but
rather consist of sophisticated combinations of the receptor signals. The objective of this section is to provide a
brief of the paths that some of this information takes.
2.2. VISUAL SYSTEM
45
Once the optical image on the retina is transduced

into chemical and electrical signals in the photoreceptors, the amplitude-modulated signals are converted into
frequency-modulated representations at the ganglion-cell
and higher levels. In these neural cells, the magnitude
of the signal is represented in terms of the number of
spikes of voltage per second red by the cell rather than
by the voltage dierence across the cell membrane. In
order to explain and represent the physiological properties of these cells, we will nd the concept of receptive
elds very useful.
A receptive eld is a graphical representation of the area
in the visual eld to which a given cell responds. Additionally, the nature of the response is typically indicated
for various regions in the receptive eld. For example,
we can consider the receptive eld of a photoreceptor
as a small circular area representing the size and location of that particular receptors sensitivity in the visual
eld. The Figure below shows exemplary receptive elds
for ganglion cells, typically in a center-surround antagonism. The left receptive eld in the gure illustrates a
positive central response (know as on-center). This kind
of response is usually generated by a positive input from a
single cone surrounded by a negative response generated
from several neighboring cones. Therefore, the response
of this ganglion cell would be made up of inputs from Antagonist receptive elds
various cones with both positive and negative signs. In
this way, the cell not only responds to points of light, but
serves as an edge (or more correctly, a spot) detector. In
analogy to the computer vision terminology, we can think
of the ganglion cell responses as the output of a convolution with an edge-detector kernel. The right receptive
eld of in the gure illustrates a negative central response
(know as o-center), which is equally likely. Usually, oncenter and o-center cells will occur at the same spatial
location, fed by the same photoreceptors, resulting in an
enhanced dynamic range.
On center
The lower Figure shows that in addition to spatial antagonism, ganglion cells can also have spectral opponency.
For instance, the left part of the lower gure illustrates a
red-green opponent response with the center fed by positive input from an L-cone and the surrounding fed by
a negative input from M-cones. On the other hand, the
right part of the lower gure illustrates the o-center version of this cell. Hence, before the visual information has
even left the retina, processing has already occurred, with
a profound eect on color appearance. There are other
types and varieties of ganglion cell responses, but they all
share these basic concepts.
On center
O center
O center
Spectrally and spatially antagonist receptive elds.
On their way to the primary visual cortex, ganglion cell
axons gather to form the optic nerve, which projects to the
lateral geniculate nucleus (LGN) in the thalamus. Coding in the optic nerve is highly ecient, keeping the
46
number of nerve bers to a minimum (limited by the

size of the optic nerve) and thereby also the size of the
retinal blind spot as small as possible (approximately 5
wide by 7 high). Furthermore, the presented ganglion
cells would have no response to uniform illumination,
since the positive and negative areas are balanced. In
other words, the transmitted signals are uncorrelated. For
example, information from neighboring parts of natural
scenes are highly correlated spatially and therefore highly
predictable [18] . Lateral inhibition between neighboring
retinal ganglion cells minimizes this spatial correlation,
therefore improving eciency. We can see this as a process of image compression carried out in the retina.
inputs[25] . However, because the null points of dierent

M-cells vary slightly, the population response is never really zero. This property is actually passed on to cortical
areas with predominant M-cell inputs[26] .
There are three channels of information that actually

communicate this information from the retina through the
ganglion cells to the LGN. They are dierent not only on
their chromatic properties, but also in their anatomical
substrate. These channels pose important limitations for
basic color tasks, such as detection and discrimination.
Once in the visual cortex, the encoding of visual information becomes signicantly more complex. In the same
way the outputs of various photoreceptors are combined
and compared to produce ganglion cell responses, the outputs of various LGN cells are compared and combined to
produce cortical responses. As the signals advance further up in the cortical processing chain, this process repeats itself with a rapidly increasing level of complexity
to the point that receptive elds begin to lose meaning.
However, some functions and processes have been identied and studied in specic regions of the visual cortex.
The parvocellular pathway (P-) originates with the individual outputs from L- or M-cone to midget bipolar cells.
These provide input to retinal P-cells[11] . In the fovea,
the receptive eld centers of P-cells are formed by single L- or M-cones. The structure of the P-cell receptive eld surround is still debated. However, the most
accepted theory states that the surround consists of a specic cone type, resulting in a spatially opponent receptive
eld for luminance stimuli[27] . Parvocellular layers conGiven the overlapping of the L- and M-cone absorption tribute with about 80 % of the total projections from the
spectra, their signals are also highly correlated. In this retina to the LGN[28] .
case, coding eciency is improved by combining the Finally, the recently discovered koniocellular pathway
cone signals in order to minimize said correlation. We (K-) carries mostly signals from S-cones[29] . Groups of
can understand this more easily using Principal Compo- this type of cones project to special bipolar cells, which in
nent Analysis (PCA). PCA is a statistical method used turn provide input to specic small ganglion cells. These
to reduce the dimensionality of a given set of variables are usually not spatially opponent. The axons of the small
by transforming the original variables, to a set of new ganglion cells project to thin layers of the LGN (adjacent
variables, the principal components (PCs). The rst PC to parvocellular layers)[30] .
accounts for a maximal amount of total variance in the
original variables, the second PC accounts for a maxi- While the ganglion cells do terminate at the LGN (makmal amount of variance that was not accounted for by the ing synapses with LGN cells), there appears to be a onerst component, and so on. In addition, PCs are linearly- to-one correspondence between ganglion cells and LGN
independent and orthogonal to each other in the param- cells. The LGN appears to act as a relay station for the
eter space. PCAs main advantage is that only a few of signals. However, it probably serves some visual function,
the strongest PCs are enough to cover the vast majority since there are neural projections from the cortex back
of system variability [19] . This scheme has been used with to the LGN that could serve as some type of switching
the cone absorption functions [20] and even with the nat- or adaptation feedback mechanism. The axons of LGN
urally occurring spectra[21] ,[22] . The PCs that were found cells project to visual area one (V1) in the visual cortex
in the space of cone excitations produced by natural ob- in the occipital lobe.
jects are 1) a luminance axis where the L- and M-cone
signals are added (L+M), 2) the dierence of the L- and
M-cone signals (L-M), and 3) a color axis where the S- Color Perception at the Brain In the cortex, the procone signal is dierenced with the sum of the L- and jections from the magno-, parvo-, and koniocellular pathM-cone signals (S-(L+M)). These channels, derived from ways end in dierent layers of the primary visual cortex.
a mathematical/computational approach, coincide with The magnocellular bers innervate principally layer 4C
the three retino-geniculate channels discovered in elec- and layer 6. Parvocellular neurons project mostly to 4C,
trophysiological experiments [23] ,[24] . Using these mech- and layers 4A and 6. Koniocellular neurons terminate in
anisms, visual redundant information is eliminated in the the cytochrome oxidase (CO-) rich blobs in layers 1, 2,
retina.
and 3[31] .
In the rst channel, the output of L- and M-cones is transmitted synergistically to diuse bipolar cells and then to
cells in the magnocellular layers (M-) of the LGN (not to
be confused with the M-cones of the retina)[24] . The receptive elds of the M-cells are composed of a center and
a surround, which are spatially antagonist. M-cells have In the V1 region (striate cortex), double opponent neuhigh-contrast sensitivity for luminance stimuli, but they rons - neurons that have their receptive elds both chroshow no response at some combination of L-M opponent matically and spatially opposite with respect to the on/o
2.2. VISUAL SYSTEM

regions of a single receptive eld - compare color signals
across the visual space [32] . They constitute between 5 to
10% of the cells in V1. Their coarse size and small percentage matches the poor spatial resolution of color vision
[1]
. Furthermore, they are not sensitive to the direction
of moving stimuli (unlike some other V1 neurons) and,
hence, unlikely to contribute to motion perception[33] .
However, given their specialized receptive eld structure,
these kind of cells are the neural basis for color contrast eects, as well as an ecient mean to encode color
itself[34] ,[35] . Other V1 cells respond to other types of
stimuli, such as oriented edges, various spatial and temporal frequencies, particular spatial locations, and combinations of these features, among others. Additionally,
we can nd cells that linearly combine inputs from LGN
cells as well as cells that perform nonlinear combination.
These responses are needed to support advanced visual
capabilities, such as color itself.
47
perception, visual attention, and stereopsis as well. Furthermore, recent studies have focused on other brain regions trying to nd the color area of the brain, such as
TEO[41] and PITd[42] . The relationship of these regions
to each other is still debated. To reconcile the discussion, some use the term posterior inferior temporal (PIT)
cortex to denote the region that includes V4, TEO, and
PITd[1] .
If the cortical response in V1, V2, and V4 cells is already
a very complicated task, the level of complexity of complex visual responses in a network of approximately 30
visual zones is humongous. Figure 4 shows a small portion of the connectivity of the dierent cortical areas (not
cells) that have been identied[43] .
At this stage, it becomes exceedingly dicult to explain
the function of singles cortical cells in simple terms. As a
matter of fact, the function of a single cell might not have
meaning since the representation of various perceptions
must be distributed across collections of cells throughout
the cortex.
Color Vision Adaptation Mechanisms Although researchers have been trying to explain the processing of
color signals in the human visual system, it is important
to understand that color perception is not a xed process.
Actually, there are a variety of dynamic mechanisms that
serve to optimize the visual response according to the
viewing environment. Of particular relevance to color
perception are the mechanisms of dark, light, and chromatic adaptation.
Fig. 4. (Partial) ow diagram illustrating the many streams of

visual information processes that take place in the visual cortex. It
is important to note that information can ow in both directions.
Dark Adaptation Dark adaptation refers to the change

in visual sensitivity that occurs when the level of illumination is decreased. The visual system response to reduced
There is substantially less information on the chromatic
illumination is to become more sensitive, increasing its
properties of single neurons in V2 as compared to V1.
capacity to produce a meaningful visual response even
On a rst glance, it seems that there are no major dierwhen the light conditions are suboptimal[44] .
ences of color coding in V1 and V2[36] . One exception
to this is the emergence of a new class of color-complex
cell[37] . Therefore, it has been suggested that V2 region is
involved in the elaboration of hue. However, this is still
very controversial and has not been conrmed.
Following the modular concept developed after the discovery of functional ocular dominance in V1, and considering the anatomical segregation between the P-, M-,
and K-pathways (described in Sec. 3), it was suggested
that a specialized system within the visual cortex devoted
to the analysis of color information should exist[38] . V4
is the region that has historically attracted the most attention as the possible color area of the brain. This
is because of an inuential study that claimed that V4
contained 100 % of hue-selective cells[39] . However, this
claim has been disputed by a number of subsequent studies, some even reporting that only 16 % of V4 neurons
show hue tuning[40] . Currently, the most accepted concept is that V4 contributes not only to color, but to shape
Fig. 5. Dark adaptation. During the rst 10 minutes (i.e. to the

left of the dotted line), sensitivity recovery is done by the cones.
After the rst 10 minutes (i.e. to the right of the dotted line), rods
outperform the cones. Full sensitivity is recovered after approximately 30 minutes.
48
Figure 5 shows the recovery of visual sensitivity after
transition from an extremely high illumination level to
complete darkness[43] . First, the cones become gradually more sensitive, until the curve levels o after a couple of minutes. Then, after approximately 10 minutes
have passed, visual sensitivity is roughly constant. At
that point, the rod system, with a longer recovery time,
has recovered enough sensitivity to outperform the cones
and therefore recover control the overall sensitivity. Rod
sensitivity gradually improves as well, until it becomes
asymptotic after about 30 minutes. In other words, cones
are responsible for the sensitivity recovery for the rst 10
minutes. Afterwards, rods outperform the cones and gain
full sensitivity after approximately 30 minutes.

nately, we rarely need to view the entire range of illumination levels at the same time.
At high light levels, adaptation is achieved by photopigment bleaching. This scales photon capture in the receptors and protects the cone response from saturating
at bright backgrounds. The mechanisms of light adaptation occur primarily within the retina[45] . As a matter
of fact, gain changes are largely cone-specic and adaptation pools signals over areas no larger than the diameter of individual cones[46] ,[47] . This points to a localization of light adaptation that may be as early as the receptors. However, there appears to be more than one
site of sensitivity scaling. Some of the gain changes are
extremely rapid, while others take seconds or even minThis is only one of several neural mechanisms produced utes to stabilize[48] . Usually, light adaptation takes around
in order to adapt to the dark lightning conditions as 5 minutes (six times faster than dark adaptation). This
good as possible. Some other neural mechanisms in- might point to the inuence of post-receptive sites.
clude the well-known pupil reex, depletion and regen- Figure 6 shows examples of light adaptation [43] . If we
eration of photopigment, gain control in retinal cells and would use a single response function to map the large
other higher-level mechanisms, and cognitive interpreta- range of intensities into the visual systems output, then
tion, among others.
we would only have a very small range at our disposal for
Light Adaptation Light adaptation is essentially the
inverse process of dark adaptation. As a matter of fact,
the underlying physiological mechanisms are the same for
both processes. However, it is important to consider it
separately since its visual properties dier.
Fig. 6. Light adaptation. For a given scene, the solid lines represent families of visual response curves at dierent (relative) energy levels. The dashed line represents the case where we would
adapt in order to cover the entire range of illumination, which
would yield limited contrast and reduced sensitivity.
a given scene. It is clear that with such a response function, the perceived contrast of any given scene would be
limited and visual sensitivity to changes would be severely
degraded due to signal-to-noise issues. This case is shown
by the dashed line. On the other hand, solid lines represent families of visual responses. These curves map the
useful illumination range in any given scene into the full
dynamic range of the visual output, thus resulting in the
best possible visual perception for each situation. Light
adaptation can be thought of as the process of sliding the
visual response curve along the illumination level axis until the optimum level for the given viewing conditions is
reached.
Chromatic Adaptation The general concept of chromatic adaptation consists in the variation of the height
of the three cone spectral responsivity curves. This adjustment arises because light adaptation occurs independently within each class of cone. A specic formulation of this hypothesis is known as the von Kries adaptation. This hypothesis states that the adaptation response
takes place in each of the three cone types separately
and is equivalent to multiplying their xed spectral sensitivities by a scaling constant[49] . If the scaling weights
(also known as von Kries coecients) are inversely proportional to the absorption of light by each cone type (i.e.
a lower absorption will require a larger coecient), then
von Kries scaling maintains a constant mean response
within each cone class. This provides a simple yet powerful mechanism for maintaining the perceived color of
objects despite changes in illumination. Under a number of dierent conditions, von Kries scaling provides a
good account of the eects of light adaptation on color
sensitivity and appearance[50] ,[51] .
Light adaptation occurs when the level of illumination is

increased. Therefore, the visual system must become less
sensitive in order to produce useful perceptions, given
the fact that there is signicantly more visible light available. The visual system has a limited output dynamic
range available for the signals that produce our perceptions. However, the real world has illumination levels
covering at least 10 orders of magnitude more. Fortu- The easiest way to picture chromatic adaptation is by
2.2. VISUAL SYSTEM
49
examining a white object under dierent types of illumination. For example, lets consider examining a
piece of paper under daylight, uorescent, and incandescent illumination. Daylight contains relatively far more
short-wavelength energy than uorescent light, and incandescent illumination contains relatively far more longwavelength energy than uorescent light. However, in
spite of the dierent illumination conditions, the paper
approximately retains its white appearance under all three
light sources. This is because the S-cone system becomes
relatively less sensitive under daylight (in order to compensate for the additional short-wavelength energy) and
the L-cone system becomes relatively less sensitive under
incandescent illumination (in order to compensate for the
additional long-wavelength energy)[43] .
[14] Nerger, Janice L and Cicerone, Carol M (1992). The ratio of L cones to M cones in the human parafoveal retina.
Vision research 32 (5): 879-888.
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2.3 Vestibular System

Sensory Systems
Vision
Hearing
Balance
Feeling
Smell
Taste
[39] Zeki, Semir M (1973). Colour coding in rhesus monkey

prestriate cortex. Brain research 53 (2): 422-427.
[40] Conway, Bevil R and Tsao, Doris Y (2006). Color architecture in alert macaque cortex revealed by fMRI. Cerebral Cortex 16 (11): 1604-1613.
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Wim and Orban, Guy A (2004). Search for color 'center(s)'in macaque visual cortex. Cerebral Cortex 14 (4):
353-363.
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Visual adaptation and retinal gain controls. Progress in
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In Animals
Insects & Spiders
Birds,Fish,...
2.3.1 Introduction
The main function of the balance system, or vestibular
system, is to sense head movements, especially involuntary ones, and counter them with reexive eye movements
and postural adjustments that keep the visual world stable
and keep us from falling. An excellent, more extensive
article on the vestibular system is available on Scholorpedia [1] . An extensive review of our current knowledge
about the vestibular system can be found in The Vestibular System: a Sixth Sense by J Goldberg et al [2] .
2.3. VESTIBULAR SYSTEM
2.3.2
Anatomy of the Vestibular System
Labyrinth
Together with the cochlea, the vestibular system is carried
by a system of tubes called the membranous labyrinth.
These tubes are lodged within the cavities of the bony
labyrinth located in the inner ear. A uid called perilymph lls the space between the bone and the membranous labyrinth, while another one called endolymph
lls the inside of the tubes spanned by the membranous
labyrinth. These uids have a unique ionic composition
suited to their function in regulating the electrochemical
potential of hair cells, which are as we will later see the
transducers of the vestibular system. The electric potential of endolymph is of about 80 mV more positive than
perilymph.
Since our movements consist of a combination of linear
translations and rotations, the vestibular system is composed of two main parts: The otolith organs, which sense
linear accelerations and thereby also give us information
about the heads position relative to gravity, and the semicircular canals, which sense angular accelerations.
Otoliths
The otolith organs of both ears are located in two membranous sacs called the utricle and the saccule which primary sense horizontal and vertical accelerations, respectively. Each utricle has about 30'000 hair cells, and each
saccule about 16'000. The otoliths are located at the central part of the labyrinth, also called the vestibule of the
ear. Both utricle and saccule have a thickened portion
of the membrane called the macula. A gelatinous membrane called the otolthic membrane sits atop the macula, and microscopic stones made of calcium carbonate
crystal, the otoliths, are embedded on the surface of this
membrane. On the opposite side, hair cells embedded in
supporting cells project into this membrane.
The otoliths are the human sensory organs for linear acceleration. The utricle (left) is approximately horizontally oriented; the
saccule (center) lies approximately vertical. The arrows indicate
the local on-directions of the hair cells; and the thick black lines
indicate the location of the striola. On the right you see a crosssection through the otolith membrane. The graphs have been generated by Rudi Jaeger, while we cooperated on investigations of
the otolith dynamics.
51
Semicircular Canals
Cupula
Hair cells
Endolymphatic
duct
Crista
Vestibular aerents
ph n
m
o
y
ol rati
d
En cele
ac
Head acceleration
Cross-section through ampulla. Top: The cupula spans the lumen of the ampulla from the crista to the membranous labyrinth.
Bottom: Since head acceleration exceeds endolymph acceleration, the relative ow of endolymph in the canal is opposite to
the direction of head acceleration. This ow produces a pressure
across the elastic cupula, which deects in response.
Each ear has three semicircular canals. They are half circular, interconnected membranous tubes lled with endolymph and can sense angular accelerations in the three
orthogonal planes. The radius of curvature of the human
horizontal semicircular canal is 3.2 mm [3] .
The canals on each side are approximately orthogonal to
each other. The orientation of the on-directions of the
canals on the right side are [4] :
(The axes are oriented such that the positive x-,y-,and zaxis point forward, left, and up, respectively. The horizontal plane is dened by Reids line, the line connecting
the lower rim of the orbita and the center of the external
auditory canal. And the directions are such that a rotation about that vector, according to the right-hand-rule,
excites the corresponding canal.) The anterior and posterior semicircular canals are approximately vertical, and
the horizontal semicircular canals approximately horizontal.
Each canal presents a dilatation at one end, called the
ampulla. Each membranous ampulla contains a saddleshaped ridge of tissue, the crista, which extends across it
from side to side. It is covered by neuroepithelium, with
52

+
Orientation of the semicircular canals in the vestibular system.

L / R stand for Left / Right, respectively, and H / A / P for
Horizontal / Anterior / Posterior. The arrows indicate the direction of head movement that stimulates the corresponding canal.
hair cells and supporting cells. From this ridge rises a

gelatinous structure, the cupula, which extends to the roof
of the ampulla immediately above it, dividing the interior
of the ampulla into two approximately equal parts.
Haircells
The sensors within both the otolith organs and the semicircular canals are the hair cells. They are responsible for
the transduction of a mechanical force into an electrical
signal and thereby build the interface between the world
of accelerations and the brain.
Hair cells have a tuft of stereocilia that project from their
apical surface. The thickest and longest stereocilia is the
kinocilium. Stereocilia deection is the mechanism by
which all hair cells transduce mechanical forces. Stereocilia within a bundle are linked to one another by protein strands, called tip links, which span from the side of
a taller stereocilium to the tip of its shorter neighbor in
the array. Under deection of the bundle, the tip links
act as gating springs to open and close mechanically sensitive ion channels. Aerent nerve excitation works basically the following way: when all cilia are deected toward the kinocilium, the gates open and cations, including potassium ions from the potassium rich endolymph,
ow in and the membrane potential of the hair cell becomes more positive (depolarization). The hair cell itself
does not re action potentials. The depolarization activates voltage-sensitive calcium channels at the basolateral
aspect of the cell. Calcium ions then ow in and trigger
AP
Transduction mechanism in auditory or vestibular haircell. Tilting the haircell towards the kinocilium opens the potassium ion
channels. This changes the receptor potential in the haircell. The
resulting emission of neurotransmittors can elicit an action potential (AP) in the post-synaptic cell.
the release of neurotransmitters, mainly glutamate, which

in turn diuse across the narrow space between the hair
cell and a nerve terminal, where they then bind to receptors and thus trigger an increase of the action potentials
ring rate in the nerve. On the other hand, aerent nerve
inhibition is the process induced by the bending of the
stereocilia away from the kinocilium (hyperpolarization)
and by which the ring rate is decreased. Because the
hair cells are chronically leaking calcium, the vestibular
aerent nerve res actively at rest and thereby allows the
sensing of both directions (increase and decrease of ring
rate). Hair cells are very sensitive and respond extremely
quickly to stimuli. The quickness of hair cell response
may in part be due to the fact that they must be able to
release neurotransmitter reliably in response to a threshold receptor potential of only 100 V or so.
Regular and Irregular Haircells While aerent haircells in the auditory system are fairly homogeneous,those
in the vestibular system can be broadly separated into
two groups: regular units and irregular units. Regular haircells have approximately constant interspike intervals, and re constantly proportional to their displacement. In contrast, the inter-spike interval of irregular
53
Excitation (red) and inhibition (blue) on utricle (left) and saccule

(right), when the head is in a right-ear-down orientation. The
displacement of the otoliths was calculated with the nite element
technique, and the orientation of the haircells was taken from the
literature.
Auditory haircells are very similar to those of the vestibular system. Here an electron microscopy image of a frogs sacculus haircell.
the vestibule, and its macula is oriented roughly horizontally when the head is upright. Within each macula, the
kinocilia of the hair cells are oriented in all possible directions.
haircells is much more variable, and their discharge rate

increases with increasing frequency; they can thus act as
event detectors at high frequencies. Regular and irregular haircells also dier in their location, morphology and
innervation.
Therefore, under linear acceleration with the head in the

upright position, the saccular macula is sensing acceleration components in the vertical plane, while the utricular
macula is encoding acceleration in all directions in the
horizontal plane. The otolthic membrane is soft enough
that each hair cell is deected proportional to the local
force direction. If denotes the direction of maximum
sensitivity or on-direction of the hair cell, and the gravitoinertial force, the stimulation by static accelerations is
given by
2.3.3
Signal Processing
Peripheral Signal Transduction
Transduction of Linear Acceleration The hair cells

of the otolith organs are responsible for the transduction
of a mechanical force induced by linear acceleration into stimotolith = F n

an electrical signal. Since this force is the product of gravThe direction and magnitude of the total acceleration is
ity plus linear movements of the head
then determined from the excitation pattern on the otolith
maculae.
d2 x
F = Fg + Finertial = m(g 2 )
dt
it is therefore sometimes referred to as gravito-inertial
force. The mechanism of transduction works roughly as
follows: The otoconia, calcium carbonate crystals in the
top layer of the otoconia membrane, have a higher specic density than the surrounding materials. Thus a linear acceleration leads to a displacement of the otoconia
layer relative to the connective tissue. The displacement
is sensed by the hair cells. The bending of the hairs then
polarizes the cell and induces aerent excitation or inhibition.
While each of the three semicircular canals senses only
one-dimensional component of rotational acceleration,
linear acceleration may produce a complex pattern of inhibition and excitation across the maculae of both the
utricle and saccule. The saccule is located on the medial wall of the vestibule of the labyrinth in the spherical
recess and has its macula oriented vertically. The utricle is located above the saccule in the elliptical recess of
Transduction of Angular Acceleration The three

semicircular canals are responsible for the sensing of
angular accelerations. When the head accelerates in
the plane of a semicircular canal, inertia causes the endolymph in the canal to lag behind the motion of the
membranous canal. Relative to the canal walls, the endolymph eectively moves in the opposite direction as
the head, pushing and distorting the elastic cupula. Hair
cells are arrayed beneath the cupula on the surface of the
crista and have their stereocilia projecting into the cupula.
They are therefore excited or inhibited depending on the
direction of the acceleration.
This facilitates the interpretation of canal signals: if the
orientation of a semicircular canal is described by the unit
vector n , the stimulation of the canal is proportional to
the projection of the angular velocity
onto this canal
stimcanal =
n
54
The stimulation of a human semicircular canal is proportional

to the scalar product between a vector n (which is perpendicular
to the plane of the canal), and the vector omega indicating the
angular velocity.
The horizontal semicircular canal is responsible for sensing accelerations around a vertical axis, i.e. the neck. The
anterior and posterior semicircular canals detect rotations
of the head in the sagittal plane, as when nodding, and in
the frontal plane, as when cartwheeling.
In a given cupula, all the hair cells are oriented in the same
direction. The semicircular canals of both sides also work
as a push-pull system. For example, because the right and
the left horizontal canal cristae are mirror opposites of
each other, they always have opposing (push-pull principle) responses to horizontal rotations of the head. Rapid
rotation of the head toward the left causes depolarization of hair cells in the left horizontal canals ampulla
and increased ring of action potentials in the neurons
that innervate the left horizontal canal. That same leftward rotation of the head simultaneously causes a hyperpolarization of the hair cells in the right horizontal canals
ampulla and decreases the rate of ring of action potentials in the neurons that innervate the horizontal canal of
the right ear. Because of this mirror conguration, not
only the right and left horizontal canals form a push-pull
pair but also the right anterior canal with the left posterior
canal (RALP), and the left anterior with the right posterior (LARP).
which is the eighth of twelve cranial nerves. The cell bodies of the bipolar aerent neurons that innervate the hair
cells in the maculae and cristae in the vestibular labyrinth
reside near the internal auditory meatus in the vestibular ganglion (also called Scarpas ganglion, Figure Figure
10.1). The centrally projecting axons from the vestibular
ganglion come together with axons projecting from the
auditory neurons to form the eighth nerve, which runs
through the internal auditory meatus together with the
facial nerve. The primary aerent vestibular neurons
project to the four vestibular nuclei that constitute the
vestibular nuclear complex in the brainstem.
Vestibulo-ocular reex.
Vestibulo-Ocular Reex (VOR)

An extensively studied example of function of the
vestibular system is the vestibulo-ocular reex (VOR).
The function of the VOR is to stabilize the image during rotation of the head. This requires the maintenance
of stable eye position during horizontal, vertical and torsional head rotations. When the head rotates with a certain speed and direction, the eyes rotate with the same
speed but in the opposite direction. Since head movements are present all the time, the VOR is very important
for stabilizing vision.
How does the VOR work? The vestibular system signals

how fast the head is rotating and the oculomotor system
uses this information to stabilize the eyes in order to keep
the visual image motionless on the retina. The vestibular
nerves project from the vestibular ganglion to the vestibular nuclear complex, where the vestibular nuclei integrate
signals from the vestibular organs with those from the
spinal cord, cerebellum, and the visual system. From
these nuclei, bers cross to the contralateral abducens nucleus. There they synapse with two additional pathways.
One pathway projects directly to the lateral rectus muscle of eye via the abducens nerve. Another nerve tract
projects from the abducens nucleus by the abducens interneurons to the oculomotor nuclei, which contain moCentral Vestibular Pathways
tor neurons that drive eye muscle activity, specically activating the medial rectus muscles of the eye through the
The information resulting from the vestibular system is oculomotor nerve. This short latency connection is somecarried to the brain, together with the auditory infor- times referred to as three-neuron-arc, and allows an eye
mation from the cochlea, by the vestibulocochlear nerve, movement within less than 10 ms after the onset of the

head movement.
For example, when the head rotates rightward, the following occurs. The right horizontal canal hair cells depolarize and the left hyperpolarize. The right vestibular aerent activity therefore increases while the left decreases.
The vestibulocochlear nerve then carries this information
to the brainstem and the right vestibular nuclei activity increases while the left decreases. This makes in turn neurons of the left abducens nucleus and the right oculomotor
nucleus re at higher rate. Those in the left oculomotor
nucleus and the right abducens nucleus re at a lower rate.
This results in the fact than the left lateral rectus extraocular muscle and the right medial rectus contract while the
left medial rectus and the right lateral rectus relax. Thus,
both eyes rotate leftward.
The gain of the VOR is dened as the change in the eye
angle divided by the change in the head angle during the
head turn
gain =
Eye
Head
55
hibitory pathways. Ito also argued that a message of retinal image slip going through the inferior olivary nucleus
carried by the climbing ber plays the role of an error signal and thereby is the modulating inuence of the Purkinje cells. On the other hand, Miles and Lisberger argued
that the brainstem neurons targeted by the Purkinje cells
are the site of adaptive learning and that the cerebellum
constructs the error signal that drives this adaptation.
2.3.4 Alcohol and the Vestibular System

As you may or may not know from personal experience,
consumption of alcohol can also induce a feeling of rotation. The explanation is quite straightforward, and basically relies on two factors: i) alcohol is lighter than the
endolymph; and ii) once it is in the blood, alcohol gets relatively quickly into the cupula, as the cupula has a good
blood supply. In contrast, it diuses only slowly into the
endolymph, over a period of a few hours. In combination,
this leads to a buoyancy of the cupola soon after you have
consumed (too much) alcohol. When you lie on your side,
the deection of the left and right horizontal cupulae add
up, and induce a strong feeling of rotation. The proof:
just roll on the other side - and the perceived direction of
rotation will ip around!
If the gain of the VOR is wrong, that is, dierent than

one, then head movements result in image motion on the
retina, resulting in blurred vision. Under such conditions,
motor learning adjusts the gain of the VOR to produce Due to the position of the cupulae, you will experience
more accurate eye motion. Thereby the cerebellum plays the strongest eect when you lie on your side. When you
lie on your back, the deection of the left and right cupula
an important role in motor learning.
compensate each other, and you don't feel any horizontal
rotation. This explains why hanging one leg out of the
The Cerebellum and the Vestibular System
bed slows down the perceived rotation.
It is known that postural control can be adapted to suit
specic behavior. Patient experiments suggest that the
cerebellum plays a key role in this form of motor learning. In particular, the role of the cerebellum has been
extensively studied in the case of adaptation of vestibuloocular control. Indeed, it has been shown that the gain
of the vestibulo-ocular reex adapts to reach the value of
one even if damage occur in a part of the VOR pathway
or if it is voluntary modied through the use of magnifying lenses. Basically, there are two dierent hypotheses
about how the cerebellum plays a necessary role in this
adaptation. The rst from (Ito 1972;Ito 1982) claims that
the cerebellum itself is the site of learning, while the second from Miles and Lisberger (Miles and Lisberger 1981)
claims that the vestibular nuclei are the site of adaptive
learning while the cerebellum constructs the signal that
drives this adaptation. Note that in addition to direct excitatory input to the vestibular nuclei, the sensory neurons of the vestibular labyrinth also provide input to the
Purkinje cells in the occulo-nodular lobes of the cerebellum via a pathway of mossy and parallel bers. In
turn, the Purkinje cells project an inhibitory inuence
back onto the vestibular nuclei. Ito argued that the gain
of the VOR can be adaptively modulated by altering the
relative strength of the direct excitatory and indirect in-
The overall eect is minimized in the upright head position - so try to stay up(right) as long as possible during
the party!
If you have drunk way too much, the endolymph will contain a signicant amount of alcohol the next morning more so than the cupula. This explains while at that point,
a small amount of alcohol (e.g. a small beer) balances the
dierence, and reduces the feeling of spinning.
[1] Kathleen Cullen and Soroush Sadeghi (2008).
Vestibular System.
Scholarpedia 3(1):3013.
http://www.scholarpedia.org/article/Vestibular_system.
[2] JM Goldberg, VJ Wilson, KE Cullen and DE Angelaki (2012). The Vestibular System: a Sixth Sense"".
Oxford University Press, USA. http://www.scholarpedia.
org/article/Vestibular_system.
[3] Curthoys IS and Oman CM (1987). Dimensions of the
horizontal semicircular duct, ampulla and utricle in the
human.. Acta Otolaryngol 103: 254261.
[4] Della Santina CC, Potyagaylo V, Migliaccio A, Minor LB,
Carey JB (2005). Orientation of Human Semicircular
Canals Measured by Three-Dimensional Multi-planar CT
Reconstruction.. J Assoc Res Otolaryngol 6(3): 191-206.
56
2.4 Somatosensory System
Glabrous skin
Hairy skin
Papillary Ridges
Sensory Systems
Vision
Hearing
Balance
Feeling
Smell
Taste
Implants
Models
In Animals
Insects & Spiders
Birds,Fish,...
Free nerve
ending
Merkels
receptor
Epidermis
Septa
Meissners
corpuscle
Sebaceous
gland
Dermis
Runis
corpuscle
Hair receptor
Pacinian
corpuscle
Receptors in the human skin: Mechanoreceptors can be free receptors or encapsulated. Examples for free receptors are the hair
receptors at the roots of hairs. Encapsulated receptors are the
Pacinian corpuscles and the receptors in the glabrous (hairless)
skin: Meissner corpuscles, Runi corpuscles and Merkels disks.
passage of time so that by the age of 50, the density in human digits is reduced to 10/mm. Unlike rapidly adapting
axons, slowly adapting bers respond not only to the ini2.4.1 Introduction
tial indentation of skin, but also to sustained indentation
2.4.2 Anatomy of the Somatosensory Sys- up to several seconds in duration.
Activation of the rapidly adapting Pacinian corpuscles
tem
gives a feeling of vibration, while the slowly adapting
Our somatosensory system consists of sensors in the skin Runi corpuscles respond to the lataral movement or
and sensors in our muscles, tendons, and joints. The re- stretching of skin.
ceptors in the skin, the so called cutaneous receptors, tell
us about temperature (thermoreceptors), pressure and surface texture (mechano receptors), and pain (nociceptors). Nociceptors Nociceptors have free nerve endings.
The receptors in muscles and joints provide information Functionally, skin nociceptors are either high-threshold
about muscle length, muscle tension, and joint angles. mechanoreceptors or polymodal receptors. Polymodal re(The following description is based on lecture notes from ceptors respond not only to intense mechanical stimuli,
but also to heat and to noxious chemicals. These recepLaszlo Zaborszky, from Rutgers University.)
tors respond to minute punctures of the epithelium, with
a response magnitude that depends on the degree of tisCutaneous receptors
sue deformation. They also respond to temperatures in
the range of 4060C, and change their response rates as
Mechanoreceptors Sensory information from Meiss- a linear function of warming (in contrast with the saturatner corpuscles and rapidly adapting aerents leads to ad- ing responses displayed by non-noxious thermoreceptors
justment of grip force when objects are lifted. These at high temperatures).
aerents respond with a brief burst of action potentials
Pain signals can be separated into individual components,
when objects move a small distance during the early
corresponding to dierent types of nerve bers used for
stages of lifting. In response to rapidly adapting aertransmitting these signals. The rapidly transmitted signal,
ent activity, muscle force increases reexively until the
which often has high spatial resolution, is called rst pain
gripped object no longer moves. Such a rapid response to
or cutaneous pricking pain. It is well localized and easily
a tactile stimulus is a clear indication of the role played
tolerated. The much slower, highly aective component
by somatosensory neurons in motor activity.
is called second pain or burning pain; it is poorly localized
The slowly adapting Merkels receptors are responsible for and poorly tolerated. The third or deep pain, arising from
form and texture perception. As would be expected for viscera, musculature and joints, is also poorly localized,
receptors mediating form perception, Merkels receptors can be chronic and is often associated with referred pain.
are present at high density in the digits and around the
mouth (50/mm of skin surface), at lower density in other
glabrous surfaces, and at very low density in hairy skin. Thermoreceptors The thermoreceptors have free
This innervations density shrinks progressively with the nerve endings. Interestingly, we have only two types
2.4. SOMATOSENSORY SYSTEM

of thermoreceptors that signal innocuous warmth and
cooling respectively in our skin (however, some nociceptors are also sensitive to temperature, but capable
of unamibiously signaling only noxious temperatures).
The warm receptors show a maximum sensitivity at ~
45C, signal temperatures between 30 and 45C, and
cannot unambiguously signal temperatures higher than
45C , and are unmyelinated. The cold receptors have
their maximum sensitivity at ~ 27C, signal temperatures
above 17C, and some consist of lightly myelinated
bers, while others are unmyelinated. Our sense of
temperature comes from the comparison of the signals
from the warm and cold receptors. Thermoreceptors
are poor indicators of absolute temperature but are very
sensitive to changes in skin temperature.
57
tors called muscle spindles. They are quite simple in principle, consisting of a few small muscle bers with a capsule surrounding the middle third of the bers. These
bers are called intrafusal bers, in contrast to the ordinary extrafusal bers. The ends of the intrafusal bers are
attached to extrafusal bers, so whenever the muscle is
stretched, the intrafusal bers are also stretched. The central region of each intrafusal ber has few myolaments
and is non-contractile, but it does have one or more sensory endings applied to it. When the muscle is stretched,
the central part of the intrafusal ber is stretched and each
sensory ending res impulses.
Numerous specializations occur in this simple basic organization, so that in fact the muscle spindle is one of the
most complex receptor organs in the body. Only three
of these specializations are described here; their overall
eect is to make the muscle spindle adjustable and give
Proprioceptors
it a dual function, part of it being particularly sensitive
The term proprioceptive or kinesthetic sense is used to re- to the length of the muscle in a static sense and part of it
fer to the perception of joint position, joint movements, being particularly sensitive to the rate at which this length
and the direction and velocity of joint movement. There changes.
are numerous mechanoreceptors in the muscles, the mus1. Intrafusal muscle bers are of two types. All are
cle fascia, and in the dense connective tissue of joint capmultinucleated, and the central, non-contractile resules and ligaments. There are two specialized encapsugion contains the nuclei. In one type of intrafusal
lated, low-threshold mechanoreceptors: the muscle spinber, the nuclei are lined up single le; these are
dle and the Golgi tendon organ. Their adequate stimucalled nuclear chain ber. In the other type, the nulus is stretching of the tissue in which they lie. Muscle
clear region is broader, and the nuclei are arranged
spindles, joint and skin receptors all contribute to kinesseveral abreast; these are called nuclear bag bers.
thesia. Muscle spindles appear to provide their most imThere are typically two or three nuclear bag bers
portant contribution to kinesthesia with regard to large
per spindle and about twice that many chain bers.
joints, such as the hip and knee joints, whereas joint receptors and skin receptors may provide more signicant
2. There are also two types of sensory endings in the
contributions with regard to nger and toe joints.
muscle spindle. The rst type, called the primary
Mammalian muscle spindle showing typical position in a muscle (left), neuronal connections in spinal cord (middle) and expanded schematic (right). The spindle is a stretch receptor with
its own motor supply consisting of several intrafusal muscle bres. The sensory endings of a primary (group Ia) aerent and
a secondary (group II) aerent coil around the non-contractile
central portions of the intrafusal bres. Gamma motoneurons
activate the intrafusal muscle bres, changing the resting ring
rate and stretch-sensitivity of the aerents.
Muscle Spindles Scattered throughout virtually every

striated muscle in the body are long, thin, stretch recep-
ending, is formed by a single Ia (A-alpha) ber, supplying every intrafusal ber in a given spindle. Each
branch wraps around the central region of the intrafusal ber, frequently in a spiral fashion, so these
are sometimes called annulospiral endings. The second type of ending is formed by a few smaller nerve
bers (II or A-Beta) on both sides of the primary
endings. These are the secondary endings, which are
sometimes referred to as ower-spray endings because of their appearance. Primary endings are selectively sensitive to the onset of muscle stretch but
discharge at a slower rate while the stretch is maintained. Secondary endings are less sensitive to the
onset of stretch, but their discharge rate does not decline very much while the stretch is maintained. In
other words, both primary and secondary endings
signal the static length of the muscle (static sensitivity) whereas only the primary ending signals the
length changes (movement) and their velocity (dynamic sensitivity). The change of ring frequency
of group Ia and group II bers can then be related to
static muscle length (static phase) and to stretch and
shortening of the muscle (dynamic phases).
3. Muscle spindles also receive a motor innervation.
58

The large motor neurons that supply extrafusal muscle bers are called alpha motor neurons, while the
smaller ones supplying the contractile portions of intrafusal bers are called gamma neurons. Gamma
motor neurons can regulate the sensitivity of the
muscle spindle so that this sensitivity can be maintained at any given muscle length.
Force
control
signal
Interneurons
Force (Golgi tendon organ)

Force feedback
External
forces
Driving
signal
Muscle
Length (secondary muscle-spindel aerents)

Length error (primary muscle-spindel aerents)Length &
Velocity (primary muscle-spindel aerents)velocity
feedback
Length
control
signal
Tendon
organs
Muscle force
Load
Muscle
length
Spindles
Gamma bias
Feedback loops for proprioceptive signals for the perception and

control of limb movements. Arrows indicate excitatory connections; lled circles inhibitory connections.
2.5 Olfactory System

Sensory Systems
Mammalian tendon organ showing typical position in a muscle (left), neuronal connections in spinal cord (middle) and expanded schematic (right). The tendon organ is a stretch receptor
that signals the force developed by the muscle. The sensory endings of the Ib aerent are entwined amongst the musculotendinous strands of 10 to 20 motor units.
Golgi tendon organ The Golgi tendon organ is located

at the musculotendinous junction. There is no eerent
innervation of the tendon organ, therefore its sensitivity
cannot be controlled from the CNS. The tendon organ, in
contrast to the muscle spindle, is coupled in series with
the extrafusal muscle bers. Both passive stretch and active contraction of the muscle increase the tension of the
tendon and thus activate the tendon organ receptor, but
active contraction produces the greatest increase. The
tendon organ, consequently, can inform the CNS about
the muscle tension. In contrast, the activity of the muscle spindle depends on the muscle length and not on the
tension. The muscle bers attached to one tendon organ
appear to belong to several motor units. Thus the CNS is
informed not only of the overall tension produced by the
muscle but also of how the workload is distributed among
the dierent motor units.
Vision
Hearing
Balance
Feeling
Smell
Taste
Implants
Models
In Animals
Insects & Spiders
Birds,Fish,...
2.5.1 Introduction
Probably the oldest sensory system in the nature, the olfactory system concerns the sense of smell. The olfactory system is physiologically strongly related to the
gustatory system, so that the two are often examined together. Complex avors require both taste and smell sensation to be recognized. Consequently, food may taste
dierent if the sense of smell does not work properly
Joint receptors The joint receptors are low-threshold (e.g. head cold).
mechanoreceptors and have been divided into four
groups. They signal dierent characteristics of joint Generally the two systems are classied as visceral sense
function (position, movements, direction and speed of because of their close association with gastrointestinal
movements). The free receptors or type 4 joint receptors function. They are also of central importance while
speaking of emotional and sexual functions.
are nociceptors.
2.4.3
Proprioceptive Signal Processing
Both taste and smell receptors are chemoreceptors that

are stimulated by molecules soluted respectively in mucus or saliva. However these two senses are anatomically
quite dierent. While smell receptors are distance receptors that do not have any connection to the thalamus, receptors pass up the brainstem to the thalamus and project
2.5. OLFACTORY SYSTEM
59
to the postcentral gyrus along with those for touch and

pressure sensibility for the mouth.
In this article we will rst focus on the organs composing the olfactory system, then we will characterize them
in order to understand their functionality and we will end
explaining the transduction of the signal and the commercial application such as the eNose.
1: Olfactory bulb 2: Mitral cells 3: Bone 4: Nasal Epithelium 5:

Glomerulus 6: Olfactory receptor cells
2.5.2
Sensory Organs
2.5.3 Sensory Organ Components
Similar to other sensory modalities, olfactory information

In vertebrates the main olfactory system detects odormust be transmitted from peripheral olfactory structures,
ants that are inhaled through the nose where they come
like the olfactory epithelium, to more central structures,
to contact with the olfactory epithelium, which contains
meaning the olfactory bulb and cortex. The specic stimthe olfactory receptors.
uli have to be integrated, detected and transmitted to the
Olfactory sensitivity is directly proportional to the area in brain in order to reach sensory consciousness. However
the nasal cavity near the septum reserved to the olfactory the olfactory system is dierent from other sensory sysmucous membrane, which is the region where the olfac- tems in three fundamental ways [1] :
tory receptor cells are located. The extent of this area is
a specic between animals species. In dogs, for exam1. Olfactory receptor neurons are continuously reple, the sense of smell is highly developed and the area
placed by mitotic division of the basal cells of the
2
covered by this membrane is about 75 150 cm ; these
olfactory epithelium. This is necessary due to the
animals are called macrosmatic animals. Dierently in
high vulnerability of the neurons, which are directly
humans the olfactory mucous membrane cover an area
exposed to the environment.
2
about 3 5 cm , thus they are known as microsmatic animals.
2. Due to phylogeny, olfactory sensory activity is transIn humans there are about 10 million olfactory cells, each
of which have 350 dierent receptor types composing
the olfactory mucous membrane. The 350 dierent receptors are characteristic for only one odorant type. The
bond with one odorant molecule starts a molecular chain
reaction, which transforms the chemical perception into
an electrical signal.
The electrical signal proceeds through the olfactory
nerves axons to the olfactory bulbs. In this region there
are between 1000 and 2000 glomerular cells which combine and interpret the potentials coming from dierent
receptors. This way it is possible to unequivocally characterise e.g. the coee aroma, which is composed by about
650 dierent odorants. Humans can distinguish between
about 10.000 odors.
ferred directly from the olfactory bulb to the olfactory cortex, without a thalamic relay.
3. Neural integration and analysis of olfactory stimuli may not involve topographic organization beyond
the olfactory bulb, meaning that spatial or frequency
axis are not needed to project the signal.
Olfactory Mucous Membrane
The olfactory mucous membrane contains the olfactory

receptor cells and in humans it covers an area about 3 5
cm^2 in the roof of the nasal cavity near the septum. Because the receptors are continuously regenerated it contains both the supporting cells and progenitors cells of the
The signal then goes forth to the olfactory cortex where olfactory receptors. Interspersed between these cells are
it will be recognized and compared with known odorants 10 20 millions receptor cells.
(i.e. olfactory memory) involving also an emotional re- Olfactory receptors are neurons with short and thick densponse to the olfactory stimuli.
drites. Their extended end is called an olfactory rod, from
It is also interesting to note that the human genome has which cilia project to the surface of the mucus. These
about 600 700 genes (~2% of the complete genome) neurons have a length of 2 micrometers and have between
specialized in characterizing the olfactory receptors, but 10 and 20 cilia of diameter about 0.1 micrometers.
only 350 are still used to build the olfactory system. This The axons of the olfactory receptor neurons go through
is a proof of the evolution change in the necessity of hu- the cribriform plate of the ethmoid bone and enter the
mans in using the olfaction.
olfactory bulb. This passage is in absolute the most sen-
60
sitive of the olfactory system; the damage of the cribriform plate (e.g. breaking the nasal septum) can imply
the destruction of the axons compromising the sense of
smell.

tle spatial encoding can be observed; that is, small areas
of the olfactory bulb virtually project the entire olfactory
cortex, and small areas of the cortex receive bers from
virtually the entire olfactory bulb [1] .
A further particularity of the mucous membrane is that In general the olfactory tract can be divided in ve major
with a period of a few weeks it is completely renewed.
regions of the cerebrum: The anterior olfactory nucleus,
the olfactory tubercle, the piriform cortex, the anterior
cortical nucleus of the amygdala and the entorhinal corOlfactory Bulbs
tex. Olfactory information is transmitted from primary
olfactory cortex to several other parts of the forebrain,
In humans, the olfactory bulb is located anteriorly with including orbital cortex, amygdala, hippocampus, central
respect to the cerebral hemisphere and remain connected striatum, hypothalamus and mediodorsal thalamus.
to it only by a long olfactory stalk. Furthermore in mamInteresting is also to note that in humans, the piriform
mals it is separated into layers and consists of a concencortex can be activated by sning, whereas to activate
tric lamina structure with well-dened neuronal somata
the lateral and the anterior orbitofrontal gyri of the frontal
and synaptic neuropil.
lobe only the smell is required. This is possible because in
After passing the cribriform plate the olfactory nerve general the orbitofrontal activation is greater on the right
bers ramify in the most supercial layer (olfactory nerve side than on the left side, this directly implies an asymlayer). When these axons reach the olfactory bulb the metry in the cortical representation of olfaction.
layer gets thicker and they terminate in the primary dendrites of the mitral cells and tufted cells. Both these cells
send other axons to the olfactory cortex and appear to
have the same functionality but in fact tufted cells are
2.5.4 Signal Processing
smaller and consequently have also smaller axons.
The axons from several thousand receptor neurons converge on one or two glomeruli in a corresponding zone of 2.5.5 Signal Processing
the olfactory bulb; this suggests that the glomeruli are the
unit structures for the olfactory discrimination.
Only substances which come in contact with the olfacIn order to avoid threshold problems in addition to mi- tory epithelium can excite the olfactory receptors. The
tral and tufted cells, the olfactory bulb contains also two right table shows thresholds for some representative subtypes of cells with inhibitory properties: periglomerular stances. These values give an impression of the huge sencells and granule cells. The rst will connect two dif- sitivity of the olfactory receptors.
ferent glomeruli, the second, without using any axons,
build a reciprocal synapse with the lateral dendrites of
the mitral and tufted cells. By releasing GABA the granule cell on the one side of these synapse are able to inhibits the mitral (or tufted) cells, while on the other side
of the synapses the mitral (or tufted) cells are able to excite the granule cells by releasing glutamate. Nowadays
about 8.000 glomeruli and 40.000 mitral cells have been
counted in young adults. Unfortunately this huge number
of cells decrease progressively with the age compromising the structural integrity of the dierent layers.
Olfactory Cortex
The axons of the mitral and tufted cells pass through
the granule layer, the intermediate olfactory stria and the
lateral olfactory stria to the olfactory cortex. This tract
forms in humans the bulk of the olfactory peduncle. The
primary olfactory cortical areas can be easily described
by a simple structure composed of three layers: a broad
plexiform layer (rst layer); a compact pyramidal cell somata layer (second layer) and a deeper layer composed
by both pyramidal and nonpyramidal cells (third layer)[1] .
Furthermore, in contrast to the olfactory bulb, only a lit-
It is remarkable that humans can recognize more than

10,000 dierent odors. Many odorant molecules dier
only slightly in their chemical structure (e.g. stereoisomers) but can nevertheless be distinguished.
Signal Transduction
An interesting feature of the olfactory system is that a
simple sense organ which apparently lacks a high degree
of complexity can mediate discrimination of more than
10'000 dierent odors. On the one hand this is made
possible by the huge number of dierent odorant receptor. The gene family of the olfactory receptor is in fact
the largest family studied so far in mammals. On the other
hand, the neural net of the olfactory system provides with
its 1800 glomeruli a large two dimensional map in the
olfactory bulb that is unique to each odorant. In addition, the extracellular eld potential in each glomerulus
oscillates, and the granule cells appear to regulate the frequency of the oscillation. The exact function of the oscillation is unknown, but it probably also helps to focus the
olfactory signal reaching the cortex [1] .
2.6. GUSTATORY SYSTEM

Smell measurement
Olfaction consists of a set of transformations from physical space of odorant molecules (olfactory physicochemical space), through a neural space of information processing (olfactory neural space), into a perceptual space
of smell (olfactory perceptual space).[3] The rules of these
transforms depend on obtaining valid metrics for each of
those spaces.
61
[2] Ganong, W. F., & Barrett, K. E. (2005). Review of medical physiology (Vol. 22). New York: McGraw-Hill Medical.
[3] Haddad, Ra; Lapid, Hadas; Harel, David; Sobel, Noam (August 2008).
Measuring smells.
Current Opinion in Neurobiology 18 (4): 438444.
doi:10.1016/j.conb.2008.09.007.
[4] Glomerular Activity Response Archive
Olfactory perceptual space As the perceptual space

represent the input of the smell measurement, its aim
is to describe the odors in the most simple possible way. 2.6 Gustatory
Odor are ordered so that their reciprocal distance in space
confers them similarity. This mean that the more two
Sensory Systems
odors are near each other in this space the more are they
expected to be similar. This space is thus dened by so
called perceptual axes characterized by some arbitrarily Vision
Hearing
chosen unit odors.
Balance
Feeling
Olfactory neural space As suggested by its name the Smell
neural space is generated from neural responses. This Taste
gives rise to an extensive database of odorant-induced activity, which can be used to formulate an olfactory space
where the concept of similarity serves as a guiding principle. Using this procedure dierent odorants are expected
to be similar if they generate a similar neuronal response. Implants
This database can be navigated at the Glomerular Activity Models
Response Archive [4] .
In Animals
Olfactory physicochemical space The need to identify the molecular encryption of the biological interaction, makes the physicochemical space the most complex
one of the olfactory space described so far. R. Haddad
suggest that one possibility is to span this space would to
represent each odorant by a very large number of molecular descriptors by use either a variance metric or a distance metric.[3] In his rst description single odorants
may have many physicochemical features and one expects
these features to present themselves at various probabilities within the world of molecules that have a smell. In
such metric the orthogonal basis generated from the description of the odorant leads to represent each odorant
by a single value. While in the second, the metric represents each odorant with a vector of 1664 values, on
the basis of Euclidean distances between odorants in the
1664 physicochemical space. Whereas the rst metric
enabled the prediction of perceptual attributes, the second enabled the prediction of odorant-induced neuronal
response patterns.
2.5.6
References
[1] Paxinos, G., & Mai, J. K. (2004). The human nervous

system. Academic Press.
System
Insects & Spiders

Birds,Fish,...
2.6.1 Introduction
The Gustatory System or sense of taste allows us to perceive dierent avors from substances like food, drinks,
medicine etc. Molecules that we taste or tastants are
sensed by cells in our mouth, which send information to
the brain. These specialized cells are called taste cells
and can sense 5 main tastes: bitter, salty, sweet, sour and
umami (savory). All the variety of avors that we know
are combinations of molecules which fall into these categories.
Measuring the degree by which a substance presents one
of the basic tastes is done subjectively by comparing its
taste to a taste of a reference substance according to relative indexes of dierent substances. For the bitter taste
quinine (found in tonic water) is used to rate how bitter
a substance is. Saltiness can be rated by comparing to a
dilute salt solution. The sourness is compared to diluted
hydrochloric acid (H+Cl-). Sweetness is measured relative to sucrose. The values of these reference substances
are dened as 1.
62
Bitter
Umami (savory or tasty)
(Coee, mate, beer, tonic water etc.)
(Cheese, soy sauce etc.)
It is considered by many as unpleasant. In general bitterness is very interesting because a large number of bitter
compounds are known to be toxic so the bitter taste is
considered to provide an important protective function.
Plant leafs often contain toxic compounds. Herbivores
have a tendency to prefer immature leaves, which have
higher protein content and lower poison levels than mature leaves. It seems that even if the bitter taste is not very
pleasant at rst, there is a tendency to overcome this aversion because coee and drinks containing rich amount
of caeine and are widely consumed. Sometimes bitter
agents are added to substances to prevent accidental ingestion.
Recently, monosodium glutamate (umami) has been

added as the fth taste. This taste signals the presence
of L-glutamate and it is a very important for the Eastern
cuisines.
2.6.2 Sensory Organs

Tongue and Taste Buds
Salty
(Table salt)
The salty taste is primarily produced by the presence of
cations such as Li+ (lithium ions), K+ (potassium ions)
and more commonly Na+ (sodium). The saltiness of substances is compared to sodium chloride, which is typically
used as table salt (Na+Cl-). Potassium chloride K+Cl- is
the principal ingredient used in salt substitutes and has an
index of 0.6 (see bellow part 5) compared to 1 of Na+Cl-.
Sour
(Lemon, orange, wine, spoiled milk and candies containing citric acid)
Sour taste can be mildly pleasant and it is linked to salty
avor but more exacerbated. Typically sour are fruits,
which are over-riped, spoiled milk, rotten meat, and other
spoiled foods, which can be dangerous. It also tastes acids
(H+ ions) which taken in large quantities can cause irre- Human tongue
versible tissue damage. Sourness is rated compared to
hydrochloric acid (H+Cl-), which has a sourness index of Taste cells are epithelial and are clustered in taste buds
located in the tongue, soft palate, epiglottis, pharynx and
1.
the esophagus the tongue being the primary organ of the
Gustatory System.
Sweet
(Sucrose (table sugar), cake, ice cream etc.)
Sweetness is regarded as a pleasant sensation and is produced by the presence of mostly sugars. Sweet substances
are rated relative to sucrose, which has an index of 1.
Nowadays there are many articial sweeteners in the market, these include saccharin, aspartame and sucralose but
it is still not clear how these substitutes activate the receptors.
Taste buds are located in papillae along the surface of

the tongue. There are three types of papillae in human:
fungiform located in the anterior part containing approximately ve taste buds, circumvallate papillae which are
bigger and more posterior than the previous ones and
the foliate papillae that are in the posterior edge of the
tongue. Circumvallate and foliate papillae contain hundreds of taste buds. In each taste bud there are dierent types of cells: basal, dark, intermediate and light
cells. Basal cells are believed to be the stem cells that
give rise to the other types. It is thought that the rest of
2.6. GUSTATORY SYSTEM
63
2.6.3 Transduction of Taste

As mentioned before we distinguish between 5 types of
basic tastes: bitter, salty, sour, sweet and umami. There
is one type of taste receptor for each avor known and
each type of taste stimulus is transduced by a dierent
mechanisms. In general bitter, sweet and umami are detected by G protein-coupled receptors and salty and sour
are detected via ion channels.
Bitter
Schematic drawing of a taste bud
the cells correspond to dierent stages of dierentiation

where the light cells are the most mature type of cells. An
alternative idea is that dark, intermediate and light cells
correspond to dierent cellular lineages. Taste cells are
short lived and are continuously regenerated. They contain a taste pore at the surface of the epithelium where
they extend microvilli, the site where sensory transduction takes place. Taste cells are innervated by bers of
primary gustatory neurons. They contact sensory bers
and these connections resemble chemical synapses, they
are excitable with voltage-gated channels: K+, Na+ and
Ca+ channels capable of generating action potentials. Although the reaction from dierent tastants varies, in general tastants interact with receptors or ion channels in the
membrane of a taste cells. These interactions depolarize
the cell directly or via second messengers and in this way
the receptor potential generates action potentials within
the taste cells, which lead to Ca2+ inux through Ca2+
voltage-gated channels followed by the release of neurotransmitters at the synapses with the sensory bers.
Bitter compounds act through G protein coupled receptors (GPCRs) also known as a seven-transmembrane domains, which are located in the walls of the taste cells.
Taste receptors of type 2 (T2Rs) which is a group of
GPCRs is thought respond to bitter stimuli. When the
bitter-tasting ligand binds to the GPCR it releases the
G protein gustducin, its 3 subunits break apart and activate phosphodiesterase, which in turn converts a precursor within the cell into a secondary messenger, closing the
K+ channels. This secondary messenger stimulates the
release of Ca2+, contributing to depolarization followed
by neurotransmitter release. It is possible that bitter substances that are permeable to the membrane are sensed
by mechanisms not involving G proteins.
Salt
The amiloride-sensitive epithelial sodium channel
(ENaC), a type of ion channel in the taste cell wall,
allows Na+ ions to enter the cell down an electrochemical gradient, altering the membrane potential of the
taste cells by depolarizing the cell. This leads to an
opening of voltage-gated Ca2+ channels, followed by
neurotransmitter release.
Sour
The sour taste signals the presence of acidic compounds

(H+ ions) and there are three receptors: 1) The ENaC,
(the same protein involved in salty taste). 2) There are
The idea that the tongue is most sensitive to certain tastes also H+ gated channels; one is the K+ channel, which alin dierent regions was a long time misconception, which lows K+ outux of the cell. H+ ions block these so the
has now been proved to be wrong. All sensations come K+ stays inside the cell. 3) A third channel undergoes a
from all regions of the tongue.
conguration change when a H+ attaches to it leading to
an opening of the channel and allowing an inux of Na+
down the concentration gradient into the cell, leading to
the opening of a voltage gated Ca2+ channels. These
Supertasters
three receptors work in parallel and lead to depolarization of the cell followed by neurotransmitter release.
An average person has about 5'000 taste buds. A supertaster is a person whose sense of taste is signicantly
more sensitive than average. The increase in the response Sweet
is thought to be because they have more than 20000 taste
buds, or due to an increased number of fungiform papil- Sweet transduction is mediated by the binding of a sweet
tastant to GPCRs located in the apical membrane of the
lae.
Tongue map
64
taste cell. Saccharide activates the GPCR, which releases

gustducin and this in turn activates cAMP (cyclic adenylate monophosphate). cAMP will activate the cAMP kinase that will phosphorylate the K+ channels and eventually inactivate them, leading to depolarization of the cell
and followed by neurotransmitter release.
Spicy food
(black peppers, chili peppers, etc.)
It is not a basic taste because this sensation does not arise

from taste buds. Capsaicin is the active ingredient in spicy
food and causes hotness or spiciness when eaten. It
stimulates temperature bers and also nociceptors (pain)
in the tongue. In the nociceptors it stimulates the release
Umami (Savory)
of substance P, which causes vasodilatation and release
of histamine causing hiperalgesia (increased sensitivity to
Umami receptors involve also GPCRs, the same way as pain).
bitter and sweet receptors. Glutamate binds a type of the
metabotropic glutamate receptor mGlurR4 causing a G- In general basic tastes can be appetitive or aversive deprotein complex to activate a secondary receptor, which pending on the eect that the food has on us but also
ultimately leads to neurotransmitter release. In particular essential to the taste experience are the presentation of
how the intermediate steps work, is currently unknown. food, color, texture, smell, previous experiences, expectations, temperature and satiety.
2.6.4
Signal Processing
In humans, the sense of taste is transmitted to the brain

via three cranial nerves. The VII facial nerve carries information from the anterior 2/3 part of the tongue and
soft palate. The IX nerve or glossopharyngeal nerve carries taste sensations from the posterior 1/3 part of the
tongue and the X nerve or vagus nerve carries information
from the back of the oral cavity and the epiglottis.
The gustatory cortex is the brain structure responsible for
the perception of taste. It consists of the anterior insula on
the insular lobe and the frontal operculum on the inferior
frontal gyrus of the frontal lobe. Neurons in the gustatory
cortex respond to the ve main tastes.
Taste cells synapse with primary sensory axons of the
mentioned cranial nerves. The central axons of these neurons in the respective cranial nerve ganglia project to rostral and lateral regions of the nucleus of the solitary tract
in the medulla. Axons from the rostral (gustatory) part of
the solitary nucleus project to the ventral posterior complex of the thalamus, where they terminate in the medial
half of the ventral posterior medial nucleus. This nucleus
projects to several regions of the neocortex, which include
the gustatory cortex.
Gustatory cortex neurons exhibit complex responses to
changes in concentration of tastant. For one tastant, the
same neuron might increase its ring and for an other tastant, it may only respond to an intermediate concentration.
2.6.5
Taste and Other Senses
In general the Gustatory Systems does not work alone.

While eating, consistency and texture are sensed by the
mechanoreceptors from the somatosensory system. The
sense of taste is also correlated with the olfactory system
because if we lack the sense of smell it makes it dicult
to distinguish the avor.
2.6.6 Taste disorders

Ageusia (complete loss of taste)
Ageusia is a partial or complete loss in the sense of taste
and sometimes it can be accompanied by the loss of smell.
Dysgeusia (abnormal taste)
Is an alteration in the perception associated with the sense
of taste. Tastes of food and drinks vary radically and
sometimes the taste is perceived as repulsive. The causes
of dysgeusia can be associated with neurologic disorders.
Chapter 3
Sensory Systems in Non-Primates

3.1 NonPrimates
3.1.1 Zebra Finches: Neural Mechanism

for Song Learning
Introduction
Primates are animals belonging to the class of mammals.

Primates include humans and the nonhuman primates,
the apes, monkeys, lemurs, tree-shrews, lorises, bush babies and tarsiers. They are characterized by a voluminous
and complicated forebrain. Most have excellent sight and
are highly adapted to an arboreal existence, including in
some species the possession of a prehensile tail. Non primates on the other hand often posses smaller brains. But
as we learn more about the rest of the animal world, its
becoming clear that non-primates are pretty intelligent
too. Some examples include pigs, octopus, and crows.[1]
In many branches of mythology, the crow plays a shrewd
trickster, and in the real world, crows are proving to be
quite a clever species. Crows have been found to engage
in feats such as tool use, the ability to hide and store
food from season to season, episodic-like memory, and
the ability to use personal experience to predict future
conditions.
As it turns out, being piggy is actually a pretty smart
tactic. Pigs are probably the most intelligent domesticated animal on the planet. Although their raw intelligence is most likely commensurate with a dog or cat, their
problem-solving abilities top those of felines and canine
pals.
If pigs are the most intelligent of the domesticated
species, octopuses take the cake for invertebrates. Experiments in maze and problem-solving have shown that they
have both short-term and long-term memory. Octopuses
can open jars, squeeze through tiny openings, and hop
from cage to cage for a snack. They can also be trained
to distinguish between dierent shapes and patterns. In a
kind of play-like activity (one of the hallmarks of higher
intelligence species) octopuses have been observed repeatedly releasing bottles or toys into a circular current
in their aquariums and then catching them.
Over the past four decades songbirds have become a

widely used model organism for neuroscientists studying
complex sequential behaviours and sensory-guided motor learning. Like human babies, young songbirds learn
many of the sounds they use for communication by imitating adults. One songbird in particular, the zebra nch
(Taeniopygia guttata), has been the focus of much research because of its proclivity to sing and breed in captivity and its rapid maturation. The song of an adult
male zebra nch is a stereotyped series of acoustic signals with structure and modulation over a wide range of
time scales, from milliseconds to several seconds. The
adult zebra nch song comprises a repeated sequence of
sounds, called a motif, which lasts about a second. The
motif is composed of shorter bursts of sound called syllables, which often contain sequences of simpler acoustic
elements called notes as shown in Fig.1. The songbirds
learning system is a very good model to study the sensorymotor integration because the juvenile bird actively listens to the tutor and modulates its own song by correcting
for errors in the pitch and oset. The neural mechanism
and the architecture of the song bird brain which plays a
crucial role in learning is similar to the language processing region in frontal cortex of humans. Detailed study of
the hierarchical neural network involved in the learning
process could provide signicant insights into the neural
mechanism of speech learning in humans.
Illustration of the typical song structure & learning

phases involved in song bird.
Song-learning proceeds through a series of stages, beginning with sensory phase where the juvenile bird just listens to its tutor (usually its father) vocalizing, often without producing any song-like vocalization itself. The bird
uses this phase to memorize a certain structure of the tutor song, forming the neural template of the song. Then
it enters the sensorimotor phase, where it starts babbling
the song and correcting its errors using auditory feedback.
65
66
Figure 1: Illustration of the typical song structure & learning

phases involved in song bird. Upper panel: Phases involved in
the song learning process. Middle panel: Structure of a crystallized song a,b,c,d,e denote the various syllable in the song. Lower
panel: Evolution of the song dynamics during learning.
CHAPTER 3. SENSORY SYSTEMS IN NON-PRIMATES

which plays a signicant role in vocal learning. The
motor control pathway includes Hyperstriatum Ventrale,
pars Caudalis (HVC), Robust Nucleus of Acropallium
(RA), Tracheosyringeal subdivision of the hypoglossal
nucleus (nXIIts) and Syrinx. This pathway is necessary
for generating the required motor control signals which
produce highly structured songs and coordinating breathing with singing. The anterior forebrain pathway includes Lateral magnocellular nucleus of anterior nidopallium (LMAN), Area X (X) and the medial nucleus of
dorsolateral thalamus (DLM). This pathway plays a crucial role in song learning in juveniles, song variability in
adults and song representation. The auditory pathway includes substantia nigra (SNc) and the ventral tegmental
area (VTA), which plays a crucial role in auditory inputs
processing and analyzing the feedback error. The muscles of the syrinx are innervated by a subset of motor
neurons from nXIIts. A primary projection to the nXIIts
descends from neurons in the forebrain nucleus RA. Nucleus RA receives motor-related projections from another
cortical analogue, nucleus HVC, which in turn receives
direct input from several brain areas, including thalamic
nucleus uvaeformis (Uva).
The earliest attempt to recreate the template of the tutor song is highly noisy, unstructured and variable and it
is called sub-song. An example is shown in the spectrogram in Fig.1. Through the subsequent days the bird enters a plastic phase where there is a signicant amount
of plasticity in the neural network responsible for generating highly structured syllables and the variability is
reduced in the song. By the time they reach sexual maturity, the variability is substantially eliminateda process
called crystallizationand the young bird begins to produce a normal adult song, which can be a striking imitation of the tutor song (Fig.1). Thus, the gradual reduction
of song variability from early sub-song to adult song, together with the gradual increase in imitation quality, is
an integral aspect of vocal learning in the songbird. In
the following sections we will explore several parts of the
avian brain and the underlying neural mechanisms that
are responsible for this remarkable vocal imitation obFigure 2. Architecture of the song bird brain & various pathways
served in these birds.
carrying motor and auditory feedback signals.
Hierarchical Neural Network involved in the generation of song sequences

Neural Mechanism for the generation of highly structured & temporally precise syllable pattern
It is important to understand the neuroanatomy of the
songbird in detail because it provides signicant infor- Nuclei HVC and RA are involved in the motor control of
mation about the learning mechanisms involved in vari- song in a hierarchical manner (Yu and Margoliash 1996).
ous motor and sensory integration pathways. This could Recordings in singing zebra nches have shown that HVC
ultimately shed light on the language processing and vo- neurons that project to RA transmit an extremely sparse
cal learning in humans. The exact neuroanatomical data pattern of bursts: each RA-projecting HVC neuron genabout human speech processing system is still unknown erates a single highly stereotyped burst of approximately
and songbird anatomy and physiology will enable us to 6 ms duration at one specic time in the song (Hahnloser,
make plausible hypotheses. The comparison of the mam- Kozhevnikov et al. 2002). During singing, RA neurons
malian brain and a songbird (avian) brain is made in the generate a complex sequence of high-frequency bursts of
nal section of this chapter in (Fig. 6). The pathway ob- spikes, the pattern of which is precisely reproduced each
served in the avian brain can be broadly divided into mo- time the bird sings its song motif (Yu and Margoliash
tor control and anterior forebrain pathway as shown in 1996). During a motif, each RA neuron produces a fairly
(Fig.2). The auditory pathway provides the error feed- unique pattern of roughly 12 bursts, each lasting ~10 ms
back signals which leads to potentiation or depression (Leonardo and Fee 2005). Based on the observations that
of the synaptic connections involved in motor pathways, RA-projecting HVC neurons generate a single burst of
3.1. NONPRIMATES
spikes during the song motif and that dierent neurons
appear to burst at many dierent times in the motif, it
has been hypothesized that these neurons generate a continuous sequence of activity over time (Fee, Kozhevnikov
et al. 2004, Kozhevnikov and Fee 2007). In other words,
at each moment in the song, there is a small ensemble of
HVC (RA) neurons active at that time and only at that
time (Figure 3), and each ensemble transiently activates
(for ~10 ms) a subset of RA neurons determined by the
synaptic connections of HVC neurons in RA (Leonardo
and Fee 2005). Further, in this model the vector of muscle activities, and thus the conguration of the vocal organ, is determined by the convergent input from RA neurons on a short time scale, of about 10 to 20 ms. The
view that RA neurons may simply contribute transiently,
with some eective weight, to the activity of vocal muscles is consistent with some models of cortical control of
arm movement in primates (Todorov 2000). A number
of studies suggest that the timing of the song is controlled
on a millisecond-by-millisecond basis by a wave, or chain,
of activity that propagates sparsely through HVC neurons.
This hypothesis is supported by an analysis of timing variability during natural singing (Glaze and Troyer 2007) as
well as experiments in which circuit dynamics in HVC
were manipulated to observe the eect on song timing.
Thus, in this model, song timing is controlled by propagation of activity through a chain in HVC; the generic
sequential activation of this HVC chain is translated, by
the HVC connections in RA, into a specic precise sequence of vocal congurations.
67
control the muscles of the vocal apparatus during song
(Yu and Margoliash 1996, Hahnloser, Kozhevnikov et al.
2002, Suthers and Margoliash 2002). Lesion of HVC or
RA causes immediate loss of song (Vicario and Nottebohm 1988). Other areas in the anterior forebrain pathway (AFP) appear to be important for song learning but
not production, at least in adults. The AFP is regarded
as an avian homologue of the mammalian basal ganglia
thalamocortical loop (Farries 2004). In particular, lesion of area LMAN (lateral magnocellular nucleus of
the nidopallium) has little immediate eect on song production in adults, but arrests song learning in juveniles
(Doupe 1993, Brainard and Doupe 2000). These facts
suggest that LMAN plays a role in driving song learning, but the locus of plasticity is in brain areas related to
song production, such as HVC and RA. Doya and Senjowski in 1998 proposed a tripartite schema, in which
learning is based on the interactions between actor and
a critic (Fig.4B). The critic evaluates the performance of
the actor at a desired task. The actor uses this evaluation
to change in a way that improves its performance. To
learn by trial and error, the actor performs the task differently each time. It generates both good and bad variations, and the critics evaluation is used to reinforce the
good ones. Ordinarily it is assumed that the actor generates variations by itself. However, the source of variation
is external to the actor. We will call this source the experimenter. The actor was identied with HVC, RA, and the
motor neurons that control vocalization. The actor learns
through plasticity at the synapses from HVC to RA (Fig.
4C). Based on evidence of structural changes like axonal
growth and retraction that take place in the HVC to RA
projection during song learning, this view is widely regarded as a plausible mechanism. For the experimenter
& critic, Doya and Senjowski turned to the anterior forebrain pathway, hypothesizing that the critic is Area X and
the experimenter is LMAN.
Biophysically realistic synaptic plasticity rules underlying song learning mechanism
Figure 3. Mechanisms of sequence generation in the adult song

motor pathway. Illustration of the hypothesis that RA-projecting
HVC (HVC(RA)) neurons burst and activate each other sequentially in groups of 100 to 200 coactive neurons. Each group of
HVC neurons drives a distinct ensemble of RA neurons to burst.
The neurons converge with some eective weight at the level of
the motor neurons to activate syringeal muscles.
Synaptic Plasticity in Posterior Forebrain Pathway is

a potential substrate for vocal learning
A number of song-related avian brain areas have been discovered (Fig. 4A). Song production areas include HVC
(Hyperstriatum Ventrale, pars Caudalis) and RA (robust
nucleus of the arcopallium), which generate sequences
of neural activity patterns and through motor neurons
Comparison between Mammalian & Songbird brain

architecture
The avian Area X is homologous to the mammalian
basal ganglia (BG) and includes striatal and pallidal cell
types. The BG forms part of a highly conserved anatomical loop-through several stations, from cortex to the BG
(striatum and pallidum), then to thalamus and back to
cortex. Similar loops are seen in the songbird: the cortical analogue nucleus LMAN projects to Area X, the striatal components of which project to the thalamic nucleus
DLM, which projects back to LMAN. Striatal components accounts for reward basing learning and reinforcement learning. The neuron types and its functionality are
exactly comparable in Area X of birds to basal ganglia in
humans as shown (in Fig.6). The close anatomical similarity motivates us to learn the song bird brain in more
68
Figure 6. Comparison of mammalian and avian basal ganglia

forebrain circuitry.
Farries, M. A. (2004). The avian song system in comparative perspective. Ann N Y Acad Sci 1016: 61-76.
Figure 4. Plasticity in Specic pathways enabling learning. (A)

Avian song pathways and the tripartite hypotheses. A: avian
brain areas involved in song production and song learning. Premotor pathway (open) includes areas necessary for song production. Anterior forebrain pathway (lled) is required for song
learning but not for song production. (B) Tripartite reinforcement learning schema: the actor produces behaviour; the experimenter sends uctuating input to the actor, producing variability
in behaviour that is used for trial-and-error learning; the critic
evaluates the behaviour of the actor and sends a reinforcement
signal to it. For birdsong, the actor includes premotor song production areas HVC and RA. (C) Plastic and empiric synapses.
RA receives synaptic input from both HVC and LMAN. We will
call the HVC synapses plastic, in keeping with the hypothesis
that these synapses are the locus of plasticity for song learning.
Fee, M. S., A. A. Kozhevnikov and R. H. Hahnloser

(2004). Neural mechanisms of vocal sequence generation in the songbird. Ann N Y Acad Sci 1016: 153170.Glaze, C. M. and T. W. Troyer (2007). Behavioral measurements of a temporally precise motor code
for birdsong. J Neurosci 27(29): 7631-7639.
Hahnloser, R. H., A. A. Kozhevnikov and M. S. Fee
(2002). An ultra-sparse code underlies the generation
of neural sequences in a songbird. Nature 419(6902):
65-70.
Kozhevnikov, A. A. and M. S. Fee (2007). Singingrelated activity of identied HVC neurons in the zebra
nch. J Neurophysiol 97(6): 4271-4283.
Leonardo, A. and M. S. Fee (2005). Ensemble coding
of vocal control in birdsong. J Neurosci 25(3): 652-661.
Seung, H. S. (2003). Learning in spiking neural networks by reinforcement of stochastic synaptic transmission. Neuron 40(6): 1063-1073.
Suthers, R. A. and D. Margoliash (2002). Motor control

detail because with this we can nally achieve some sig- of birdsong. Curr Opin Neurobiol 12(6): 684-690.
nicant understanding of the speech learning in humans Todorov, E. (2000). Direct cortical control of muscle
and treat many speech related disorders with higher pre- activation in voluntary arm movements: a model. Nat
cision.
Neurosci 3(4): 391-398.
Vicario, D. S. and F. Nottebohm (1988). Organization
of the zebra nch song control system: I. Representation
of syringeal muscles in the hypoglossal nucleus. J Comp
Brainard, M. S. and A. J. Doupe (2000). Auditory feed- Neurol 271(3): 346-354.
back in learning and maintenance of vocal behaviour. Yu, A. C. and D. Margoliash (1996). Temporal hierNat Rev Neurosci 1(1): 31-40.
archical control of singing in birds. Science 273(5283):
Dembo, A. and T. Kailath (1990). Model-free dis- 1871-1875.
References
tributed learning. IEEE Trans Neural Netw 1(1): 58-70.

Doupe, A. J. (1993). A neural circuit specialized for 3.1.2
vocal learning. Curr Opin Neurobiol 3(1): 104-111.
Octopus
3.1. NONPRIMATES
Introduction
One of the most interesting non-primate is the octopus.
The most interesting feature about this non-primate is its
arm movement. In these invertebrates, the control of the
arm is especially complex because the arm can be moved
in any direction, with a virtually innite number of degrees of freedom. In the octopus, the brain only has to
send a command to the arm to do the actionthe entire
recipe of how to do it is embedded in the arm itself. Observations indicate that octopuses reduce the complexity
of controlling their arms by keeping their arm movements
to set, stereotypical patterns. To nd out if octopus arms
have minds of their own, the researchers cut o the nerves
in an octopus arm from the other nerves in its body, including the brain. They then tickled and stimulated the
skin on the arm. The arm behaved in an identical fashion
to what it would in a healthy octopus. The implication is
that the brain only has to send a single move command to
the arm, and the arm will do the rest.
69
voluntary movement is embedded within the neural circuitry of the arm itself.[2]
Arm Movements in Octopus
In the hierarchical organization in octopus, the brain only
has to send a command to the arm to do the action. The
entire recipe of how to do it is embedded in the arm itself.
By the use of the arms octopus walks, seizes its pray, or
rejects unwanted objects and also obtains a wide range of
mechanical and chemical information about its immediate environment.
Octopus arms, unlike human arms, are not limited in their

range of motion by elbow, wrist, and shoulder joints. To
accomplish goals such as reaching for a meal or swimming, however, an octopus must be able to control its
eight appendages. The octopus arm can move in any direction using virtually innite degrees of freedom. This
ability results from the densely packed exible muscle
In this chapter we discuss in detail the sensory system of bers along the arm of the octopus.
an octopus and focus on the sensory motor system in this Observations indicate that octopuses reduce the complexnon-primate.
ity of controlling their arms by keeping their arm movements to set, stereotypical patterns.[3] For example, the
reaching movement always consists of a bend that propagates along the arm toward the tip. Since octopuses
always use the same kind of movement to extend their
arms, the commands that generate the pattern are stored
in the arm itself, not in the central brain. Such a mechanism further reduces the complexity of controlling a exible arm. These exible arms are controlled by an elaborate peripheral nervous system containing 5 107 neurons distributed along each arm. 4 105 of these are
motor neurons, which innervate the intrinsic muscles of
the arm and locally control muscle action.
Whenever it is required, the nervous system in octopus
generates a sequence of motor commands which in turn
produces forces and corresponding velocities making the
limb reach the target. The movements are simplied by
The Common Octopus, Octopus vulgaris.
the use of optimal trajectories made through vectorial
summation and superposition of basic movements. This
Octopus - The intelligent non-primate Octopuses requires that the muscles are quite exible.
have two eyes and four pairs of arms, and they are bilaterally symmetric. An octopus has a hard beak, with its
mouth at the center point of the arms. Octopuses have no The Nervous System of the Arms
internal or external skeleton (although some species have
a vestigial remnant of a shell inside their mantle), allow- The eight arms of the octopus are elongated, tapering,
ing them to squeeze through tight places. Octopuses are muscular organs, projecting from the head and regularly
among the most intelligent and behaviorally exible of all arranged around the mouth. The inner surface of each
arm bears a double row of suckers, each sucker alternatinvertebrates.
row. There are about 300
The most interesting feature of the octopuses is their arm ing with that of the opposite
[4]
suckers
on
each
arm.
movements. For goal directed arm movements, the nervous system in octopus generates a sequence of motor
commands that brings the arm towards the target. Control of the arm is especially complex because the arm can
be moved in any direction, with a virtually innite number of degrees of freedom. The basic motor program for
The arms perform both motor and sensory functions.

The nervous system in the arms of the octopus is represented by the nerve ganglia, subserving motor and interconnecting functions. The peripheral nerve cells represent the sensory systems. There exists a close functional
70
relationship between the nerve ganglia and the peripheral Six main nerve centers lie in the arm and are responsible
nerve cells.
for the performance of these sets of muscles. The axial
nerve cord is by far the most important motor and integrative center of the arm. The eight cords one in each
General anatomy of the arm The muscles of the arm arm contains altogether 3.5 108 neurons. Each axial
can be divided into three separate groups, each having cord is linked by means of connective nerve bundles with
a certain degree of anatomical and functional indepen- ve sets of more peripheral nerve centers, the four intradence:
muscular nerve cords, lying among the intrinsic muscles
of the arm, and the ganglia of the suckers, situated in the
peduncle just beneath the acetabular cup of each sucker.
1. Intrinsic muscles of the arm,
All these small peripheral nerves contain motor neurons
and receive sensory bers from deep muscle receptors
3. Acetabulo-brachial muscles (connects the suckers to which play the role of local reex centers. The motor innervation of the muscles of the arm is thus provided not
the arm muscles).
only by the motor neurons of the axial nerve cord, which
receives pre-ganglionic bers from the brain, but also by
Each of these three groups of muscles comprises three these more peripheral motor centers.
muscle bundles at right angles to one another. Each bundle is innervated separately from the surrounding units
and shows a remarkable autonomy.In spite of the absence Sensory Nervous system The arms contain a complex
of a bony or cartilaginous skeleton, octopus can produce and extensive sensory system. Deep receptors in the three
arm movements using the contraction and relaxation of main muscle systems of the arms, provide the animal with
dierent muscles. Behaviorally, the longitudinal muscles a widespread sensory apparatus for collecting information
shorten the arm and play major role in seizing objects from muscles. Many primary receptors lie in the epithecarrying them to mouth, and the oblique and transverse lium covering the surface of the arm. The sucker, and
muscles lengthen the arms and are used by octopus for particularly its rim, has the greatest number of these senrejecting unwanted objects.
sory cells, while the skin of the arm is rather less sensitive.
2. Intrinsic muscles of the suckers, and
Several tens of thousands of receptors lie in each sucker.

Three main morphological types of receptors are found
in arms of an octopus. These are round cells, irregular
multipolar cells, and tapered ciliated cells. All these elements send their processes centripetally towards the ganglia. The functional signicance of these three types of
receptors is still not very well known and can only be conjectured. It has been suggested that the round and multipolar receptors may record mechanical stimuli, while
ciliated receptors are likely to be chemo-receptors.
The ciliated receptors do not send their axons directly to
the ganglia but the axons meet encapsulated neurons lying underneath the epithelium and make synaptic contacts
with the dendritic processes of these. This linkage helps
in reduction of input between primary nerve cells. Round
and multipolar receptors on the other hand send their axons directly to the ganglia where the motor neurons lie.
Functioning of peripheral nervous system in arm

movements
Cross section of an octopus arm: The lateral roots innervate the

intrinsic muscles, the ventral roots the suckers.
Behavioral experiments suggest that information regarding the movement of the muscles does not reach the learning centers of the brain, and morphological observations
prove that the deep receptors send their axons to peripheral centers such as the ganglion of the sucker or the intramuscular nerve cords.[5] The information regarding the
stretch or movement of the muscles is used in local reexes only.
3.1. NONPRIMATES
71
When the dorsal part of the axial nerve cord that contains the axonal tracts from the brain is stimulated by electrical signals, movements in entire arm are still noticed.
The movements are triggered by the stimulation which is
provided and is not directly driven by the stimuli coming from the brain. Thus, arm extensions are evoked by
stimulation of the dorsal part of the axial nerve cord. In
contrast, the stimulation of the muscles within the same The lateral line sensory organ shown on a shark.
area or the ganglionic part of the cord evokes only local
muscular contractions. The implication is that the brain
only has to send a single move command to the arm, and way back to their home streams, because they remember
what they smell like. Especially ground dwelling sh have
the arm will do the rest.
a very strong tactile sense in their lips and barbels. Their
A dorsally oriented bend propagates along the arm caus- taste buds are also located there. They use these senses
ing the suckers to point in the direction of the movement. to search for food on the ground and in murky waters.
As the bend propagates, the part of the arm proximal to
the bend remains extended. For further conformations Fish also have a lateral line system, also known as the latthat an octopus arm has a mind of its own, the nerves in eralis system. It is a system of tactile sense organs located
an octopus arm have been cut o from the other nerves in the head and along both sides of the body. It is used to
in its body, including the brain. Movements resembling detect movement and vibration in the surrounding water.
normal arm extensions were initiated in amputated arms
by electrical stimulation of the nerve cord or by tactile
Function
stimulation of the skin or suckers.
It has been noted that the bend propagations are more
readily initiated when a bend is created manually before
stimulation. If the fully relaxed arm is stimulated, the initial movement is triggered by the stimuli, which follows
the same bend propagation. The nervous system of the
arm thus, not only drives local reexes but controls complex movements involving the entire arm.
Fish use the lateral line sense organ to sense prey and
predators, changes in the current and its orientation and
they use it to avoid collision in schooling.
Coombs et al. have shown [1] that the lateral line sensory
organ is necessary for sh to detect their prey and orient
towards it. The sh detect and orient themselves towards
movements created by prey or a vibrating metal sphere
These evoked movements are almost kinematically iden- even when they are blinded. When signal transduction in
tical to the movements of freely behaving octopus. When the lateral lines is inhibited by cobalt chloride application,
stimulated, a severed arm shows an active propagation of the ability to target the prey is greatly diminished.
the muscle activity as in natural arm extensions. MoveThe dependency of sh on the lateral line organ to avoid
ments evoked from similar initial arm postures result in
collisions in schooling sh was demonstrated by Pitcher
similar paths, while dierent starting postures result in
et al. in 1976, where they show that optically blinded sh
dierent nal paths.
can swim in a school of sh, while those with a disabled
As the extensions evoked in denervated octopus arms are lateral line organ cannot [2].
qualitatively and kinematically similar to natural arm extensions, an underlying motor program seems to be controlling the movements which are embedded in the neu- Anatomy
romuscular system of the arm, which does not require
The lateral lines are visible as two faint lines that run along
central control.
either side of the sh body, from its head to its tail. They
are made up of a series of mechanoreceptor cells called
neuromasts. These are either located on the surface of the
3.1.3 Fish
skin or are, more frequently, embedded within the lateral
line canal. The lateral line canal is a mucus lled structure
Fish are aquatic animals with great diversity. There are that lies just beneath the skin and transduces the exterover 32000 species of sh, making it the largest group of nal water displacement through openings from the outside
vertebrates.
to the neuromasts on the inside. The neuromasts themMost sh possess highly developed sense organs. The selves are made up of sensory cells with ne hair cells
eyes of most daylight dwelling sh are capable of color vi- that are encapsulated by a cylindrical gelatinous cupula.
sion. Some can even see ultra violet light. Fish also have These reach either directly into the open water (common
a very good sense of smell. Trout for example have spe- in deep sea sh) or into the lymph uid of the lateral line
cial holes called nares in their head that they use to reg- canal. The changing water pressures bend the cupula, and
ister tiny amounts of chemicals in the water. Migrating in turn the hair cells inside. Similar to the hair cells in all
salmon coming from the ocean use this sense to nd their vertebrate ears, a deection towards the shorter cilia leads
72
to a hyperpolarization (decrease of ring rate) and a deection in the opposite direction leads to depolarization
(increase of ring rate) of the sensory cells. Therefore
the pressure information is transduced to digital information using rate coding that is then passed along the lateral
line nerve to the brain. By integrating many neuromasts
through their aerent and eerent connections, complex
circuits can be formed. This can make them respond to
dierent stimulation frequencies and consequently coding for dierent parameters, like acceleration or velocity
[3].

recordings from these lines in the common cuttlesh
(Sepia ocinalis) and the brief squid (Lolliguncula brevis) have identied them as an invertebrate analogue to
the mechanoreceptive lateral lines of sh and aquatic amphibians [5].
Crustaceans:
Another convergence to the sh lateral line is found
in some crustaceans. Contrary to sh, they dont have
the mechanosensory cells on their body, but have them
spaced at regular intervals on long trailing antennae.
These are held parallel to the body. This forms two lateral lines parallel to the body that have similar properties
to those of sh lateral lines and are mechanically independent of the body [6].
Mammals:
Some scales of the lateral line (center) of a Rutilus rutilus
In aquatic manatees the postcranial body bears tactile

hairs. They resemble the mechanosensory hairs of naked
mole rats. This arrangement of hair has been compared to
the sh lateral line and complement the poor visual capacities of the manatees. Similarly, the whiskers of harbor
seals are known to detect minute water movements and
serve as a hydrodynamic receptor system. This system is
far less sensitive than the sh equivalent. [7]
3.1.4 Flies
Introduction
In sharks and rays, some neuromasts have undergone an

interesting evolution. They have evolved into electroreceptors called ampullae of Lorenzini. They are mostly
concentrated around the head of the sh and can detect a
change of electrical stimuli as small as 0.01 microvolt [4].
With this sensitive instrument these sh are able to detect
tiny electrical potentials generated by muscle contractions
and can thus nd their prey over large distances, in murky
waters or even hidden under the sand. It has been suggested that sharks also use this sense for migration and
orientation, since the ampullae of Lorenzini are sensitive
enough to detect the earths electromagnetic eld.
Halteres of the Crane y
Halteres are sensory organs present in many ying insects.

Widely thought to be an evolutionary modifcation of the
rear pair of wings on such insects, halteres provide gyroscopic sensory data, vitally important for ight. Although
the y has other relevant systems to aid in ight, the visual
Convergent Evolution
system of the y is too slow to allow for rapid maneuvers.
Additionally, to be able to y adeptly in low light conCephalopods:
ditions, a requirement to avoid predation, such a sensory
Cephalopods such as squids, octopuses and cuttlesh have system is necessary. Indeed, without halteres, ies are
lines of ciliated epidermal cells on head and arms that incapable of sustained, controlled ight. Since the 18th
resemble the lateral lines of sh. Electrophysiological century, scientists have been aware of the role halteres
3.1. NONPRIMATES
73
play in ight, but it was only recently that the mechanisms matic changes in the ight dynamics. Halteres have been
by which they operate have been better explored. [6] [7]
shown to have extremely fast response times, allowing
these ight changes to be performed much more quickly
than if the y were to rely on its visual system. In order
Anatomy
to distinguish between dierent rotational components,
such as pitch and roll, the y must be able to combine
The haltere evolved from the rearmost of two pairs of signals from the two halteres, which must not be coinwings. While the rst has maintained its usage for ight, cident (coincident signals would diminish the ability of
the posterior pair has lost its ight functions and has the y to dierentiate the rotational axes). The halteres
adopted a slightly dierent shape. The haltere is visu- are capable of contributing to image stabilization, as well
ally comprised of three structural components: a knob- as in-ight attitude control, which was established by nushaped end, a thin shaft, and a slightly wider base. The merous authors noting a reaction from the head and wings
knob contains approximately 13 innervated hairs, while to inputs from the components of the rotation rate vector.
the base contains two chordotonal organs, each inner- contributions from halteres to head and neck movements
vated by about 20-30 nerves. Chordotonal organs are have been noted, explaining their role in gaze stabilizasense organs thought to be solely responsive to extension, tion. The y therefore uses input from the halteres to esthough they remain relatively unknown. The base is also tablish where to xate its gaze, an interesting integration
covered by around 340 campaniform sensilla, which are of the two senses.
small bers which respond preferentially to compression
in the direction in which they are elongated. Each of these
bers is also innervated. Relative to the stalk of the hal- Mathematics
tere, both the chordotonal organs and the campaniform
sensilla have an orientation of approximately 45 degrees, Recordings have indicated that halteres are capable of
which is optimal for measuring bending forces on the responding to stimuli at the same (double-wingbeat)
haltere. The halteres move contrary (anti-phase) to the frequency as Coriolis forces, the proof of concept
wings during ight. The sensory components can be cat- that allows further mathematical analysis of how these
egorized into three groups [8] ): those sensitive to vertical measurements can occur. The vector cross-product of
oscillations of the haltere, including the dorsal and ven- the halteres angular velocity and the rotation of the
tral scapal plates, dorsal and ventral Hicks papillae (both body provide the Coriolis force vector to the y. This
the plates and papillae are subcategories of the aforemen- force is at the same frequency as the wingbeat in both
tioned campaniform sensilla), and the small chordotonal the pitch and roll planes, and is doubly fast in the yaw
organ. The basal plate (another manifestation of the sen- plane. Halteres are capable of providing a rate damping
silla) and the large chordotonal organ are sensitive to gy- signal to aect rotations. This is because the Coriolis
roscopic torque acting on the haltere, and there is also a force is proportional to the ys own rotation rate. By
population of undierentiated papillae which are respon- measuring the Coriolis force, the halteres can send an
sive to all strains acting on the base of the haltere. This appropriate signal to their aliated muscles, allowing the
provides an additional method for ies to distinguish be- y to properly control its ight. The large amplitude of
tween the direction of force being applied to the haltere. haltere motion allows for the calculation of the vertical
Genetics As Homeobox genes were being discovered
and explored for the rst time, it was found that the deletion or inactivation of the Hox gene Ultrabithorax (Ubx)
causes the halteres to develop into a normal pair of wings.
This was a very compelling early result as to the nature of
Hox genes. Manipulations to the Antennapedia gene can
similarly cause legs to become severely deformed, or can
cause a set of legs to develop instead of antennae on the
head.
Function
and horizontal rates of rotation. Because of the large

disparity in haltere movement between vertical and
horizontal movement, 1 , the vertical component of the
rotation rate, generates a force of double the frequency
of the horizontal component. It is widely thought that
this twofold frequency dierence is what allows the y to
distinguish between the vertical and horizontal components. If we assume that the haltere moves sinusoidally,
a reasonably accurate approximation of its real-world
behavior, the angular position can be modeled as:
= 2 sin(t) where is the haltere beat frequency,
and the amplitude is 180, a close approximation to the
real life range of motion. The body rotational velocities
can be computed, given the known rates (the roll, pitch,
and yaw components are labeled below with 1, 2, and 3,
respectively) from the two halteres ( being the left and
being the right haltere) reference frames, respective
to the body of the y with the following calculations [7] :
The halteres function by detecting Coriolis forces, sensing the movement of air across the potentially rotating
y body. Studies have indicated that the angular velocity
of the body is encoded by the Coriolis forces measured
by the halteres [8] . Active halteres can recruit any neigh+c3
W2 =
boring units, inuencing nearby muscles and causing dra- W1 = 2b3sin()
b3 c3
2 cos()
74
c1
W3 = b1 +
2
represents the haltere angle of rotation from the body

plane, and the terms are, as mentioned, the angular
velocity of the haltere with respect to the body. Knowing
this, one could roughly simulate input to the halteres
using the equation for forces on the end knob of a haltere:
F = mg mai maF m i ri mi (i
ri ) 2mi vi
m is the mass of the knob of the haltere, g is the acceleration due to gravity, ri, vi,} and ai are the position, velocity,
and acceleration of the knob relative to the body of the y
in the i direction, aF is the ys linear acceleration, and
and are the angular velocity and acceleration components for the direction i, respectively, of the y in space.
The Coriolis force is simulated by the 2m vi term. Because the sensory signal generated is proportional to the
forces exerted on the halteres, this would allow the haltere signal to be simulated. If attempting to reconcile the
force equation with the rotational component equations,
it is worthwhile to remember that the force equation must
be calculated separately for both halteres.
3.1.5
Butteries
in their function: proprioceptors are sensitive to forces

generated by the insect itself and exteroreceptors to external forces. These receptors allow detection of sound
via the vibrations of particles when sound is transmitted
though a medium such as air or water. Far-eld sounds
refer to the phenomenon when air particles transmit the
vibration as a pressure change over a long distance from
the source. Near-eld sounds refer to sound close to
the source, where the velocity of the particles can move
lightweight structures. Some insects have visible hearing
organs such as the ears of noctuoid moths, whereas other
insects lack a visible auditory organ, but are still able to
register sound. In these insects the Johnstons Organ
plays an important role for hearing.
Johnstons organ
The Johnstons Organ (JO) is a chordotonal organ present
in most insects. Christopher Johnston was the rst who
described this organ in mosquitoes, thus the name Johnstons Organs [11] . Quarterly Journal of Microscopical
Science. 1855, Vols. s1-3, 10, pp. 97-102.. This organ is located at the stem of the insects antenna. It
has developed the highest degree of complexity in the
Diptera (two-wings), for which hearing is of particular
importance [10] . The JO consists of organized base sensory units called scolopidia (SP). The number of scolopidia varies among the dierent animals. JO has various
mechanosensory functions, such as detection of touch,
gravity, wind and sound, for example in honeybees JO
( 300 SPs) is responsible to detect sound coming from
another dancing honeybee [12] . In male mosquitoes (
7000 SPs) JO is used to detect and locate female ight
sound for mating behavior [13] . . The antenna of these
insects is specialized to capture near-eld sound. It acts
as a physical mechanotransducer.
Anatomy of the Johnstons Organ A typical insect

antenna has three basic segments: the scape (base), the
The sense of balance of butteries sits at the base of the antennae. pedicel (stem) and the agellum [14] . Some insects have
a bristle at the third segment called an arista. Figure 1
Butteries and moth keep their balance with Johnstons shows the Drosophila antenna. For the Drosophila the
organ: this is an organ at the base of a butterys antennae, antenna segment a3 ts loosely into the sockets on segand is responsible for maintaining the butterys sense of ment a2 and can rotate when sound energy is absorbed
[15]
balance and orientation, especially during ight.
. This leads to stretching or compression of JO neurons of the scolopidia. In Diptera the JO scolopidia are
located in the second antennal segment a2 the pedicel
3.1.6 Johnstons organ
(Yack, 2004). JO is not only associated with sound perception (exteroreceptor), it can also function as a proprioIntroduction
ceptors giving information on the orientation and position
of the agellum relative to the pedicel [16] .
The perception of sound for some insects is important
for mating behavior, e.g. Drosophila [9] . The ability Structure of a Scolopedia
of hearing in Insecta and Crustacea is given by chordotonal organs: mechanoreceptors, which respond to me- A scolopidia is the base sensory unit of the JO. A scolochanical deformation [10] . These chordotonal organs are pidia comprises four cell types [10] : (1) one or more bipowidely distributed throughout the insects body and dier lar sensory cell neurons, each with a distal dendrite; (2)
3.1. NONPRIMATES
Figure 1: Left: Frontal view of the Drosophila antenna. The

scolopidia in the second segment (a2, pedicel) with their neurons
are illustrated. Sound energy absorption leads to vibration of the
arista and rotation of the third segment a3. The rotation leads to
deformation of the scolopidia, leading to activation or deactivation. Right: The antenna located on the head of the Drosophila
is shown. (adapted from [15] ).
a scolopale cell enveloping the dendrite; (3) one or more

attachment cells associated with the distal region of the
scolopale cell; (4) one or more glial cells surrounding the
proximal region of the sensory neuron cell body. The
scolopale cell surrounds the sensory dendrite (cilium) and
forms with this the scolopale lumen / receptor lymph cavity. The scolopale lumen is tightly sealed. The cavity is
lled with a lymph, which is thought to have high potassium content and low sodium content, thus closely resembling the endolymph in the cochlea of mammals. Scolopidia are classied according dierent criteria. The cap
cell produces an extracellular cap, which envelopes the
cilia tips and connects them to the third antennal segment
a3 [17] .
Type 1 and Type 2 scolopidia dier by the type of ciliary
segment in the sensory cell. In Type 1 the cilium is of uniform diameter, except for a distal dilation at around 2/3
along its length. The cilium inserts into a cap rather than
into a tube. In Type 2 the ciliary segment has an increasing diameter into a distal dilation, which can be densely
packed with microtubules. The distal part ends in a tube.
Mononematic and amphinematic scolopidia dier by the
extracellular structure associated with the scolopale cell
and the dendritic cilium. Mononematic scolopidia have
the dendritic tip inserted into a cap shape which is an electron dense structure. In amphinematic scolopidia the tip
is enveloped by an electron-dense tube. Monodynal and
Heterodynal scolopidia are distinguished in their number
of sensory neurons. Monodynal scolopidia have a single
sensory cell and heterodynal ones have more than one.
75
are heterodynal and contain two or three neurons, thus
the JO comprises around 480 neurons. It is the largest
mechanosensory organ of the fruit y [9] . Perception by
JO of male Drosophila courtship songs (produced by their
wings) makes females reduce locomotion and males to
chase each other forming courtship chains [19] . JO is not
only important to perceive sound, but also to gravity [20]
and wind [21] sensing. Using GAL4 enhancer trap lines
in the JO showed that JO neurons of ies can be categorized anatomically into ve subgroups, A-E [18] . Each has
a dierent target area of the antennal mechanosensory
and motor centre (AMMC) in the brain (see Figure 2).
Kamikouchi et al. showed that the dierent subgroups
are specialized to distinct types of antennal movement [9] .
Dierent groups are used for sound and gravity response.
Neural activities in the JO To study JO neurons activities it is possible to observe intracellular calcium signals in the neurons caused by antenna movement [9] . Furthermore ies should be immobilized (e.g. by mounting on a coverslip and immobilizing the second antennal segment to prevent muscle-caused movements). The
antenna can be actuated mechanically using an electrostatic force. The antenna receiver vibrates when sound
energy is absorbed and deects backwards and forwards
when the Drosophila walks. Deecting and vibrating the
antenna yields dierent activity patterns in the JO neurons: deecting the receiver backwards with a constant
force gives negative signals in the anterior region and positive ones in the posterior region of the JO. Forward deection produces the opposite behavior. Courtship songs
(pulse song with a dominant frequency of 200Hz) evoke
broadly distributed signals. The opposite patterns for the
forward and backward deection reect the opposing arrangements of the JO neurons. Their dendrites connect
to anatomically distinct sides of the pedicel: the anterior
and posterior sides of the receiver. Deecting the receiver
forwards stretches the JO neurons in the anterior region
and compresses neurons in the posterior one. From this
is can be concluded that JO neurons are activated (i.e.
depolarized) by stretch and deactivated (i.e. hyperpolarized) by compression.
Dierent JO neurons A JO neuron usually targets

only one zone of the AMMC, and neurons targeting the
same zone are located in characteristic spatial regions
within JO [18] . Similar projecting neurons are organized
into concentric rings or paired clusters (see Figure 2A).
JO studied in the fruit y (Drosophila melanogaster) Vibration sensitive neurons for sound perception A
and B neurons (AB) were activated maximally by receiver
The JO in Drosophila consists of an array of approxi- vibration between 19 Hz and 952 Hz. This response
mately 277 scolopidia located between the a2/a3 joint was frequency dependent. Subgroup B showed larger reand the a2 cuticle (a type of an outer tissue layer) [18] . sponse to low-frequency vibrations. Thus subgroup A is
The scolopidia in Drosophila are mononematic [15] . Most responsible for the high-frequency responses.
76
Deection sensitive neurons for gravity and wind perception C and E showed maximal activity for static receiver deection. Thus these neurons provide information about the direction of a force. They have a larger displacement threshold of the arista than the neurons of AB
[21]
. Nevertheless CE neurons can respond to small displacement of the arista (e.g. gravitational force): gravity
displaces the arista-tip by 1 m (see S1 of [9] ). They also
respond to larger displacement caused by air-ow (e.g.
wind) [21] . Zone C and E neurons showed distinct sensitivity to air ow direction, which causes deection of
the arista in dierent directions. Air ow applied to the
front of the head resulted in strong activation in zone E
and little activation in zone C. Air ow applied from the
rear showed the opposite result. Air ow applied to the
side of the head yielded in zone C in ipsilaterally activation and in zone E in contralaterally one. The dierent
activation allows the Drosophila to sense from which direction the wind comes. It is not known whether the same
subgroups-CE neurons mediate wind and gravity detection or if there are more sensitive CE neurons for gravity
detection and less sensitive CE neurons for wind detection
[9]
. A proof that wild-type Drosophila melanogaster can
perceive gravity is that the ies tend to y upwards against
the force vector of gravitation (negative gravitaxis) after
getting shaken in a test tube. When the antennal aristae were ablated this negative gravitaxis behavior vanished, but not the phototaxis behavior (ies y towards
light source). Removing also the second segment, i.e.
where the JO is located, the negative gravitaxis behavior came present again. This shows that when JO is lost,
Drosophila can still perceive gravitational force through
other organs, for example mechanoreceptors on neck or
legs. These receptors were shown to be responsible for
gravity sensing in other insect species [22] .
Silencing specic neurons It is possible to silence selectively subgroups of JO neurons using tetanus toxin
combined with subgroup-specic GAL4 drivers and
tubulin-GAL80. The latter is a temperature-sensitive
GAL4 blocker. With this it could be conrmed that neurons of subgroup CE are responsible for gravitaxis behavior. Elimination of neurons of subgroups CE did not
impair the ability of hearing [21] . Silencing subgroup B
impaired the males response to courtship songs, whereas
silencing groups CE or ACE did not [9] . Since subgroup A
was found to be involved in hearing (see above) this result
was unexpected. From dierent experiment, in which the
sound-evoked compound action potential (sum of action
potentials) were investigated the conclusion was drawn
that subgroup A is required for nanometer-range receiver
vibrations as imposed by faint songs of courting males.
Origin of dierence of the subgroups
Figure 2: A) left: Neurons of dierent subgroups A-E are illustrated in the JO. right: The corresponding target zones of the subroups are shown in the AMMC. B) Simplied circuitry of the auditory (zone AB) and deection sensitive (zone CE) system. These
two systems separated similar as in vertebrates. Neurons of zone
A have target zones in the AMMC, vlprs and SOG. Vlpr stands
for ventrolateral protocerebrum, SOG for suboesophageal ganglion, A for anterior, D for dorsal, M for medial. (adapted from
Figure 2.10 of [15] ).
opposing connection sites on the receiver. Thus for e.g.

forward deection some neurons get stretched whereas
others get compressed, which yields dierent response
characteristics (opposing calcium signals). The dierence for vibration- and deection-sensitive neurons may
come from distinct molecular machineries for transduction (i.e. adapting or non-adapting channels and NompCdependent or not). Sound-sensitive neurons express the
mechanotransducer channel NompC (no mechanoreceptor potential C, also known as TRPN1) channel whereas
subgroups CE are independent of NompC [9] . In addition
JO neurons of subgroup AB transduce dynamic receiver
vibrations, but adapt fast for static receiver deection (i.e.
they respond phasically) [23] . Neurons of subgroups CE
showed a sustained calcium signal response during the
static deection (i.e. they respond tonically). The two
distinct behaviors show that there are transduction channels with distinct adaption characteristics, which is also
known for the mammalian cochlea or mammalian skin
(i.e. tonically activated Merkel calls and rapidly adapting
Meissners corpuscles) [21] .
Dierences in gravitation and sound perception in

the brain Neurons of subgroups A and B target on one
As mentioned above the anatomically dierent subgroups side zones of the primary auditory centre in the AMMC
of JO neurons have dierent functions [9] . The neurons and on the other side the inferior part of ventrolateral prodo attach to the same antennal receiver, but they dier in tocerebrum (VLP) (see Figure 2B)). These zones show
3.1. NONPRIMATES
many commissural connections between themselves and
with the VLP. For neurons of subgroups CE almost no
commissural connection between the target zones were
found, nor connections to the VLP. Neurons associated
with the zones of subgroup CE descended or ascended
from the thoracic ganglia. This dierence in the AB and
CE neurons projection reminds strongly on the separate
vertebrate projection of the auditory and vestibular pathways in mammals [15] .
Johnstons Organ in honeybees
Solitary bee (Anthidium orentinum): the Johnstons organs on

the head are head are clearly visible.
The JO in bees is also located in the pedicel of the antenna and used to detect near eld sounds [12] . In a hive
some bees perform a waggle dance, which is believed
to inform conspecics about the distance, direction and
protability of a food source. Followers have to decode
the message of the dance in the darkness of the hive, i.e.
visual perception is not involved in this process. Perception of sound is a possible way to get the information of
the dance. The sound of a dancing bee has a carrier frequency of about 260 Hz and is produced by wing vibrations. Bees have various mechanosensors, such as hairs
on the cuticle or bristles on the eyes. Dreller et al. found
that the mechanosensors in JO are responsible for sound
perception in bees [12] . Nevertheless hair sensors could
still be involved in detection of further sound-sources,
when the amplitude is too low to vibrate the agellum.
Dreller et al. trained bees to associate sound signals with
a sucrose reward. After the bees were trained some of the
mechanosensors were abolished on dierent bees. Then
the bees ability to associate the sound with the reward
was tested again. Manipulating the JO yielded loss of the
learnt skill. Training could be done with a frequency of
265 Hz, but also of 10 Hz, which shows that JO is also
involved in low-frequency hearing. Bees with only one
antenna made more mistakes, but were still better than
bees that had ablated both antennas. Two JO in each antenna could help followers to calculate the direction of
the dancing bee. Hearing could also be used by bees in
other contexts, e.g. to keep a swarming colony together.
77
The decoding of the waggle dance is not only done by auditory perception, but also or even more by electric eld
perception. JO in bees allows detection of electric elds
[24]
. If body parts are moved together, bees accumulate
electric charge in their cuticle. Insects respond to electric
elds, e.g. by a modied locomotion (Jackson, 2011).
Surface charge is thought to play a role in pollination, because owers are usually negatively charged and arriving
insects have a positive surface charge [24] . This could help
bees to take up pollen. By training bees to static and modulated electric elds, Greggers et al. showed that bees can
perceive electric elds [24] . Dancing bees produce electric elds, which induce movements of the agellum 10
times more strongly than the mechanical stimulus of wing
vibrations alone. The vibrations of the agellum in bees
are monitored with JO, which responds to displacement
amplitudes induced by oscillation of a charged wing. This
was proven by recording compound action potential responses from JO axons during electric eld stimulation.
Electric eld reception with JO does not work without antenna. Whether also other non-antennal mechanoreceptors are involved in electric eld reception has not been
excluded. The results of Greggers et al. suggest that electric elds (and with it JO) are relevant for social communication in bees.
Importance of JO (and chordotonal organs in general) for research

Chordotonal organs, like JO, are only found in Insecta and
Crustacea [10] . Chordotonal neurons are ciliated cells [25] .
Genes that encode proteins needed for functional cilia are
expressed in chordotonal neurons. Mutations in the human homologues result in genetic diseases. Knowledge
of the mechanisms of ciliogenesis can help to understand
and treat human diseases which are caused by defects in
the formation or function of human cilia. This is because the process of controlling neuronal specication in
insects and in vertebrates is based on highly conserved
transcription factors, which is shown by the following
example: Atonal (Ato), a proneural transcription factor,
species chordotonal organ formation. The mouse orthologue Atoh1 is necessary for hair cell development in the
cochlea. Mice which expressed a mutant Atoh1 phenotype, which are deaf, can be cured by the atonal gene of
Drosophila. Studying chordotonal organs in insects can
lead to more insights of mechanosensation and cilia construction. Drosophila is a versatile model to study the
chordotonal organs [26] . The fruit y is easy and inexpensive to culture, produces large numbers of embryos,
can be genetically modied in numerous ways and has a
short life cycle, which allows investigating several generations within a relative short time. In addition comes
that most of the fundamental biological mechanisms and
pathways that control development and survival are conserved across Drosophila and other species, such as humans.
78
3.1.7
Spiders Visual System
teristically arranged in three or four rows across the prosomas carapace. Overall, 99% of all spiders have eight
eyes and of the remaining 1% almost all have six. SpiIntroduction
ders with only six eyes lack the principal eyes, which
While the highly developed visual systems of some spi- are described in detail below.
der species have been subject to extensive studies since The pairs of eyes are called anterior median eyes
many decades, terms like animal intelligence or cogni- (AME), anterior lateral eyes (ALE), posterior median
tion were not usually used in the context of spider stud- eyes (PME), and posterior lateral eyes (PLE). The large
ies. Instead, spiders were traditionally portrayed as rather principal eyes facing forward are the anterior median
simple, instinct driven animals (Bristowe 1958, Savory eyes, which provide the highest spatial resolution to a spi1928), processing visual input in pre-programmed pat- der, at the cost of a very narrow eld of view. The smaller
terns rather than actively interpreting the information re- forward-facing eyes are the anterior lateral eyes with a
ceived from their visual apparatus towards appropriate re- moderate eld of view and medium spatial resolution.
actions. While Although this still seems to be the case The two posterior eye pairs are rather peripheral, secin a majority of spiders, which primarily interact with ondary eyes with wide eld of view. They are extremely
the world through tactile sensation rather than by visual sensitive and suitable for low-light conditions. Spiders
cues, some spider species have shown surprisingly intelli- use their secondary eyes for sensing motion, while their
gent use of their eyes. Considering its limited dimensions principal eyes allow shape and object recognition. In conwithin the body, a spiders optical apparatus and visual trast to insect vision, a visually-based spiders brain is alprocessing perform extremely well.[27] Recent research most completely devoted to vision, as it receives only the
points towards a very sophisticated use of visual cues in a optic nerves and consists of only the optic ganglia and
spiders world when investigating topics such as the com- some association centers. The brain is apparently able
plex hunting schemes of the vision-guided jumping spi- to recognize object motion, but even more to also clasders (Salticidae) taking huge leaps of up to 30 times their sify the counterpart into a potential mate, rival or prey by
own body length onto prey or a wolf spiders (Lycosi- seeing legs (lines) at a particular angle to the body. Such
dae) ability to visually recognize asymmetries in poten- stimulus will result in a spider displaying either courtship
tial mates. Even in the case of the night-active Cupi- or threatening signs respectively.
ennius salei (Ctenidae), relying primarily on other sensory organs, or the ogre-faced Dinopis hunting at night
by spinning small webs and throwing them at approaching A Spiders eyes
prey, the visual system is still highly developed. Findings
like these are not only fascinating but are also inspiring Although spider eyes may be described as camera eyes,
other scientic and engineering elds such as robotics and they are very dierent in their details from the camera
eyes of mammals or any other animals. In order to t
computer-guided image analysis.
a high-resolution eye into such a small body, neither an
insects compound eyes nor spherical eyes, as we humans
General structure of a spiders visual system
have them, would solve the problem. The ocelli found in
spiders are the optically better solution, as their resolution is not limited by refractive eects at the lens which
would be the case with compound eyes. When replacing the eye of a spider by a compound eye of the same
resolving power, it would simply not t into the spiders
prosoma. By using ocelli, the spatial acuity of some spiders is more similar to that of a mammal than to that of
an insect, with a huge size dierence and only a few thousand photocells, e.g. in a jumping spiders eye, as compared to more than 150 million photocells in the human
retina.
A spiders anatomy primarily consists of two major body
segments, the prosoma and the opisthosoma, which are
also known as the cephalothorax and abdomen, respectively. All extremities as well as the sensory organs including the eyes are located in the prosoma. Other than
the visual system of arthropods featuring compound eyes,
modern arachnid eyes are ocelli (simple eyes consisting of
a lens covering a vitreous uid-lled pit with a retina at
the bottom), of which spiders have six or eight, charac-
Principal eyes The anterior median eyes (AME),

which are present in most spider species, are also called
the principal eyes. Details about the principal eyes structure and its components are illustrated in the gure below and are explained in the following by going through
the AME of the jumping spider Portia (family Salticidae), which is famous for its high-spatial-acuity eyes and
vision-guided behavior despite its very small body size of
4.5-9.5 mm.
3.1. NONPRIMATES
79
Principal eye retina movements Such spectacular visual abilities come at a price within small animals as the
jumping spiders: The retina in each of Portias principal
eyes has only 2-5 eld of view, while its fovea even captures only 0.6 eld of view. This results from the principal retina having elongated boomerang-like shapes which
span about 20 vertically and only 1 horizontally, corresponding to about six receptor rows. This severe limitation is compensated by sweeping the eye tube over the
whole image of the scene using eye muscles, of which
jumping spiders have six. These are attached to the outside of the principal eye tube and allow the same three
degrees of freedom horizontal, vertical, rotation as in
When a light beam enters the principal eye it rstly passes human eyes. Principal retinae can move by as much as
a large corneal lens. This lens features a long focal length 50 horizontally and vertically and rotate about the optienabling it to magnify even distant objects. The com- cal axis (torsion) by a similar amount.
bined eld of view of the two principal eyes corneal
lenses would cover about 90 in front of the salticid spi- Spiders making sophisticated use of visual cues move
der, however a retina with the desired acuity would be their principal eyes retinae either spontaneously, in sactoo large to t inside a spiders eye. The surprising so- cades xating the fovea on a moving visual target
lution is a small, elongated retina, which lies behind a (tracking), or by scanning, which serves presumably
long, narrow tube and a second lens (a concave pit) at its for pattern recognition. It seems today, that spiders scan
end. Such combination of a corneal lens (with a long focal a scene sequentially by moving the eye-tube in complex
length) and a long eye tube (magnifying the image from patterns, allowing it to process high amounts of visual inthe corneal lens) resembles a telephoto system, making formation despite their very limited brain capacities.
the pair of principal eyes similar to a pair of binoculars. The spontaneous retinal movements, so-called miThe salticid spider captures light beams successively on crosaccades, are a mechanism thought to prevent the
four retina layers of receptors, which lie behind each photoreceptor cells of the anterior-median eyes from
other (in contrast, the human retina is arranged in only adapting to a motionless visual stimulus. Cupiennius spione plane). This structure allows not only a larger number ders, which feature 4 eye muscles - two dorsal and two
of photoreceptors in a conned area but also enables color ventral ones continuously perform such microsaccades
vision, as the light is split into dierent colours (chro- of 2 to 4 in the dorso-median direction, lasting about 80
matic aberration) by the lens system. Dierent wave- ms (when xed to a holder). The 2-4 of microsaccadic
lengths of light thus come into focus at dierent dis- movements match closely to Cupiennius angle of about
tances, which correspond to the positions of the retinas 3 between the receptor cells, supporting the idea of its
layers. While salticids discern green (layer 1 ~580 nm, function preventing adaption. In contrast, retinal movelayer 2 ~520-540 nm), blue (layer 3 ~480-500 nm) ments elicited by mechanical stimulation (directing an air
and ultraviolet (layer 4 ~360 nm) using their principal pu onto the tarsus of the second walking leg) can be coneyes, it is only the two rearmost layers (layers 1 and 2) siderably larger than the spontaneous retinal movements,
which allow shape and form detection due to their close with deections up to 15. Such stimulus increases eye
muscle activity from being spontaneously active at 12
receptor spacing.
1 Hz at the resting level to 80 Hz with the air pu stimuAs in human eyes, there is a central region in layer 1 lation applied. Active retinal movement of the two princalled the fovea, where the inter-receptor spacing was cipal eyes is however never activated simultaneously durmeasured to about 1 m. This was found to be optimal, ing such experiments and no correlation exists between
as the telephoto optical system provides images precise the two eyes regarding their direction either. These two
enough to be sampled in this resolution, but any closer mechanisms, spontaneous microsaccades as well as active
spacing would reduce the retinas sampling quality due to peering by active retinal movement, seemingly allow
quantum-level interference between adjacent receptors. spiders to follow and analyze stationary visual targets eEquipped with such eyes, Portia exceeds any insect by far ciently using only their principal eyes without reinforcing
when it comes to visual acuity: While the dragony Sym- the saccadic movements by body movements.
petrum striolatus has the highest acuity known for insects
(0.4), the acuity of Portia is ten times higher (0.04) with However, there is another factor inuencing visual capacmuch smaller eyes. The human eye with 0.007 acuity is ities of a spiders eye, which is the problem of keeping obonly ve times better than Portias. With such visual pre- jects at dierent distances in focus. In human eyes, this is
cision, Portia would be technically able to discriminate solved by accommodation, i.e. changing the shape of the
two objects which are 0.12 mm apart from a distance of lens, but salticids take a dierent approach: the recep200 mm. The spatial acuity of other salticid eyes is usu- tors in layer 1 of their retina are arranged on a staircase
at dierent distances from the lens. Thus, the image of
ally not far behind that of Portia.[28][29][30]
80
any object, whether a few centimeters or some meters

in front of the eye, will be in focus on some part of the
layer-1 staircase. Additionally, the salticid can swing the
eye tubes side to side without moving the corneal lenses
and will thus sweep the staircase of each retina across the
image of the corneal lense, sequentially obtaining a sharp
image of the object.
The resulting visual performance is impressive: Jumping
spiders such as Portia focus accurately on an object at distances between 2 centimeters to innity, being able to see
up to about 75 centimeters in practice. The time needed
to recognize objects is however relatively long (seemingly
in the range of 10-20 s) because of the complex scanning process needed to capture high-quality images from
such tiny eyes. Due to this limitation, it is very dicult
for spiders such as Portia to identify much larger predators fast enough because of the predators size, making
the small spider an easy prey for birds, frogs and other
predators.[31][32]
Blurry vision for distance estimation An unexpected
nding recently surprised researchers, when it was shown
that jumping spiders use a technique called blurry vision
to estimate their distance to previously recognized prey
before taking a jump. Where humans achieve depth perception using binocular vision and other animals do so by
moving their heads around or measuring ultrasound responses, jumping spiders perform this task within their
principal eyes. As in other jumping spider species, the
principal eyes of Hasarius adansoni feature four retinal
layers with the two bottom ones featuring photocells responding to green impulses. However, green light will
only ever focus sharply on the bottom one, layer 1, due
to its distance from the inner lens. Layer 2 would receive
focused blue light, however these photoreceptor cells are
not sensitive to blue and receive a fuzzy green image instead. Interestingly, the amount of blur depends on the
distance of an object from the spiders eye the closer
it is, the more out of focus it will appear on the second
retina layer. At the same time, the rst retina layer 1 always receives a sharp image due to its staircase structure.
Jumping spiders are thus able to estimate depth using a
single unmoving eye by comparing the images of the two
bottom retina layers. This was conrmed by letting spiders jump at prey in an arena ooded with green light
versus red light of equal brightness. Without the ability
to use the green retina layers, jumping spiders would repeatedly fail to judge distance accurately and miss their
jump.
around its body. The anterior and posterior lateral eyes

(i.e. secondary eyes) only feature a single type of visual
cells with a maximum spectral sensitivity for green colored light of ~535-540 nm wavelength. The number and
arrangement of secondary eyes diers signicantly between or even within dierent spider families, as does
their structure: Large secondary eyes can contain several thousand rhabdomeres (the light-sensitive parts of the
retina) and support hunters or nocturnal spiders with their
high sensitivity to light, while small secondary eyes contain at most a few hundred rhabdomeres and only providing basic movement detection. Dierently from the
principal eyes which are everted (the rhabdomeres point
towards the light), the secondary eyes of a spider are inverted, i.e. their rhabdomeres point away from the light,
as is the case for vertebrates like the human eye. Spatial
resolution of the secondary eyes e.g. in the extensively
studied Cupiennius salei is greatest in horizontal direction, enabling the spider to analyse horizontal movements
well even with the secondary eyes, while vertical movement may not be especially important when living in a
at world.
The reaction time of jumping spiders lateral eyes is comparably slow and amounts to 80-120 ms, measured with a
3-sized (inter-receptor angle) square stimulus travelling
past the animals eyes. The minimum stimulus travel distances, until the spider reacts, are 0.1 at a stimulus velocity of 1/s, 1 at 9/s and 2.5 at 27/s. This means that
a jumping spiders visual system detects motion even if
an object is travelling only a tenth of the secondary eyes
inter-receptor angle at slow speed. If the stimulus gets
Secondary eyes In contrast to the principal eyes re- even smaller to a size of only 0.5, responds occur only
sponsible for object analysis and discrimination, a spi- after long delays, indicating that they lie at the spiders
ders secondary eyes act as motion detectors and there- limit of perceivable motion.
fore do not feature eye muscles to analyze a scene more Secondary eyes of (night-active) spiders usually feature a
extensively. Depending on their arrangement on the spi- tapetum behind the rhabdomeres, which is a layer of crysders carapace, secondary eyes enable the animal to have tals reecting light back to the receptors to increase visual
panoramic vision detecting moving objects almost 360 sensitivity. This allows night-hunting spiders to have eyes
3.1. NONPRIMATES
81
with an aperture as large as f/0.58 enabling them to capture visual information even in ultra-low-light conditions.
Secondary eyes containing a tapetum thus easily reveal
a spiders location at night when illuminated e.g. by a
ashlight.[33][34]
the principal eyes moved involuntarily whenever a secondary eye detected motion within its visual eld. This
activity increase of the principal eye muscles, compared
to no stimulation presented, would not change when covering the principal eyes with black paint, but would stop
with the secondary eyes masked. Thus it is now clear, that
only the input received from secondary eyes controls prinCentral nervous system and visual processing in the cipal eye muscle activity. Also, a spiders principal eyes
brain
do not seem to be involved in motion detection, which is
only the secondary eyes responsibility.
As anywhere in neuroscience, we still know very little
Other experiments using dual-channel telemetric regisabout a spiders central nervous system (CNS), especially
tration of the eye muscle activities of Cupiennius have
regarding its functioning in visually controlled behavior.
shown that the spider actively peers into the walking diOf all the spiders, the CNS of Cupiennius has been studrection: The ipsilateral retina of the principal eyes was
ied most extensively, focusing mainly on the CNS strucmeasured to shift with respect to the walking direction
ture. As of today, only little is known about electrophysibefore, during and after a turn, while the contralateral
ological properties of central neurons in Cupiennius, and
retina remained in its resting position. This happened ineven less about other spiders in this regard.
dependently from the actual light conditions, suggesting
The structure of a spiders nervous system is closely a voluntary peering initiated by the spiders brain.
related to its bodys subdivisions, but instead of being
spread all over the body, the nervous tissue is enormously
concentrated and centralized. The CNS is made up of two Pattern recognition using principal eyes
paired, rather simple nerve cell clusters (ganglia), which
are connected to the spiders muscles and sensory systems
by nerves. The brain is formed by fusion of these ganglia
in the head segments ahead of and behind the mouth and
lls the prosoma largely with nervous tissue, while no ganglia exist in the abdomen. Looking at the spiders brain,
it receives direct inputs from only one sensory system, the
eyes - unlike any insects and crustaceans. The eight optic
nerves enter the brain from the front and their signals are
processed in two optic lobes in the anterior region of the
brain. When a spiders behavior is especially dependent
on vision, as in the case of the jumping spider, the optic ganglia contribute up to 31% of the brains volume,
indicating the brain to be almost completely devoted to
vision. This score still amounts to 20% for Cupiennius,
whereas other spiders like Nephila and Ephebopus come
in at only 2%.
The distinction between principal and secondary eyes
persists in the brain. Both types of eyes have their own visual pathway with two separate neuropil regions fullling
distinct tasks. Thus spiders evidently process the visual
information provided by their two eye types in parallel,
with the secondary eyes being specialized for detecting
horizontal movement of objects and the principal eyes
being used for the detection of shape and texture.
Two visual systems in one brain
While principal and secondary eyesight seems to be distinct in spiders brains, surprising inter-relations between
both visual systems in the brain are known as well. In
visual experiments principal eye muscle activity of Cupiennius was measured while covering either its principal
or secondary eyes. When stimulating the animals in a
white arena with short sequences of moving black bars,
Recognition of shape and form by jumping spiders is believed to be accomplished through a scanning process
of the visual eld, which consists of a complex set of
rotations (torsional movements) and translations of the
anterior-median eyes retinae. As described in the section Principal eye retina movements, a spiders retinae
are narrow and shaped like boomerangs, which can be
matched with straight features by sweeping over the visual
scene. When investigating a novel target, the eyes scan it
82
in a stereotyped way: By moving slowly from side to side
at speeds of 3-10 per second and rotating through 25,
horizontal and torsional retina movement allows the detection of dierently positioned and rotated lines. This
method can be understood as template matching where
the template has elongated shape and produces a strong
neural response whenever the retina matches a straight
feature in the scene. This identies a straight line with
little or no further processing necessary.
A computer vision algorithm for straight line detection
as an optimization problem (da Costa, da F. Costa) was
inspired by the jumping spiders visual system and uses
the same approach of scanning a scene sequentially using
template matching. While the well-known Hough Transform allows robust detection of straight visual features in
an image, its eciency is limited due to the necessity to
calculate a good part or even the whole parameter space
while searching for lines. In contrast the alternative approach used in salticid visual systems suggests searching
the visual space by using a linear window, which allows
adaptive searching schemes during the straight line search
process without the need to systematically calculate the
parameter space. Also, solving the straight line detection in such a way allows to understand it as an optimization problem, which makes ecient processing by computers possible. While it is necessary to nd appropriate
parameters controlling the annealing-based scanning experimentally, the approach taking a jumping spiders path
of straight line detection was proven to be very eective,
especially with properly set parameters.[35]
Visually-guided behavior
Discernment of visual targets The ability of discerning between slightly dierent visual targets has been
shown for Cupiennius salei, although this species relies
mainly on its mechanosensory systems during prey catching or mating behavior. When presenting two targets at a
distance of 2 m to the spider, its walking path depends on
their visual appearance: Having to choose between two
identical targets such as vertical bars, Cupiennius shows
no preference. However the animal strongly prefers a vertical bar to a sloping bar or a V-shaped target.

The discrimination of dierent targets has been shown
to be only possible with the principal eyes uncovered,
while the spider is able to detect the targets using any of
the eyes. This suggests that many spiders anterior-lateral
(secondary) eyes are capable of much more than simply
object movement detection. With all eyes covered, the
spider exhibits totally undirected walking paths.
Placing Cupiennius in total darkness however results not
only in undirected walks but also elicits a change of gait:
Instead of using all eight legs the spider will only walk
with six and employ the rst legs as antennae, comparable
to a blind persons cane. In order to feel the surroundings
the extended forelegs are moved up and down as well as
sideways. This is specic to the rst leg pair only, inuenced solely by the visual input when the normal room
light is switched to the invisible infrared light.
Vision-based decision making in jumping spiders

The behavior of jumping spiders after having detected
movement with the eyes depends on three factors: the targets size, speed and distance. If it has more than twice
the spiders size, the object is not approached and the spider tries to escape if it comes towards her. If the target has adequate size, its speed is visually analyzed using the secondary eyes. Fast moving targets with a speed
of more than 4/s are chased by jumping spiders, guided
by her anterior-lateral eyes. Slower objects are carefully
approached and analyzed with the anterior-median (i.e.
principal) eyes to determine whether it is prey or another
spider of the same species. This is seemingly achieved
by applying the above described straight line detection,
to nd out whether a visual target features legs or not.
While jumping spiders have shown to approach potential
prey of appropriate characteristics as long as it moves,
males are pickier in deciding whether their current counterpart might be a potential mate.
Potential mate detection Experiments have shown

that drawings of a central dot with leg-like appendages on
the sides will result in courtship displays, suggesting that
visual feature extraction is used by jumping spiders to detect the presence and orientation of linear structures in the
target. Additionally, a spiders behavior towards a considered conspecic spider depends on dierent factors such
as sex and maturity of both involved spiders and whether
it is mating time. Female wolf spiders, Schizocosa ocreata, even discern asymmetries in male secondary sexual
characters when choosing their mate, possibly to avoid
developmental instability in their ospring. Conspicuous
tufts of bristles on a males forelegs, which are used for visual courtship signaling, appear to inuence female mate
choice and asymmetry of these body parts in consequence
of leg loss and regeneration apparently reduces female receptivity to such male spiders.[36]
3.1. NONPRIMATES
Secondary eye-guided hunting A jumping spiders
stalking behavior when hunting insect prey is comparable to a cat stalking birds. If something moves within
the visual eld of the secondary eyes, they initiate a turn
to bring the larger, forward-facing pair of principal eyes
into position for classifying the objects shape into mate,
rival or prey. Even very small, low contrast dot stimuli
moving at slow or fast speeds elicit such orientation behavior. Like Cupiennius, jumping spiders are also able
to use their secondary eyes for more sophisticated tasks
than just motion detection: Presenting visual prey cues to
salticids with only visual information from the secondary
eyes available and both primary eyes covered, results in
the animal exhibiting complete hunting sequences. This
suggests that the anterior lateral eyes of jumping spiders
may be the most versatile components of their visual system. Besides detecting motion, the secondary eyes obviously also feature a spatial acuity which is good enough
to direct complete visually-guided hunting sequences.
83
principal eyes than usual (as sketched in the gure on
the right) elicited dierent behavior. Presenting virtual
salticid prey with only one anterior-median eye or a regular lure with two enlarged secondary eyes elicited cryptic
stalking behavior suggesting successful recognition of a
salticid, while P. mbriata froze less often when faced by
a Cyclops-like lure (a single principal eye centered between the two secondary eyes). Lures with square-edged
principal eyes were usually not classied as a salticid, indicating that the shape of the principal eyes edges are an
important cue to identify fellow salticids.[37]
Jumping decisions from visual features Spiders in

the genus Phidippus have been tested within a study for
their willingness to cross inhospitable open space by placing visual targets on the other side of a gap. It was found
that whether the spider takes the risk of crossing open
ground or not is mainly dependent on factors like distance
to target, relative target size compared to distance and the
targets color and shape. In independent test runs, the spider moved to tall, distant targets equally often as to short,
close targets, with both objects appearing equally sized
on the spiders retina. When giving the choice of moving to either white or green grass-like targets, the spiders
consistently chose the green target irrespective of its contrast with the background, thus proving their ability to use
color discernment in hunting situations.[38]
Prey face recognition Visual cues also play an important role for jumping spiders (salticids) when discriminating between salticid and non-salticid prey using principal eyesight. To this end a salticid preys large principal eyes provide critical cues, to which the jumping spider Portia mbriata reacts by exhibiting cryptic stalking
tactics before attacking (walking very slowly with palps
retracted and freezing when faced). This behavior is
only used when identifying a prey as salticid. This was
exploited in experiments presenting computer-rendered,
realistic three-dimensional lures with modied principal
eyes to Portia mbriata. While intact virtual lures resulted in cryptic stalking, lures without or with smaller
Identifying microhabitat traits by visual cues Presented with manipulated real plants and photos of plants,
Psecas chapoda (a bromeliad-dwelling salticid spider) is
able to detect a favorable microhabitat by visually analyzing architectural features of the host plants leaves and
rosette. By using black-and-white photos, any potential
inuence of other cues, such as color and smell, on host
plant selection by the spider could be excluded during a
study, leaving only shape and form as discerning characteristics. Even when having to decide solely from photographs, Psecas chapoda consistently preferred rosetteshaped plants (Agavaceae) with narrow and long leaves
84
over dierently looking plants, which proves that some [16] Baker, Dean Adam and Beckingham, Kathleen Mary and
Armstrong, James Douglas. 2007. Functional dissection
spider species are able to evaluate and distinguish physiof the neural substrates for gravitaxic maze behavior in
cal structure of microhabitats only on the basis of shape
[39]
Drosophila melanogaster. Journal of Comparative Neufrom visual cues of plant traits.
rology. 2007, Vol. 501, 5, pp. 756-764
3.1.8
References
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Chapter 4
Appendix
4.1 Authors
Structural dierences of cone 'oil-droplets in the

light and dark adapted retina of Poecilia reticulata
P., Yvette W. Kunz and Christina Wise
This list contains the names of all the authors that have
contributed to this text. If you have added, modied or
contributed in any way, please add your name to this list.
Advances in organ biology, Volume 10, Pages 1-395

(2005)
<http://www.search.eb.com/eb/art-53283>"optic
chiasm: visual pathways. Online Art. Encyclopdia Britannica Online.
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Color atlas of physiology,Despopoulos, A. and Silbernagl, S.,2003, Thieme
Visual System
http://www.yorku.ca/eye/
Neurotransmitter systems in the retina, Ehinger, B.,

Retina, 2-4, 305, 1982
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Auditory System
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BiologyPages/
Intraoperative Neurophysiological Monitoring, 2nd

Edition, Aage R. Mller, Humana Press 2006, Totowa, New Jersey, pages 55-70
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sensesweb/
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1993, in: Cummings Otolaryngology: Head and
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Louis
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Script Ver 1.3 March 2010, T. Haslwanter, Upper
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(1 May 2000). Nature Neuroscience 3 (5): 431432.
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Okubo, Tadashi; Clark, Cheryl; Hogan, Brigid L.M.
(February 2009). Cell Lineage Mapping of Taste
Bud Cells and Keratinocytes in the Mouse Tongue
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Colour spectrum produced by a prism
Yarmolinsky, David A.; Zuker, Charles S.; Ryba,

Nicholas J.P. (October 2009). Common Sense
about Taste: From Mammals to Insects. Cell 139
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The colour triangle is often used to illustrate the colourmixing eect. The triangle entangles the visible spectrum, and a white dot is located in the middle of the triangle. Because of additive colour mixing property of red
(700nm), green(546nm) and blue(435nm), every colour
can be produced by mixing those three colours.
4.3.2 Colour Models
Zhao, Grace Q.; Zhang, Yifeng; Hoon, Mark A.;

Chandrashekar, Jayaram; Erlenbach, Isolde; Ryba,
Nicholas J.P.; Zuker, Charles S. (October 2003).
The Receptors for Mammalian Sweet and Umami
4.3.3 History of Sensory Systems
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This Wikibook was started by engineers studying at ETH
Kandel, E., Schwartz, J., and Jessell, T. (2000) Prin- Zurich as part of the course Computational Simulations
ciples of Neural Science. 4th edition. McGraw Hill, of Sensory Systems. The course combines physiology
with an emphasis on the sensory systems, programming
New York.
and signal processing. There is a plethora of information
regarding these topics on the internet and in the literature, but theres a distinct lack of concise texts and books
4.3 Appendix
on the fusion of these 3 topics. The world needs a structured and thorough overview of biology and biological
systems from an engineering point of view, which is what
4.3.1 Spectrum
this book is trying to correct. We will start o with the
If light passes through a prism, a colour spectrum will be Visual System, focusing on the biological and physiologformed at the other end of the prism ranging from red to ical aspects, mainly because this will be used in part to
violet. The wavelength of the red light is from 650nm to grade our performance in the course. The other part be700nm, and the violet light is at around 400nm to 420nm. ing the programming aspects have already been evaluated
This is the EM range detectable for the human eye.
and graded. It is the authors wishes that eventually in-
88
The RGB color-triangle
formation on physiology/biology, signal processing AND

programming shall be added to each of the sensory systems. Also we hope that more sections will be added to
extend the book in ways previously not thought of.
The original title of the Wikibook, Biological Machines,
stressed the technical aspects of sensory system. However, as the wikibook evolved it became a comprehensive
overview of human sensory systems, with additional emphasis on technical aspects of these systems. This focus
is better represented with Sensory Systems, the new wikibook title since December 2011.
In 2015, the content became too big for the original structure. Neurosensory Implants and Computer Models
became separate chapters, and the Non-Primates section was split, into Arthropods and Other Animals.
CHAPTER 4. APPENDIX
Chapter 5
Text and image sources, contributors, and

licenses
5.1 Text
Sensory Systems/Introduction Source: https://en.wikibooks.org/wiki/Sensory_Systems/Introduction?oldid=3122955 Contributors:
CommonsDelinker, Thomas.haslwanter, QuiteUnusual, Dirk Hnniger, JackBot, QUBot, Stas000D, Wieralee, Atcovi and Anonymous:
6
Sensory Systems/NeuralSimulation Source: https://en.wikibooks.org/wiki/Sensory_Systems/Computer_Models/NeuralSimulation?
oldid=3122951 Contributors: Thomas.haslwanter, QuiteUnusual, JackBot, Dling007, Isabelletan and Anonymous: 4
Sensory Systems/Auditory System Source: https://en.wikibooks.org/wiki/Sensory_Systems/Auditory_System?oldid=3122948 Contributors: Thomas.haslwanter, Adrignola, Skela, Rega~enwikibooks, JackBot, S2709pr, Syum90 and Anonymous: 12
Sensory Systems/Visual System Source: https://en.wikibooks.org/wiki/Sensory_Systems/Visual_System?oldid=3122959 Contributors:
Thomas.haslwanter, Adrignola, Skela, Psimmler, Salomonw, JackBot and Anonymous: 2
Sensory Systems/Vestibular System Source: https://en.wikibooks.org/wiki/Sensory_Systems/Vestibular_System?oldid=2832230 Contributors: Thomas.haslwanter, Adrignola, Skela, Avicennasis and Anonymous: 2
Sensory Systems/Somatosensory System Source: https://en.wikibooks.org/wiki/Sensory_Systems/Somatosensory_System?oldid=
3122958 Contributors: Thomas.haslwanter, Adrignola, Skela, JackBot, Tolva and Anonymous: 5
Sensory Systems/Olfactory System Source: https://en.wikibooks.org/wiki/Sensory_Systems/Olfactory_System?oldid=3122957 Contributors: Jomegat, Thomas.haslwanter, Adrignola, Skela, Zurlos, JackBot and AlphaPsi
Sensory Systems/Gustatory System Source: https://en.wikibooks.org/wiki/Sensory_Systems/Gustatory_System?oldid=2774382 Contributors: Thomas.haslwanter, Adrignola, Skela and Anonymous: 1
Sensory Systems/NonPrimates Source: https://en.wikibooks.org/wiki/Sensory_Systems/NonPrimates?oldid=3122956 Contributors:
CommonsDelinker, Thomas.haslwanter, JackBot, Harrybrowne1986, QUBot, GerickINI, Nikhilbiyani, Goeldi ma, Sdiether, Mdzung and
Anonymous: 6
Sensory Systems/Authors Source:
https://en.wikibooks.org/wiki/Sensory_Systems/Authors?oldid=3121065 Contributors:
Thomas.haslwanter, Adrignola, Skela, Psimmler, Rega~enwikibooks, AlphaPsi, Nikhilbiyani, Mbuerki, J sun, Goeldi ma, Arturomoncadatorres, Sdiether, Dat72787, SteM90, Andani23, Duguyue100, CSSKG, Isabelletan, Mgirr and Anonymous: 4
Sensory Systems/Sources Source: https://en.wikibooks.org/wiki/Sensory_Systems/Sources?oldid=2750256 Contributors:
Thomas.haslwanter, Adrignola, Skela, Pole from sweden, Avicennasis, Rega~enwikibooks, MartinPoulter and Anonymous: 1
Sensory Systems/Appendix Source:
Thomas.haslwanter, Adrignola and Skela
https://en.wikibooks.org/wiki/Sensory_Systems/Appendix?oldid=2764782
A mu,
Contributors:
5.2 Images
File:5_Salticid_eye_movement.png Source: https://upload.wikimedia.org/wikipedia/commons/b/b8/5_Salticid_eye_movement.png License: CC BY-SA 3.0 Contributors: Own work Original artist: Sdiether
File:6_Discernment_of_visual_targets_by_Cupiennius_salei.png Source: https://upload.wikimedia.org/wikipedia/commons/8/82/6_
Discernment_of_visual_targets_by_Cupiennius_salei.png License: CC BY-SA 3.0 Contributors: Own work Original artist: Sdiether
File:7_Principal_eye_characteristics_influence_stalking_behavior_in_Portia_fimbriata.jpg Source: https://upload.wikimedia.org/
wikipedia/commons/b/b6/7_Principal_eye_characteristics_influence_stalking_behavior_in_Portia_fimbriata.jpg License: CC BY-SA
3.0 Contributors: Own work Original artist: Sdiether
File:8_Phidippus_clarus_female_preying_on_fly.jpg Source: https://upload.wikimedia.org/wikipedia/commons/6/6e/8_Phidippus_
clarus_female_preying_on_fly.jpg License: CC BY 2.0 Contributors: http://www.flickr.com/photos/23233631@N00/2959226433/in/
photolist-5vuNVp-5vz7RL Original artist: David Hill
89
90
CHAPTER 5. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES
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https://upload.wikimedia.org/wikipedia/commons/2/22/A_crocodiles_eye_
%287825799462%29.jpg License: CC BY 2.0 Contributors: A crocodiles eye Original artist: Alias 0591 from the Netherlands
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3.0 Contributors: Own work Original artist: Arturomoncadatorres
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Contributors: Own work Original artist: Original by en:User:Chris 73, updated by en:User:Diberri, converted to SVG by tiZom
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elegans.jpg License: CC BY-SA 2.5 Contributors: Transferred from en.wikipedia to Commons.
Original artist: The original uploader was Kbradnam at English Wikipedia
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SemicircularCanal.svg License: CC BY-SA 3.0 Contributors: Own work Original artist: Thomas.haslwanter
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Human_Ear_en.svg License: CC BY 2.5 Contributors: Perception SpaceThe Final Frontier, A PLoS Biology Vol. 3, No. 4, e137
doi:10.1371/journal.pbio.0030137 (Fig. 1A/Large version), vectorised by Inductiveload Original artist: Chittka L, Brockmann
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Original artist: Alvesgaspar
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electromagnetic_opacity.svg License: Public domain Contributors: Vectorized by User:Mysid in Inkscape, original NASA image from
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Contributors: Own work Original artist: E vidal
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Source:
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Big-eared-townsend-fledermaus.jpg License: Public domain Contributors: http://www.blm.gov/nv/st/en.html Original artist: PDUSGov, exact author unknown
File:Bird_lore_(1913)_(14562557107).jpg Source:
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29_%2814562557107%29.jpg License: Public domain Contributors: https://www.flickr.com/photos/internetarchivebookimages/
14562557107/ also at Wisconsin Historical society page on passenger pigeon photographs and photo page Original artist: J. G. Hubbard,
Internet Archive Book Images
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3.0 Contributors: Own work Original artist: darklama
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png License: Public domain Contributors: Transferred from en.wikipedia to Commons by Wadester16 using CommonsHelper. Original
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BY-SA 4.0 Contributors: Own work Original artist: Dling007
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Source:
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(www.micro2macro.net) Facebook Youtube
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title='File:Cochlea-crosssection.png'>Cochlea-crosssection.png</a>. Modications made by Fred the Oyster. Original artist: Cochleacrosssection.png: Original uploader was Oarih at en.wikipedia
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5.2. IMAGES
91
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Sylvie Renaud, Johannes Schemmel, Gert Cauwenberghs, John Arthur, Kai Hynna, Fopefolu Folowosele, Sylvain Saighi, Teresa SerranoGotarredona, Jayawan Wijekoon, Yingxue Wang, and Kwabena Boahen
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Public domain Contributors: Transferred from en.wikibooks; transferred to Commons by User:Adrignola using CommonsHelper.
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Sensory Systems

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Sensory Systems

Physiology & Computer Simulations

Keep it simple: Unicellular Creatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Not so simple: Three-hundred-and-two Neurons . . . . . . . . . . . . . . . . . . . . . . .

General principles of Sensory Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Principles of Information Processing in the Nervous System . . . . . . . . . . . . . . . . .

Simulating Action Potentials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Hodgkin Huxley equation

Modeling the Action Potential Generation: The Fitzhugh-Nagumo model . . . . . . . . . .

Simulating a Single Neuron with Positive Feedback

Simulating a Simple Neural System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

The Development and Theory of Neuromorphic Circuits . . . . . . . . . . . . . . . . . . . . . . .

Current Events in Neuromorphic Engineering . . . . . . . . . . . . . . . . . . . . . . . .

Transistor Structure & Physics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Basic static circuits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

The NEURON simulation environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Neuron with Python . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Sensory Systems in Humans

Anatomy of the Auditory System

Auditory Signal Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Anatomy of the Visual System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Anatomy of the Vestibular System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Alcohol and the Vestibular System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Anatomy of the Somatosensory System . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Proprioceptive Signal Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Sensory Organ Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Taste and Other Senses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Sensory Systems in Non-Primates

Zebra Finches: Neural Mechanism for Song Learning . . . . . . . . . . . . . . . . . . . .

Spiders Visual System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

History of Sensory Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Text and image sources, contributors, and licenses

And such unicellular organisms can be amazingly smart:

1.1.2 Not so simple: Three-hundred-andtwo Neurons

General principles of Sensory Systems

Based on the example of the visual system, the general

Types of sensory transducers

All sensory systems are based on

Golgi organs: in the tendons

the Processing of this information by our nervous

3. Light-receptors (visual system): here we have

And the generation of a resulting Action.

While the underlying physiology restricts the maximum

Heat-sensors (maximum sensitivity at ~ 45C,

5. Electro-receptors: for example in the bill of the

Now what distinguishes neurons from other cells in the

A conductile stage, the axon: once the cell body

1.1.6 Principles of Information Processing

Olfactory system - to signal sweet or sour

Auditory system - to signal frequency

a) Dendrites, b) Soma, c) Nucleus, d) Axon hillock, e) Sheathed

Sensory information is rarely based on the signal nerve.

The structure of the connections between nerve cells is

1.3 Simulating Action Potentials

The action potential is the stereotypical voltage change

Female Monarch buttery

- On the other hand, we must not learn too fast, either.

Action potential Time dependence

With the mechanisms described below, an incoming

1.3. SIMULATING ACTION POTENTIALS

where Pi denotes the permeability of Ion i, and I the

Occasionally ion channels directly connect two cells,

(Kv )closed (Kv )open

Since n is the probability that the channel is open, the

# -- coding: utf-8 -- import numpy as np import