Dominance and access to the food resource

Tutorial: Processing videos to assess the time individuals spent at the feeder
Lilianas internship
2014.02.26

MAIN GOAL
assess the time each individual spent at the feeder to investigate the access to the food resource in relation of an individuals dominance score.

Objectives
For two hours of feeding per video maximum:
Record the time each individual spent in the periphery area = OUT zone Record the time each individual spent in the feeder area = IN zone Record with a binomial variable (0 = feed on the edge; 1= feed inside the feeder) whether each individual are feeding from the edge of the feeder or from inside = Feed.in

This one feeds inside the IN zone and you will have to write 1 in the feed.in column because it is feeding inside the feeder

Zone IN

Zone OUT

Files and software

Download the latest version of VLC (free) Open VA resource alim 2013-2014 _ L Open the video you have to process with VLC
NOTES:
1. If you cannot read the video smoothly from the hardware using VLC, you may need to copy the video first on your computer if this does not solve the pb, that means your graphic card is not powerful enough which means we will have to find another computer Try to be organized, keep track of videos you have processed already etc Maybe create an excel file where you list all the videos you have to analyze and a variable showing if you did it or not It is also quite interesting to have written the bout of time where birds are seen at the feeder OR more convinient, the bout of time where no birds are around (it helps if we have to look at the video again)

2.

VLC tips
Use the key - to slow down a playback Use the key + to accelerate a playback The more you press these keys, the faster/slower the video is played. Use the keyboard main tab to pause the playback When no bird are around, move the cursor forward from about 10s (not more otherwise you may miss things)

Before you press the start button

From file: VA resource alim 2013-2014 _ L
Enter year, month, day, col, processor (= your initial) time start, time end, duration of the video (if less than 2hrs,
note it and process the video until the end, if > 2hrs, do only 2hrs: its painful enough!).

Have a look at my behavioural observation file to extract the ID of the birds I have observed around. It will facilitate the ID determination from the
video Filter per colony

How to write colour IDs

BK = BLACK DB = DARK BLUE EG = EMERALD GREEN FP = FLUO PINK LB = LIGHT BLUE LG = LIGHT GREEN OR = ORANGE PS = PINK STRIPE (black band with fluo-pink stripes) RE = RED VI = VIOLET WH = WHITE WS = WHITE STIPE (black band with white stripes) YE = YELLOW

How to write colour IDs

Colour IDs have to be written with the following order Upper left; Lower left; upper right; lower right
Left hand side is the left leg of the bird (on the left when you look at the back of the bird)
For instance: the bird on the pic is YEWHYEM

How to write colour IDs

One more example: This one is WHREYEM

How to write ID with missing ring

UR = Code for missing ring (UnRing) If the colour ring above the metal ring is missing, always write URM If one colour is missing from the leg with no metal ring, always write the color code first ORUR or DBUR or REUR or LBUR etc
Example: ORURURM has one colour missing and one orange band on the left hand side and just a metal ring on the right hand side.

 For example: This one is EGURYEM

Be aware of
Light Blue (LB) and White (WH) are very very tricky, hard to differentiate on videos, make sure
you do not have birds that differ only from those colours. If it is the case and you have trouble, email/skype me (i.e. at colony 27 there are a LBORORM and a WHORORM)

DB and BK can also be a bit tricky when the light is not

good but usually, the exposure change and the confusion vanishes

Be very careful not to omit any time and to enter time correctly

 For example: This one is LBLBYEM and not WHWHYEM luckily,

in that colony there is no WHWHYEM so it makes thing easier

Example of video processing

With the next slides, I have attempted to describe you as best as possible how I proceed to process a video (so what you should do!) In that example, we are looking at what happens from 1hr 08 min 15 sec after we started the camera & positioned the feeder under the colony To simplify, I used A,B,C,D,E,F instead of Colour IDs

Example of video processing

C B D E

1h08m15s

Yr 2013 2013 2013 2013

Mth 09 09 09 09

Day 9 9 9 9

Col 33 33 33 33

Proc . MR MR MR MR

AM/ PM PM PM PM PM

IN/ OUT OUT OUT OUT OUT

ID. Col A B D E

Start 1:06:09 1:07:52 1:08:02 1:07:08

End

Duration

Total Video 02:00:00 02:00:00 02:00:00 02:00:00

Fee d.in

2013 2013 2013

2013 2013

09 09 09
09 09

9 9 9
9 9

33 33 33
33 33

MR MR MR
MR MR

PM PM PM
PM PM

OUT OUT IN
IN IN

F C A
B D

1:02:05 1:08:01 1:08:10

1:08:12 1:08:07

02:00:00 02:00:00 02:00:00

02:00:00 02:00:00

1. A few seconds before 1:08:15, these 6 individuals were all in the OUT zone. A,B,D,E,F,E jumped over the green hoop and stayed at least 2 sec in the OUT zone therefore we enter for each of them at what time they entered the OUT zone, we specified it is the OUT zone considered here and we precise the ID. The table should look like the one above

Example of video processing

C B D E

1h08m15s

Yr 2013 2013 2013 2013

Mth 09 09 09 09

Day 9 9 9 9

Col 33 33 33 33

Proc . MR MR MR MR

AM/ PM PM PM PM PM

IN/ OUT OUT OUT OUT OUT

ID. Col A B D E

Start 1:06:09 1:07:52 1:08:02 1:07:08

End 1:08:10 1:08:12 1:08:07

Duration =End-Start 00:00:20 00:00:05

Total Video 02:00:00 02:00:00 02:00:00 02:00:00

Fee d.in

2013 2013 2013

2013 2013

09 09 09
09 09

9 9 9
9 9

33 33 33
33 33

MR MR MR
MR MR

PM PM PM
PM PM

OUT OUT IN
IN IN

F C A
B D

1:02:05 1:08:01 1:08:10

1:08:12 1:08:07

02:00:00 02:00:00 02:00:00

02:00:00 02:00:00

2. But then individuals A,B,D leaves the OUT zone (at respectively 1:08:10, 1:08:12 and 1:08:07 to start feeding directly from the feeder, standing on the edge for B,D. In the middle of the feeder for A Enter the time they left the OUT zone inside the End column for each individual. Use these times as a Start time for the IN zone for each of those 3 individuals Also, individual A is feeding inside the feeder so do not forget to write 1 in the feed.in column. Careful, it is very easy to forget a End time, always check that the number of birds you see in each zone (IN and OUT correspond to the data entry with no End time yet.

C D B

1h08m29s

Yr 2013 2013 2013 2013

Mth 09 09 09 09

Day 9 9 9 9

Col 33 33 33 33

Proc . MR MR MR MR

AM/ PM PM PM PM PM

IN/ OUT OUT OUT OUT OUT

ID. Col A B D E

Start 1:06:09 1:07:52 1:08:02 1:07:08

End 1:08:10 1:08:12 1:08:07

Duration =End-Start 00:00:20 00:00:05

Total Video 02:00:00 02:00:00 02:00:00 02:00:00

Fee d.in

2013 2013 2013

2013 2013 2013

09 09 09
09 09 09

9 9 9
9 9 9

33 33 33
33 33 33

MR MR MR
MR MR MR

PM PM PM
PM PM PM

OUT OUT IN
IN IN OUT

F C A
B D D

1:02:05 1:08:01 1:08:10

1:08:12 1:08:07 1:08:29 1:08:29

02:00:00 02:00:00 02:00:00

02:00:00 02:00:00

3. At 1:08:29 A, B are still in the IN zone D left the IN zone, we need to create a new OUT entry C, E, F, are still in the OUT zone.

C D B

A
F
1h08m37s

C D B

1h09m17s

5. At 1:09:17 A is still in the IN zone (he may not be inside the feeder anymore but as he went at least feeding from inside once during this bout, we keep the variable 1) C is still in the OUT zone D is still in the IN zone but went inside the feeder type 1 in the feed.in column E left the OUT zone and the whole feeding area enter End time in the OUT entry for this ind. F left the OUT zone to feed in the IN zone from the edge. enter End time in the OUT entry and create a new IN entry with this same time for this ind.

B left the IN zone to feed in the OUT zone enter End time in the IN entry and create a new OUT entry with this same time for this ind.

Yr 2013 2013 2013 2013

Mth 09 09 09 09

Day 9 9 9 9

Col 33 33 33 33

Proc . MR MR MR MR

AM/ PM PM PM PM PM

IN/ OUT OUT OUT OUT OUT

ID. Col A B D E

Start 1:06:09 1:07:52 1:08:02 1:07:08

End 1:08:10 1:08:12 1:08:07 1:09:17

Duration =End-Start 00:00:20 00:00:05 00:00:09

Total Video 02:00:00 02:00:00 02:00:00 02:00:00

Fee d.in

2013 2013 2013

2013 2013 2013 2013 2013 2013

09 09 09
09 09 09 09 09 09

9 9 9
9 9 9 9 9 9

33 33 33
33 33 33 33 33 33

MR MR MR
MR MR MR MR MR MR

PM PM PM
PM PM PM PM PM PM

OUT OUT IN
IN IN OUT IN IN OUT

F C A
B D D D F B

1:02:05 1:08:01 1:08:10

1:08:12 1:08:07 1:08:29 1:08:37 1:09:17 1:09:17

1:09:17

00:07:12

02:00:00 02:00:00 02:00:00 1

1:09:17 1:08:29 1:08:37

00:01:05 00:00:22 00:00:08

02:00:00 02:00:00 02:00:00 02:00:00 02:00:00 02:00:00 1

Check: We have 3 birds that are supposed to be still in the IN zone YES We have 2 birds that are supposed to be in the OUT zone YES

More rules
Suppose individual E comes back to the OUT zone jumping over the hoop and then crossing the OUT zone quickly to directly reach the IN zone It is quite time consuming to create new row/entry for such behaviour So if a bird stays < 2 sec in a zone, do not create a new entry for that zone. Use the time the ind enters/leaves the first zone it crossed as a start time. Another rule, sometime they move from the edge just for a bit and come back to the feeder, if this is < 2 sec, do not end the IN entry to create a new OUT entry and then again a new IN entry

General advices
BE PATIENT! Do not rush this analysis otherwise it is prone to mistakes! And we need accurate data!
I know it can be painful, believe me, I am doing very intense videos at the moment for which I can spend sometime 15min processing 1min of video because there are a lot of movements between zones and a lot of birds! I have been as kind to you as possible and I have spared you the most intense colonies!

When they are many birds at the same time, I found sometime easier just to follow one bird (i.e. focal obs) at the time for that crazy bout and then play the bout again and focus on a second bird

General advices
When your eyes start to be very red, your brain painful and your nerves at the edge of a breakdown Sit back, breath, relax, enjoy a coffee take a break and come back to it once youve calm down

Priorities
Start by colony 21 and colony 81 I will send you a list of 5 video ID for each colony. You will start with those, then probably 5 more. That means you will have to analyze 20 videos of 2 hours

Good luck!!!!!!!!!!!!!!!
If you have any questions margaux.rat@gmail.com and I am usually on skype for emergency (username: margaux.rat)