Aperio FL Quick Start Guide

This guide gives a quick overview of using the Aperio FL slide scanner. For detailed information on
operation and maintenance, see the Aperio FL Users Guide.

Red stop button

Slide tray door

LCD status
Green start button

Slide tray
access

The main power switch is on the back of the scanner. Your scanner number is also located on the back (for example,
SS6301). The magnification changer control is inside the access door on the left of the unit.

Starting the Scanner

Turn on the equipment in this order:
1. Press the power switch on the external light source to the On (|) position.
2. Press the main power switch on the back of the scanner to the On (|) position.
3. Press the power buttons on the front panel of the scanner control workstation and on the computer monitor.
A Windows logon screen may appear; if it does, press Ctrl+Alt+Del on the keyboard. Log in with the user name and
password provided during scanner installation. If your administrator has changed the default password (a recommended
security practice), contact your administrator if you do not know the new password.
The scanner takes approximately three minutes to initialize and place the stage mechanism in the home position. The light
source takes approximately four minutes to initialize. When the scanner has completed these processes, the status screen
on the front of the scanner reads Scanner Ready.

Aperio FL Quick Start Guide, Revision B Leica Biosystems Imaging, Inc. 2013

Aperio FL Quick Start Guide

Because of the special characteristics of fluorescence scanning, you must not use automatic scanning.
Manually step through the scanning steps using the Aperio FL Console. After setting scanning
parameters in the Console, you can then use the Console One Touch button or the scanner automatic
scan button to complete the scan. If automatically selecting focus points (by using the Console Focus
Points tab Auto Select button) does not provide satisfactory results, use the Console tools to manually
add focus points.

Changing Optical Filters in the Filter Wheel

Standard filters can be used with dimensions of 25 mm diameter and 5.0 mm thickness.
To change a filter in the filter wheel:
1. Open the side access door on the left of the scanner.
2. Rotate the filter wheel until the numbered position you want to use is in front of you. The number indicates the
wheel position of the filter just above the label.

Filter wheel in position 1

3. If a filter is already in that position, place your finger in the notch behind the filter and your thumb on the front rim
of the filter and pull it toward you to remove it. Do NOT touch the glass portion of the filter, but only its rim!
4. To insert a filter, hold it by the rim only and push it into the filter receptacle on the wheel. Note that it must be
inserted in the proper orientation. (The arrow on the filter rim must point in the same direction as the light path.)
If you happen to touch the glass surface of the filter, it is very important that you clean it immediately. See the Aperio FL
Users Guide for details.
It is a good idea to wear lint-free gloves when handling filters to protect the filter surface.
After you close the access door, the scanner will automatically move the filter wheel back to its home position.

Aperio FL Quick Start Guide, Revision B Leica Biosystems Imaging, Inc. 2013

Aperio FL Quick Start Guide

Changing Filter Cubes in the Filter Cube Turret

To change a filter cube in the filter cube turret:
1. Start the scanner Console program.
2. In the Console, go to the Tools menu and click Configure.
3. On the Configuration window, click the Cube Turret tab.

4. To remove a filter cube, add a filter cube to an empty position, or change a filter cube in the scanner, you must move
the appropriate cube position in the turret to the loading position. To do this, select the filter cube position number
in the Move the filter number into load position drop-down list or double-click it on the cube turret map shown
on this tab. (The scanner LCD tells you that it is Loading cube x.)
5. When the filter cube position has been moved to the access position, open the side access door on the left of
the scanner. The filter cube you want to change (or the empty position in which you want to insert a filter cube) is
directly in front of you.
6. If a filter cube is in this position, slide it down the dovetail fitting to remove it.
7. Insert the new filter cube by sliding it up the dovetail fitting. The arrow on the numbered label points to the dovetail
for that turret position.

Aperio FL Quick Start Guide, Revision B Leica Biosystems Imaging, Inc. 2013

Aperio FL Quick Start Guide

Filter cube in turret position # 1

Dovetail for turret position #6

Associating Fluorochromes and Optical Filters in the Console

All fluorochromes, excitation filters and filter cubes must be defined in the Console.
1. Start the Console program.
2. In the Console, go to the Tools menu and click Configure.
3. Click the Dyes tab to see the list of pre-defined dyes and to create new ones. (See the Aperio FL Console Users
Guide for details.)

Aperio FL Quick Start Guide, Revision B Leica Biosystems Imaging, Inc. 2013

Aperio FL Quick Start Guide

4. Click the Filter Wheel tab to see what filters are defined for your filter wheel and to change them:

You can use this tab to delete filters, remove them from the wheel, or to move filters on the wheel. Make sure this
configuration matches the physical installation of filters in the filter wheel!
5. Click the Cube Turret tab to see what filter cubes are defined for the filter cube turret and to change filter cubes:

You can use this tab to define new filter cubes, remove filter cubes from the turret, and move filter cubes on the
turret. Make sure this configuration matches the physical installation of filter cubes in the cube turret!
For details on using these configuration tools, see Configuration Options in the Aperio FL Console Users Guide.

Aperio FL Quick Start Guide, Revision B Leica Biosystems Imaging, Inc. 2013

Aperio FL Quick Start Guide

Loading Slides
Glass slides should be clean and labels must not hang over the edges before loading in the slide tray.
When loading a slide, remove the slide tray from the scanner and position the slide in the tray with the cover slip facing up
and the slide label oriented to the left.
Re-insert the slide tray into the scanner, ensuring it is seated properly.

Using the Console

1. Start the Console either by double-clicking the Console icon on the desktop or by clicking Start in the Windows
taskbar and then selecting All Programs > ScanScope > ScanScope Console.
2. Use the picture on the Console Start tab to monitor and modify slide status (for example, when you remove a slide
from the slide tray) by right-clicking on the desired slide.
3. Hold the cursor over a particular slide to view information about that slide once it has been scanned.
As you proceed through scanning, various status screens are displayed; at any time you may click on the Start tab to modify
tray and slide status.
The graphic on the Start tab gives you information on the scanning status of your slides:

Here are the color codes that can appear on the Start tab tray graphic:

Category
Snapshots

Slide State

Color Code

Needs Snapshot A slide is in the queue to

get a snapshot, but the snapshot has not yet
been made.

White with blue diagonal lines

Has Snapshot A snapshot was made of

this slide and it is available to be visited and
reviewed.

Light blue

Visited A snapshot was made of this slide and Dark blue

the snapshot has been reviewed.
Failed Snapshot Scanner attempted to get a
snapshot of this slide but the snapshot failed.

White with red diagonal lines

Aperio FL Quick Start Guide, Revision B Leica Biosystems Imaging, Inc. 2013

Aperio FL Quick Start Guide

Category

Scanning

Rack Contents

Slide State

Color Code

Locked Another Console user is reviewing

this slides snapshot at this time, so you cannot
make changes to it.

Yellow with black diagonal lines

Scanning This slide is being scanned.

Yellow with the word

SCANNING

Scanned The slide was scanned and the

scanner was able to focus the tissue.

Green

Review The slide was scanned but the

scanner may not have been able to focus the
tissue.

Orange

Failed Scanner attempted to scan this slide,

but the scan failed.

Red

Unknown The state of this tray position is

Gray
unknown. It may contain a slide, but if so a
snapshot has not been made of it nor has it been
scanned
Empty No slide is in this tray location.

White

The scanning status colors displayed on the Console Start tab graphic indicate how well the scanner was able to focus the
tissue on the slide. Although a well-focused slide is likely to result in a better image than a poorly-focused slide, status
colors should not be interpreted as an absolute indicator of image quality.
Instead, they should be used as a diagnostic tool alerting you to possible problems with a scan. Regardless of the scan
status color displayed by the Console, all slides should be reviewed for acceptable image quality.
For more information on using the Console, on judging scan quality, and on snapshots, refer to the Aperio FL Console Users
Guide.

Starting Scanning
Make sure the scanner side door is closed and that there is at least one slide on the tray.

Set Scanning Parameters

Use the Console to perform the following steps (See the Aperio FL Console Users Guide for detailed instructions):
1. On the Console Start tab graphic, right-click the slide tray position containing the slide you want to scan and select
Set Current Slide.
2. Click Manual Loadon the new screen, click Manual Scan to get the macro image of the slide (you can
optionally enter a slide name on this screen).
3. Click OK to advance to the Scan Area tab.
4. Set the scan area by selecting the tissue or cell area you want to scan.

Aperio FL Quick Start Guide, Revision B Leica Biosystems Imaging, Inc. 2013

Aperio FL Quick Start Guide

5. Position the calibration point to an area that does not contain tissue or cells.
6. Select the channels and define what fluorochromes (dyes) were used on the specimen and what filters and filter
cubes to use for the slide.
7. Determine exposure times for each channel.
8. Place focus points on the specimen.
9. Perform calibration.
Click Start Scan to start the scan.

To Pause or Stop Scanning

1. Press the red scanner button and wait for the LCD to display Scanner Ready. Or, click Stop on any of the Console
tabs.
2. Now you may pull out the slide tray and change slides. When done, re-insert the slide tray.
3. Modify slide status as necessary on the Console Start tab by right-clicking on the slide position on the Start tab
graphic and selecting the appropriate command (such as Slide Removed).
4. Manually set up the scan parameters for the new slide as listed in the previous section.

Organizing eSlides
After a slide is scanned, the image is automatically added to the eSlide Manager default data group. To view your eSlides:
1. Open an Internet browser.
2. Access eSlide Manager by typing the appropriate host name or IP address in the URL address box of the browser. If
you are not sure what address to enter, contact your network administrator for help.
3. On the login screen, enter your user name and password and click User Login.
4. On the main eSlide Manager page, click List All eSlides to see all scanned slides.

Troubleshooting
If scanning stops unexpectedly, try these steps:
`` Restart the scanner Controllerclick on the Aperio Service Manager icon
Restart Services, and then select Restart Controller Service.

in the Windows taskbar, select

`` If that does not restart the scanning, turn off power to the scanner; wait five seconds and turn power back on.
Restart the Controller.
`` If that does not restart the scanning, reboot the Windows workstation.
If an error occurs, please send an email message to TechServices@LeicaBiosystems.com noting the following:
`` Scanner serial number (for example, SS6031)
`` Approximate time of the error or when it was noticed
`` Brief description of what you saw and what action you took

Aperio FL Quick Start Guide, Revision B Leica Biosystems Imaging, Inc. 2013

Aperio FL Quick Start Guide

`` Let us know if you were able to resume scanning

If email is not available, please call (866) 478-3999 and leave the above information in a voice mail.

For More Information

The Aperio user guides have been installed on your scanner workstation. To access them, double-click the Documentation
icon on your desktop. From the displayed list of guides, click the title of the guide you want to open.
If you are new to using the scanner, the following guides will help you get started:

To learn about...
Using your Aperio FL instrument

Refer to...
Aperio FL Users Guide
In addition to operation information, this guide also contains
important maintenance information and specifications.

Safety instructions

Aperio Fluorescence Scanner Safety Instructions

Using the Console software to scan slides

Aperio FL Console Users Guide

Viewing eSlides

ImageScope Users Guide

Using eSlide Manager to manage your digital

pathology information, including your eSlides

eSlide Manager Administrators Guide

eSlide Manager Operators Guide

Analyzing eSlides

Aperio ePathology Image Analysis Users Guide

Aperio FL Quick Start Guide, Revision B Leica Biosystems Imaging, Inc. 2013

Aperio FL Quick Start Guide

Aperio FL Quick Start Guide

MAN-0145, Revision B | 18 October 2013
This document applies to eSlide Manager Release 12 and later.

Copyright Notice
Copyright 2006-2013 Leica Biosystems Imaging, Inc. All rights reserved.

Customer Resources
For the latest information on Leica Biosystems Aperio ePathology products and services, please visit www.LeicaBiosystems.com/ePathology.

Disclaimers
Use normal care in maintaining and using the eSlide Manager servers. Interrupting network connections or turning off the eSlide Manager and
DSR servers while they are processing data (such as when they are analyzing eSlides or generating an audit report) can result in data loss.

This manual is not a substitute for the detailed operator training provided by Leica Biosystems Imaging or for other advanced instruction. Leica
Biosystems Imaging Field Representatives should be contacted immediately for assistance in the event of any instrument malfunction. Installation
of hardware should only be performed by a certified Leica Biosystems Imaging Service Engineer.

ImageServer is intended for use with the SVS file format (the native format for eSlides created by scanning glass slides with the scanner).
Educators will use Aperio ePathology software to view and modify eSlides in Composite WebSlide (CWS) format.

Trademarks and Patents

Aperio and ScanScope are registered trademarks and Genie, ImageScope, Aperio ePathology Solutions, eSlideShare, and eSlide Manager are
trademarks of Leica Biosystems Imaging, Inc. All other trade names and trademarks are the property of their respective holders.

Aperio ePathology products are protected by U.S. Patents: 6,711,283; 6,917,696; 7,035,478; 7,116,440; 7,257,268; 7,428,324; 7,457,446; 7,463,761;
7,502,519; 7,518,652; 7.602.524, 7,646,496; 7,738,688 and licensed under one or more of the following U.S. Patents: 6,101,265; 6,272,235;
6,522,774; 6,775,402; 6,396,941; 6,674,881; 6,226,392; 6,404,906; 6,674,884; and 6,466,690.

Contact Information Leica Biosystems Imaging, Inc.

Headquarters
Leica Biosystems Imaging, Inc.
1360 Park Center Drive
Vista, CA 92081
United States

Customer Support

General Information

US/Canada Tel: +1 (866) 478-3999 (toll free)

Direct International Tel: +1 (760) 539-1150

US/Canada Tel: +1 (866) 478-4111 (toll free)

Direct International Tel: +1 (760) 539-1100

US/Canada/Worldwide Email:
TechServices@LeicaBiosystems.com

Email: ePathology@LeicaBiosystems.com

Tel: +1 (866) 478-4111 (toll free)

Direct International Tel: +1 (760) 539-1100

European Union Authorized Representative

CEPartner4U
Esdoornlann 13
351DB, Maarn
The Netherlands

10

Aperio FL Quick Start Guide, Revision B Leica Biosystems Imaging, Inc. 2013