Leica Aperio AT2 DX User manual

Aperio AT2 DX
MAN-0351, Revision B | 13 April 2020
User’s Guide

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 20202
Aperio AT2 DX User’s Guide
Copyright Notice
ÌCopyright © 2019-2020 Leica Biosystems Imaging, Inc. All Rights Reserved. LEICA and the Leica logo are registered trademarks of Leica
Microsystems IR GmbH. Aperio is a trademark of the Leica Biosystems group of companies in the USA and optionally in other countries. Other
logos, product and/or company names might be trademarks of their respective owners.
ÌThis product is protected by registered patents. For a list of patents, contact Leica Biosystems.
Customer Resources
ÌFor the latest information on Leica Biosystems Aperio products and services, please visit www.LeicaBiosystems.com/Aperio.
Disclaimers
ÌUse normal care in maintaining and using your MDDS. Interrupting network connections or turning off the MDDS while it is writing scanned
images can result in data loss.
ÌCaution: Federal (U.S.) law restricts this device to sale by or on the order of an appropriately licensed healthcare practitioner.
ÌThis 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.
ÌThe barcode decoding software used by Aperio scanners was provided by Honeywell International, Inc.
Contact Information – Leica Biosystems Imaging, Inc.
Headquarters Customer Support General Information
Leica Biosystems Imaging, Inc.
1360 Park Center Drive
Vista, CA 92081
USA
Tel: [phone] (toll free)
Direct International Tel: [phone]
Contact your local support representative
with any query and service request.
https://www.leicabiosystems.com/service-
support/technical-support/
US/Canada Tel: [phone] (toll free)
Direct International Tel: [phone]
Email: [email protected]
23AT2DX

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 2020 3
Customer Service Contacts
Please contact the office for your country for technical assistance.
Australia:
96 Ricketts Road
Mount Waverly, VIC 3149
AUSTRALIA
Tel: [phone] (toll free)
Between 8:30 AM-5 PM, Monday-Friday, AEST
Email: [email protected]
Austria:
Leica Biosystems Nussloch GmbH
Technical Assistance Center
Heidelberger Strasse 17
Nussloch 69226
GERMANY
Tel: [phone] (toll free)
In-country Tel: [phone]
Email: [email protected]
België/Belgique:
Tel: [phone] (toll free)
In-country Tel: [phone]
Email: [email protected]
Canada:
Tel: [phone] (toll free)
Direct International Tel: [phone]
Email: T[email protected]
China:
17F, SML Center No. 610 Xu Jia Hui Road, Huangpu District
Shanghai, PRC PC:200025
CHINA
Tel: [phone]
Fax: [phone]
Email: [email protected]
Remote Care email: [email protected]
Danmark:
Tel: [phone] (toll free)
In-country Tel: [phone]
Email: [email protected]
Deutschland:
Leica Biosystems Nussloch GmbH
Technical Assistance Center
Heidelberger Strasse 17
Nussloch 69226
GERMANY
Tel: [phone] (toll free)
In-country Tel: [phone]
Email: [email protected]
Eire:
Tel: [phone] (toll free)
In-country Tel: [phone]
Email: [email protected]
España:
Tel: [phone] (toll free)
In-country Tel: [phone]
Email: [email protected]
France:
Tel: [phone] (toll free)
In-country Tel: [phone]
Email: [email protected]
Italia:
Tel: [phone] (toll free)
In-country Tel: [phone]
Email: [email protected]
Japan:
1-29-9 Takadannobaba, Sinjuku-ku
Tokyo 169-0075
JAPAN
Nederland:
Tel: [phone] (toll free)
In-country Tel: [phone]
Email: [email protected]

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 20204
New Zealand:
96 Ricketts Road
Mount Waverly, VIC 3149
AUSTRALIA
Tel: [phone] (toll free)
Between 8:30 AM-5 PM, Monday-Friday, AEST
Email: [email protected]
Portugal:
Tel: [phone] (toll free)
In-country Tel: [phone]
Email: [email protected]
The Russian Federation
BioLine LLC
Pinsky lane 3 letter A
Saint Petersburg 197101
THE RUSSIAN FEDERATION
Tel: [phone] (toll free)
In-country Tel: [phone]
Email: [email protected]
Sweden:
Tel: [phone] (toll free)
In-country Tel: [phone]
Email: [email protected]
Switzerland:
Tel: [phone] (toll free)
In-country Tel: [phone]
Email: [email protected]
United Kingdom:
Tel: [phone] (toll free)
In-country Tel: [phone]
Email: [email protected]
USA:
Tel: [phone] (toll free)
Direct International Tel: [phone]
Email: T[email protected]

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 2020 5
1 Introduction ...................................................................................................................... 8
Intended Use...................................................................................................................................9
Image Viewing Restrictions for Primary Diagnosis....................................................................................9
If You Need Help..............................................................................................................................9
Symbols and Warnings....................................................................................................................10
Instrument Warnings....................................................................................................................... 11
Compliance Specifications................................................................................................................ 11
Installation ................................................................................................................................... 11
2 Startup and Shutdown................................................................................................... 12
System Startup..............................................................................................................................12
System Shutdown ..........................................................................................................................12
Calibration and Verification...............................................................................................................13
3 Preparing for Scanning ................................................................................................. 14
Training........................................................................................................................................14
Slide Preparation Tips......................................................................................................................14
Tissue Preparation ......................................................................................................................14
Staining....................................................................................................................................14
Slide Preparation ........................................................................................................................14
Coverslips .................................................................................................................................15
Label Issues ..............................................................................................................................15
Glass Slide Quality Control ...............................................................................................................16
4 Scanning Slides ............................................................................................................. 17
Scanner Controls............................................................................................................................17
Scanning Parameters ......................................................................................................................18
Starting the Console .......................................................................................................................18
Barcode Requirement......................................................................................................................18
Manually Entering a Barcode.........................................................................................................19
Multiple Slide Scanning Using the AutoLoader......................................................................................19
Replacing a Rack ........................................................................................................................19
Contents

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 20206
Contents
Loading a Slide into the Slide Tray......................................................................................................19
Basic Concepts ..............................................................................................................................20
Batch View................................................................................................................................21
Quick Reference .........................................................................................................................22
Viewing Scan Status ...................................................................................................................23
Batch Scanning..............................................................................................................................23
Fine-Tuning Batch Scanning ..........................................................................................................25
Scan Batch Tasks........................................................................................................................25
Manually Scanning a Slide ...............................................................................................................27
Using Snapshots ............................................................................................................................28
Working with Focus Points ...............................................................................................................29
Automatically Adding Focus Points .................................................................................................29
Calibration....................................................................................................................................30
Z-Stack Scanning ...........................................................................................................................31
About the Z-Stack Scanning Window ..............................................................................................32
Basic Z-Stack Settings .................................................................................................................32
Advanced Z-Stack Settings ...........................................................................................................33
Saving Z-Stack Settings as a Slide Setting........................................................................................33
Viewing Z-Stacks........................................................................................................................33
5 Image Quality Review .................................................................................................... 34
Image Quality Review......................................................................................................................34
Data Entry ....................................................................................................................................34
6 Using the AutoLoader.................................................................................................... 35
Microscope Slide Types ...................................................................................................................35
Slide Preparation............................................................................................................................35
Loading Slides into the AutoLoader ....................................................................................................36
Inspecting the AutoLoader and Racks..................................................................................................38
7 Quality Control and Maintenance................................................................................. 39
Maintenance Schedule....................................................................................................................39
Restart the Scanner Controller Service ................................................................................................40
Perform a Presnap ..........................................................................................................................40
Set Line Camera Gains ....................................................................................................................40
Clean the Objective.........................................................................................................................41
Removing the Objective................................................................................................................41
Installing the Objective ................................................................................................................41
Clean the Scanner ..........................................................................................................................42
Cleaning the Scanner Casing .........................................................................................................42

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 2020 7
Contents
Cleaning the Scanner Interior ........................................................................................................42
Cleaning the Slide Tray on the Stage ...............................................................................................42
Cleaning the AutoLoader ..............................................................................................................42
Cleaning the AutoLoader Racks......................................................................................................43
Recalibrate the AutoLoader Slide-in-Rack Sensor...................................................................................43
Change the Aperio Service Account Password and Update ApService.........................................................45
Changing the Aperio Service Account Password.................................................................................45
Updating the Aperio Service Credentials ..........................................................................................46
A Troubleshooting ............................................................................................................. 49
General Troubleshooting ..................................................................................................................49
AutoLoader Troubleshooting .............................................................................................................50
Carousel Status Light Red or Blinking Red ........................................................................................50
Slide on Stage ...........................................................................................................................51
Stalled AutoLoader Carousel or Rack Lift..........................................................................................52
Unable to Load AutoLoader Carousel...............................................................................................53
Motion Control ..............................................................................................................................53
Magnification Changer Troubleshooting...............................................................................................53
Recovering from a Motion Fault.........................................................................................................54
B Specications................................................................................................................. 55
Recommended Operating Environment ................................................................................................55
AC Power .....................................................................................................................................55
Transporting or Moving the Aperio AT2 DX ...........................................................................................55
Decommissioning and Disposal .........................................................................................................55
Long Term Storage..........................................................................................................................55
Aperio AT2 DX Hardware Specifications ..............................................................................................56
AutoLoader Specifications................................................................................................................56
Scanner Control Workstation Software Specifications.............................................................................57
System Requirements......................................................................................................................57
Environment Specifications...............................................................................................................57
C Aperio AT2 DX Safety Instructions ............................................................................... 58
Index ..................................................................................................................................... 60
Symbols................................................................................................................................ 63

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 20208
This Aperio AT2 DX scanner has been configured for and is part of the Aperio AT2 DX System, which includes:
`The Aperio AT2 DX scanner, including a control/viewing workstation and calibrated monitors
`Console scanning software
`One or more Aperio AT2 DX Viewing Stations including two calibrated monitors for each station
`Aperio ImageScope DX viewer
For a complete description of this system and the workflow for using it, refer to the Aperio AT2 DX System Overview.
The monitors provided with the Aperio AT2 DX System have been calibrated at the factory and may
require periodic re-calibration in the field by authorized Leica Biosystems technicians. Contact your
Leica Biosystems Technical Services representative for information. Do not attempt to change the
monitor display settings as doing so may interfere with the monitor calibration.
The Aperio AT2 DX System must only be used with the Aperio AT2 DX Viewing Stations provided as
part of the system.
The Aperio AT2 DX slide scanner has been manufactured to the highest quality standards. Refer to “Appendix C: Aperio
AT2 DX Safety Instructions” on page 58 for important information on safely operating your scanner—following these
safety guidelines will protect your unit and provide optimal operation.
Note that annual servicing is required to maintain scanner performance.
This equipment is intended to be used by trained, knowledgeable, licensed operators/technicians. Appropriate good
laboratory practices or other policies and procedures required by your institution must be followed in support of slide
preparation, processing, storage, and disposal.
Use this equipment only for this purpose and in the manner described in this guide.
1 Introduction

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 2020 9
Chapter 1: Introduction
Intended Use
The Aperio AT2 DX System is an automated digital slide creation and viewing system. The Aperio AT2 DX System is
intended for in vitro diagnostic use as an aid to the pathologist to review and interpret digital images of surgical pathology
slides prepared from formalin-fixed paraffin embedded (FFPE) tissue. The Aperio AT2 DX System is not intended for use with
frozen section, cytology, or non-FFPE hematopathology specimens.
The Aperio AT2 DX System is composed of the Aperio AT2 DX scanner, the Aperio ImageScope DX review application
and display. The Aperio AT2 DX System is for creation and viewing of digital images of scanned glass slides that would
otherwise be appropriate for manual visualization by conventional light microscopy. It is the responsibility of a qualified
pathologist to employ appropriate procedures and safeguards to assure the validity of the interpretation of images obtained
using the Aperio AT2 DX System.
Image Viewing Restrictions for Primary Diagnosis
The images produced by the Aperio AT2 DX scanner are for diagnostic use within the Aperio AT2 DX System only. Images
opened outside the system with non-cleared Aperio viewers will display an error alerting the user that these images cannot
be used for primary diagnosis.
Non-cleared Aperio viewers include:
`Aperio ImageScope (all non-DX versions)
`Aperio WebViewer
`Aperio WebScope
`Aperio ePathViewer
If You Need Help
Refer to “Appendix A: Troubleshooting” on page 49 for troubleshooting tips. For further technical support, contact your
local Leica Biosystems office. Training is also available from Leica Biosystems. Refer to page 3 of this manual for contact
information.

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 202010
Chapter 1: Introduction
Symbols and Warnings
The following symbols are used throughout the documentation to alert you to potential danger in operating the scanner.
Symbol Description
The exclamation point within an equilateral triangle is intended to alert you to the presence of
important operating and maintenance (servicing) instructions.
The lightning flash with arrowhead symbol within an equilateral triangle is intended to alert you to the
presence of uninsulated “dangerous voltage” within the product’s enclosure that may be of sufficient
magnitude to constitute a risk of electric shock to persons.
The flat surface with waves symbol within an equilateral triangle is intended to alert you to the
presence of hot surfaces which could cause burn damage.
Caution: Federal (U.S.) law restricts this device to sale by or on the order of an appropriately licensed healthcare practitioner.
IMPORTANT
If the scanner is used in any manner not specified in this documentation, the protection provided by the equipment may be
impaired.
WARNING: This equipment generates, uses and can radiate radio frequency energy. If not installed and used in accordance
with the instructions in this manual it may cause interference to radio communications. It has been tested and found to
comply with the limits for a Class A computing device (pursuant to Subpart B of Part 15 FCC Rules), which are designed to
provide reasonable protection against such interference when operated in a commercial environment.

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 2020 11
Chapter 1: Introduction
Instrument Warnings
WARNING: TO REDUCE THE RISK OF FIRE OR ELECTRIC SHOCK, DO NOT EXPOSE THE
SCANNER TO RAIN OR MOISTURE.
MISUSE OF ELECTRICAL EQUIPMENT CAN CAUSE ELECTROCUTION, BURNS, FIRES, AND
OTHER HAZARDS.
Compliance Specifications
This device complies with Part 15 of the FCC rules. Operation is subject to the following two conditions: (1) This device may
not cause harmful interference and (2) this device must accept any interference received, including interference that may
cause undesired operation.
This device has been evaluated against and conforms to the following standards:
Feature Details
Safety
Low Voltage Directive 2006/95/EC
CAN/CSA-C22.2 No. 61010-1/R:2009
CAN/CSA-C22.2 No. 61010-2-081:2004
CAN/CSA-C22.2 No. 61010-2-101:2004
UL 61010-1/R:2008-10
EN 61010-1: 2001
IEC/EN 61010-2-081/A1:2003
IEC/EN 61010-2-101:2002
EMC EMC Directive 2004/108/EC
IEC/EN 61326-1: 2006; Class A
FCC Part 15 Sub Part B
Installation
CAUTION: Two people are required for lifting the scanner.
Installation and setup of the scanner should only be performed by a trained Leica Biosystems Technical Services
representative.

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 202012
2 Startup and Shutdown
System Startup
To start the Aperio AT2 DX scanner:
1. Press the power button on the front panel of the Aperio AT2 DX Control Station.
2. When the Windows login screen appears, log in with the Windows user name and password.
The default user name and the password were provided to your administrator on installation. We recommend that
the administrator change the user name and password after installation. Contact your administrator for assistance
with the default or updated user name and password.
3. Turn on the Aperio Image View Station monitors.
4. Press the main power switch on the back of the scanner to the On (|) position.
The scanner takes approximately three minutes to initialize and place the stage in the home position. When the
scanner completes these processes, the status screen on the front panel of the scanner reads “Scanner Ready.”
System Shutdown
To shut down the scanner:
1. Press the main power switch on the back of the scanner to the Off (O) position.
2. Close all scanner software applications and any additional Windows applications that are open.
3. Click the Windows Start button and select Shut Down.
4. Select Shutdown from the window and click OK.
5. Turn off the viewing monitors.
We advise leaving the scanner instrument powered on unless it is to be idle for more than four days.

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 2020 13
Chapter 2: Startup and Shutdown
Calibration and Verification
The Aperio AT2 DX scanner is calibrated and verified at the factory before shipment. During installation, a Leica Biosystems
technician also performs calibration and operational verification.
We recommend annual preventive maintenance, performed by Leica Biosystems Technical Services, to make sure the
scanner is operating correctly. For scanner maintenance you can perform yourself, see “Chapter 7: Quality Control and
Maintenance” on page 39.
The scanner provides automatic calibration and verification every time a slide is scanned by performing calibration during
the scan. For customer calibration instructions, see “Calibration” on page 30.
The monitors provided with the Aperio AT2 DX System have been calibrated at the factory and may
require periodic re-calibration in the field by authorized Leica Biosystems technicians. Contact your
Leica Biosystems Technical Services representative for information. Do not attempt to change the
monitor display settings, as doing so may interfere with the monitor calibration.

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 202014
This chapter contains information on preparing for scanning slides with the Aperio AT2 DX scanner.
Training
Leica Biosystems Imaging offers on-site training courses. Contact Leica Biosystems Imaging Customer Support for
information about training options.
Slide Preparation Tips
When preparing slides for scanning, you must use the procedures required by the vendors of the stains
and reagents you are using.
Well prepared slides are crucial to a successful scan. Here are some things to keep in mind that will help make sure your
scans are of the optimum quality. If after reading this section you have any questions about whether your slide preparation
techniques will provide good scan quality, contact Leica Biosystems Technical Services for assistance.
Consult the material safety data sheets for the stains and re-agents you are using, as well as your institution’s biosafety
policies and procedures regarding safely handling biological materials.
Tissue Preparation
The tissue preparation is important for scan quality. Folds in the tissue and tissue sections that are too thick will result in
out of focus images. If working with such a slide, preparation of a new slide might be required.
Staining
Reproducibility of the slide staining is important for consistent and accurate diagnosis. Make sure that the variations of the
staining process are controlled and eliminated to the greatest extent possible. Employ appropriate morphological studies
and controls as specified in the reagent manufacturers’ instructions.
Slide Preparation
The preparation of the slide is important for its scan quality and ease of scanning. Clean the slides and make sure they
are in good condition—no dirt, no fingerprints, no markings, no writing, no extra adhesive, no broken slides, no chips, no
scratches, etc. Prior to loading slides, ensure that all slides are fully cured (that is, not “wet”). For best results, all slides
scanned should have coverslips.
3 Preparing for Scanning

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 2020 15
Chapter 3: Preparing for Scanning
Before scanning the slide, make sure it is very clean. Wipe it with a clean cotton rag (don’t use chemical cleaners).
Make sure there is no glue around the edges of a slide that would cause it to stick or catch in the scanner stage area. This is
crucial for the AutoLoader.
DO NOT ATTEMPT TO SCAN DAMAGED SLIDES AS DOING SO MAY DAMAGE THE
APERIO AT2 DX SCANNER.
The tissue ideally should be located in the middle of the slide a distance from the edges
of the slide, the label and any other markings. For more details on slide specifications,
see “Aperio AT2 DX Hardware Specifications” on page 56.
It is helpful for the tissue to be placed consistently in the same location and orientation
on the slide. Some of the mechanical problems of a slide can be resolved by cleaning the
slide with a cotton tissue or trimming the sides with a razor blade. Permanent problems
with a slide may require the preparation of a new slide.
See “Coverslips” and”Label Issues” below for more information on slide preparation.
Coverslips
The quality of the scan is affected by the condition of the coverslip.
`Keep the glue that attaches the coverslip to the slide to a minimum. Excess glue makes it hard for the tissue
finder to distinguish between actual tissue and the glue. If a focus point lands on the glue, slide focus will not be
accurate.
`Make sure there are no air pockets under the coverslip.
`For best results, there should not be markings or writing on the coverslip.
`The coverslip must not hang over the side of the slide.
Label Issues
Improperly applied slide labels can cause slides to jam in the AutoLoader. Do not apply multiple labels to the same slide—
this can cause the slide to exceed the specification for slide thickness (see “AutoLoader Specifications” on page 56 for
slide specifications). Make sure that labels do not extend beyond the edges of the slide and that they do not cover any
tissue. Make sure that labels are firmly attached.
Do not apply labels to the bottom surface of the slide.
Below are examples of a slide on which multiple labels cause the slide to exceed the allowable maximum thickness and a
slide in which the label is peeling away from the slide:

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 202016
Chapter 3: Preparing for Scanning
Glass Slide Quality Control
It is the responsibility of the lab to verify the quality of the tissue preparation, the mechanics of a slide and the staining.

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 2020 17
4 Scanning Slides
This chapter contains information on scanning slides with the Aperio AT2 DX scanner.
CAUTION: Keep hands clear of the mechanical stage assemblies when the scanner is operating.
Scanner Controls
Several of the controls on this scanner not labeled below are used in other configurations of this scanner, but are not used
as part of an Aperio AT2 DX System.
LCD status
Slide tray
access

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 202018
Chapter 4: Scanning Slides
Scanning Parameters
Note that certain scanning parameters (such as image compression type) have been preselected and
cannot be changed. This ensures that your results are consistent with the Aperio clinical studies on
which the FDA clearances for the Aperio AT2 DX System were based.
Starting the Console
Start the Console by double-clicking the Console icon on the Windows Desktop or from the Windows Start menu by
clicking Start, pointing to All Programs > ScanScope, and then selecting ScanScope Console.
You can only use the Console on a workstation directly connected to the scanner.
When you first start the Console you see a connection screen that asks you to log in. Enter the user name and password
required by your MDDS. If you are not sure what user name and password to use, contact your system administrator for
help.
Barcode Requirement
For quality control, the Aperio AT2 DX System requires the use of barcodes on your slide labels to provide slide identification
information. The Aperio AT2 DX will mark as a failed scan any slide on which it was not able to read the barcode.
Barcode formats supported by this system are:
`Data Matrix
`Interleaved 2 of 5
`PDF417
`MicroPDF
`QR Code
`Code 128
If the Aperio AT2 DX scanner is unable to interpret the barcode on the label of your slide, the slide will appear on the
Console window in red to indicate the scan failed.
In this case, inspect the slide to see if that area of the slide needs to be cleaned.
If you are unable to make the barcode area of the label readable to the scanner, you can manually enter barcode data. (The
text you enter depends on your institution’s policy for what information should be in the barcode.)

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 2020 19
Chapter 4: Scanning Slides
Manually Entering a Barcode
To manually enter a barcode:
1. While using the Console, click on the slide in the rack or batch view and select the View Slide icon .
2. In the slide view window, click the down-arrow at the top of the label window to expand it.
3. Type the barcode data into the Enter Barcode Id text box and press Return.
4. Rescan the slide.
Multiple Slide Scanning Using the AutoLoader
The AutoLoader allows you to automatically scan up to 400 1-inch x 3-inch (2.54 cm by 7.62 cm) tissue slides unattended.
For information on loading slides into the AutoLoader, see “Loading Slides into the AutoLoader” on page 36. For
specifications for slides used in the AutoLoader, see “AutoLoader Specifications” on page 56.
Replacing a Rack
To replace an AutoLoader rack, eject the rack—this tells the scanner to move the rack to the access position. Then remove
the rack from the scanner, re-load it or replace it with another loaded rack, and place it back in the scanner. (See
“Chapter 6: Using the AutoLoader” on page 35 for details on placing slides in racks and using the AutoLoader.) To
eject the rack, place your cursor at the bottom of the graphic of the rack you want to eject—the Eject button appears;
click it to eject the rack.
Loading a Slide into the Slide Tray
You can scan a single slide by using the slide tray.
To load a slide in the slide tray:
1. First, make sure the slide tray is in load position by clicking the Eject button at the bottom of the Console window.
2. Place a slide into the slide tray with coverslip up and label oriented to the front.
For more information on scanning from the slide tray, see “Manually Scanning a Slide” on page 27.

Aperio AT2 DX User’s Guide, Revision B © Leica Biosystems Imaging, Inc. 202020
Chapter 4: Scanning Slides
Basic Concepts
When you first start the Console, you see the rack view, which gives information on the status of the contents of the
AutoLoader racks.
You will select slides and racks on this window.
The most important concept to understand when using the rack view is the difference between including slides in the
current scan batch and selecting slides.
Any slides in the slide positions shown in the slide tray display that have a white color are not included in the current scan
batch nor are they selected, whether or not there is a slide in that position.
Any slides in the slide positions shown in the rack view that have a status color other than white are included in the current
scan batch.
If the slide position has a status color and shows a lighter bar on the left, the slide is selected:
The dot to the left of each slide indicates the scan magnification selected for that slide. (The colors match the magnification
levels shown on the Magnification icon.)