Leica BIOSYSTEMS Aperio AT2 DX User Manual
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Leica BIOSYSTEMS Aperio AT2 DX User Manual

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Aperio AT2 DX
User's Guide
MAN-0351, Revision A | 29 July 2019

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Summary of Contents for Leica BIOSYSTEMS Aperio AT2 DX

  • Page 1 Aperio AT2 DX User’s Guide MAN-0351, Revision A | 29 July 2019...
  • Page 2 Copyright © 2019 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.
  • Page 3 Tel: 0080052700527 (toll free) In-country Tel: +31 70 413 21 00 Danmark: Email: support.nl@leicabiosystems.com Tel: 0080052700527 (toll free) In-country Tel: +45 44 54 01 01 Email: support.dk@leicabiosystems.com Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...
  • Page 4 Tel: 0080052700527 (toll free) In-country Tel: +44 1908 577 650 Email: support.uk@leicabiosystems.com USA: Tel: +1 (toll free) (844) 534-2262 Direct International Tel: +1 760 539 1150 Email: TechServices@leicabiosystems.com Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 5: Table Of Contents

    Scanning Slides ......................18 Scanner Controls ..........................18 Scanning Parameters ........................19 Starting the Console ........................19 Barcode Requirement ........................19 Manually Entering a Barcode ......................20 Multiple Slide Scanning Using the AutoLoader ..................20 Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...
  • Page 6 Restart the Scanner Controller Service ....................41 Perform a Presnap ..........................41 Set Line Camera Gains ........................41 Clean the Objective .........................42 Removing the Objective ........................42 Installing the Objective ........................42 Clean the Scanner ..........................43 Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...
  • Page 7 AutoLoader Specifications ........................57 Scanner Control Workstation Software Specifications ................58 System Requirements ........................58 Environment Specifications .......................58 Aperio AT2 DX Safety Instructions ................59 Index ............................. 61 Symbols..........................65 Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 8: Introduction

    Aperio ImageScope DX viewer Ì 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.

  • Page 9: Intended Use

    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.

  • Page 10: Symbols And Warnings

    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 A © Leica Biosystems Imaging, Inc. 2019...

  • Page 11: Instrument Warnings

    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 A © Leica Biosystems Imaging, Inc. 2019...

  • Page 12: Startup And Shutdown

    To start the Aperio AT2 DX scanner: Press the power button on the front panel of the Aperio AT2 DX Control Station. You see the McAfee encryption login window. (This utility protects the contents of the workstation hard disk by encrypting it.) You need to enter a password to unlock the hard disk.

  • Page 13: Changing The Mcafee Disk Encryption Password

    Chapter 2: Startup and Shutdown Changing the McAfee Disk Encryption Password We recommend changing the disk encryption utility password every few months to protect the Aperio AT2 DX Control Station disk contents. (For more cybersecurity recommendations, see Aperio AT2 DX System Overview.) On the main McAfee login window, select the Change password check box and then log in with your current password.

  • Page 14: Calibration And Verification

    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.

  • Page 15: Preparing For Scanning

    Preparing for Scanning 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.

  • Page 16: Coverslips

    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 A © Leica Biosystems Imaging, Inc. 2019...

  • Page 17: Glass Slide Quality Control

    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 A © Leica Biosystems Imaging, Inc. 2019...

  • Page 18: Scanning Slides

    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.

  • Page 19: Scanning Parameters

    QR Code Ì 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.

  • Page 20: Manually Entering A Barcode

    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 28. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 21: Basic Concepts

    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.) Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 22: Batch View

    To select all slides in the batch view, click at the top of the window. Ì To unselect all slides in the batch view, click at the top of the window. Ì Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 23: Quick Reference

    Selects all slides that Marks all selected Automatically sets indicator slides from scan failed to scan slides for rescanning focus points batch Selects z-stack scanning. Selects magnification of scan Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 24: Viewing Scan Status

    Eject each rack on the Console window as discussed in “Viewing Scan Status” on page 24 and replace the racks with loaded racks. Click the Scan button: Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...
  • Page 25 To see the slide in even more detail, click the magnifying glass at the top corner of the green box (which indicates the scanned area) to open the image in Aperio ImageScope DX. To return to the previous view, click the back arrow at the top of the page. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 26: Fine-Tuning Batch Scanning

    To place the rack in loading position, move the cursor to the bottom of the rack in rack view and click the Eject button: Then remove the rack, re-load it or replace it with another loaded slide rack, and place it back in the scanner. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...
  • Page 27 Magnification icon. magnification Add name or Optionally, you can name one or more selected slides and give them a description by using the description Name and Description fields. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 28: Manually Scanning A Slide

    For details on the icons in the Manual Setup section shown on the slide view window above, see the following sections of this chapter. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 29: Using Snapshots

    If the image has already been scanned, a small magnifying glass appears at the top left of the image image. Click it to open the scanned image in Aperio ImageScope DX. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 30: Working With Focus Points

    You can automatically place focus points in two ways on the slide view window. Use the Number of Focus Points slider to place a small number or large number of focus points. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 31: Calibration

    The scanner is calibrated and verified at the factory before shipment. No further manual calibration or verification is required by the customer. However, we recommend annual preventive maintenance, performed by Leica Biosystems Technical Services, to make sure the scanner is operating correctly.

  • Page 32: Z-Stack Scanning

    Z-Stack Scanning The Aperio AT2 DX can create multiple digital images of slide tissue scanned at different focal depths, creating a 3D image that you can visually navigate through much as a microscope user can navigate through different tissue focal depths by using the microscope objective fine and coarse adjustments.

  • Page 33: About The Z-Stack Scanning Window

    When satisfied with the settings, click Apply to apply the settings to the current slide and click the red X at the top of the window to close it. Click Scan on the slide view window to scan the slide. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 34: Advanced Z-Stack Settings

    Type a name for the slide setting. Click Save. Viewing Z-Stacks For information on viewing the 3-dimensional z-stack image, refer to the Aperio ImageScope DX User’s Guide. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 35: Image Quality Review

    Data Entry Data entry is automated using barcodes. When a glass microscope slide is scanned by the Aperio AT2 DX scanner, a barcode on the slide label is decoded to populate data fields in your MDDS. For information on barcode formats supported and on what to do if the scanner cannot read a barcode, see “Barcode Requirement”...

  • Page 36: Using The Autoloader

    Using the AutoLoader The Aperio AT2 DX AutoLoader is a high precision robotic device which automates the tedious and time consuming task of manually loading glass microscope slides into a scanner. As the AutoLoader involves transportation of fragile and often precious glass slides, it is critical that you read and follow these operational guidelines carefully.

  • Page 37: Loading Slides Into The Autoloader

    Console to select the rack you want to use and click the Eject button in the Console to move that rack into load position. The status light should turn green. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...
  • Page 38 Do not try to manually rotate the carousel. Note that the rack has been designed to load slides from a Sakura Tissue-Tek automatic slide stainer and coverslipper slide basket. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 39: Inspecting The Autoloader And Racks

    All grooves within the rack (sides and bottom) must be clean and smooth. Clean the racks as required with compressed air and/or cleaning solvent. Damaged racks should be replaced immediately. Clean racks frequently. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 40: Quality Control And Maintenance

    Off (0) position and disconnect the power cord to the scanner. Maintenance Schedule Call Leica Biosystems Technical Services for assistance if any maintenance task cannot be performed or indicates problems. How Often Task...

  • Page 41: Restart The Scanner Controller Service

    Go to the Console Tools menu and click Set Line Camera Gains. The scanner will automatically place focus points on the slide, check the calibration, then adjust the line camera gains as required. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 42: Clean The Objective

    We recommend cleaning the objective every month. To protect the objective, use gloves when handling it. If you are removing the objective to clean it, store the objective in the objective case supplied by Leica Biosystems when it is outside of the scanner.

  • Page 43: Clean The Scanner

    To clean the AutoLoader carousel cover and access door, use water and a mild detergent. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 44: Cleaning The Autoloader Racks

    Open the AT2 DX covers to gain access to the inside of the scanner. Locate the slide-in-rack sensor amplifier which is to the right of the AutoLoader cover. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...
  • Page 45 OTHER BUTTONS ON THE AMPLIFIER COULD PUT THE SCANNER INTO A STATE THAT CAN ONLY BE REMEDIED BY A SERVICE TECHNICIAN VISIT. Locate the Set button on the amplifier (marked in the illustration). The button is labeled “Set.” Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 46: Change The Aperio Service Account Password And Update Apservice

    Enter the new password and repeat it in the next text box. Click the arrow to proceed. Now you must go to the next section to update the service credentials. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 47: Updating The Aperio Service Credentials

    In the search box at the bottom of the pane, type services.msc. On the Services window, locate ApService: Right click on it and select Properties from the context menu. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...
  • Page 48 On the Log On tab, enter and confirm the password you used for the Aperio service account in “Changing the Aperio Service Account Password” on page 46. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...
  • Page 49 Click Apply. You see a warning that the changes won’t take effect until you stop and restart the service. Click OK on the message box to exit. and select Restart All from the context menu to restart all services. Click the Aperio Service Manager icon Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 50: Troubleshooting

    General Troubleshooting If the information below does not help you find or fix the problem you are having, for further scanner technical support contact your local Leica Biosystems office. Refer to page 3 of this manual for contact information. Symptom...

  • Page 51: Carousel Status Light Red Or Blinking Red

    This light will be green when the scanner is ready for you to remove or load racks (that is, when the racks are in load position). Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 52: Slide On Stage

    Ì error is that someone opened the carousel door while the carousel was moving—in this case, use the Console to rehome the stage. If this does not correct the error, contact Leica Biosystems Technical Services for assistance. Slide on Stage If you see a “slide on stage”...

  • Page 53: Stalled Autoloader Carousel Or Rack Lift

    If that does not work, then power the scanner off and then back on again. in the Windows task bar select Restart Services and To restart the Controller, click the Aperio Service Manager icon then select Restart Controller Service. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 54: Unable To Load Autoloader Carousel

    If you cannot scan: Open the scanner doors. Pull the magnification changer all the way out. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 55: Recovering From A Motion Fault

    Controller Service. This restarts the Controller and also homes the AutoLoader and stage. If you do not recover from this error, the quality of your scans may suffer. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 56: Specifications

    If you plan on not using the scanner for a considerable amount of time, turn it off and unplug it. (This is not necessary for normal day to day use.) If you want to store it, contact Leica Biosystems Technical Services for assistance (See pages 3-4 for contact information.)

  • Page 57: Aperio At2 Dx Hardware Specifications

    In all cases, it is up to the user to load slides which fit easily and smoothly into the AutoLoader rack. Failure to follow this advice may result in damage to specimens and/or the AutoLoader mechanism. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 58: Scanner Control Workstation Software Specifications

    Environment Specifications The Aperio AT2 DX is designed to be operated under the following environmental conditions: indoor use only, MAINS supply voltage fluctuations of up to ± 10% of 100 - 120 V and 220 - 240 V, and transient overvoltages (category II of IEC 60364-4- 443) typically present on the MAINS supply.

  • Page 59: Aperio At2 Dx Safety Instructions

    Pay particular attention to the cords at AC wall plugs and convenience receptacles and at the point where the cord enters the AC/DC adapter. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...
  • Page 60 Cleaning – Do not use liquid cleaners or aerosol cleaners. Use only a damp cloth for cleaning. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 61: Index

    20 viewing scanned image 29 requirements 19 starting 19 viewing scanned slide 30 batch view 22 z-stack scanning 32 best focus layer 32 controls 18 coverslips 16 Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...
  • Page 62 41 coverslips 16 manual scanning 20, 28 labels 16 motion control 54 slide tray access 18 motion fault 55 slide tray, loading 20 slide view window 25 Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...
  • Page 63 52 UPS 56 warning symbols 10 z-stack scanning advanced options 34 basic options 33 best focus layer 32 introduction 32 slide settings 34 Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...
  • Page 64 Index Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...

  • Page 65: Symbols

    The UV lamp within an equilateral triangle is intended to alert you to the presence of UV light within the product’s enclosure that may be of sufficient magnitude to constitute a risk to the operator. Aperio AT2 DX User’s Guide, Revision A © Leica Biosystems Imaging, Inc. 2019...
  • Page 66 www.LeicaBiosystems.com/Aperio...

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