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Leica BIOSYSTEMS Aperio AT2 DX, User Manual

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

15

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

Summary of Contents for Aperio AT2 DX

Page 1: ...Aperio AT2 DX MAN 0351 Revision A 29 July 2019 User s Guide ...

Page 2: ...ederal U S law restricts this device to sale by or on the order of an appropriately licensed healthcare practitioner Ì Ì 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 Inst...

Page 3: ...ai PRC PC 200025 CHINA Tel 86 4008208932 Fax 86 21 6384 1389 Email service cn leica microsystems com Remote Care email tac cn leica microsystems com Danmark Tel 0080052700527 toll free In country Tel 45 44 54 01 01 Email support dk leicabiosystems com Deutschland Leica Biosystems Nussloch GmbH Technical Assistance Center Heidelberger Strasse 17 Nussloch 69226 GERMANY Tel 0080052700527 toll free In...

Page 4: ...C Pinsky lane 3 letter A Saint Petersburg 197101 THE RUSSIAN FEDERATION Tel 8 800 555 49 40 toll free In country Tel 7 812 320 49 49 Email main bioline ru Sweden Tel 0080052700527 toll free In country Tel 46 8 625 45 45 Email support se leicabiosystems com Switzerland Tel 0080052700527 toll free In country Tel 41 71 726 3434 Email support ch leicabiosystems com United Kingdom Tel 0080052700527 tol...

Page 5: ...ystem Startup 12 Changing the McAfee Disk Encryption Password 13 System Shutdown 13 Calibration and Verification 14 3 Preparing for Scanning 15 Training 15 Slide Preparation Tips 15 Tissue Preparation 15 Staining 15 Slide Preparation 15 Coverslips 16 Label Issues 16 Glass Slide Quality Control 17 4 Scanning Slides 18 Scanner Controls 18 Scanning Parameters 19 Starting the Console 19 Barcode Requir...

Page 6: ...ning 32 About the Z Stack Scanning Window 33 Basic Z Stack Settings 33 Advanced Z Stack Settings 34 Saving Z Stack Settings as a Slide Setting 34 Viewing Z Stacks 34 5 Image Quality Review 35 Image Quality Review 35 Data Entry 35 6 Using the AutoLoader 36 Microscope Slide Types 36 Slide Preparation 36 Loading Slides into the AutoLoader 37 Inspecting the AutoLoader and Racks 39 7 Quality Control an...

Page 7: ...ubleshooting 50 General Troubleshooting 50 Carousel Status Light Red or Blinking Red 51 Slide on Stage 52 Stalled AutoLoader Carousel or Rack Lift 53 Unable to Load AutoLoader Carousel 54 Motion Control 54 Magnification Changer Troubleshooting 54 Recovering from a Motion Fault 55 B Specifications 56 Recommended Operating Environment 56 AC Power 56 Transporting or Moving the Aperio AT2 DX 56 Decomm...

Page 8: ... 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 59 for impo...

Page 9: ...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 Ape...

Page 10: ...ns 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 equi...

Page 11: ...ce 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 IE...

Page 12: ...soon as the system is installed so contact your administrator for the current password if it has changed 3 When the Windows login screen appears log in with the Windows user name and password The first time you turn on the workstation you will use the default user name and password User Name aperio Password Sc nscope123 We recommend your administrator change this password as soon as the system is ...

Page 13: ...ter your new password in the New password text box and type it again in the Confirm password text box 3 Click OK You cannot use a password that you ve previously used If you forget the current password contact Leica Biosystems Technical Services for assistance 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...

Page 14: ...canner maintenance you can perform yourself see Chapter 7 Quality Control and Maintenance on page 40 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 31 The monitors provided with the Aperio AT2 DX System have been calibrated at the factory and may requir...

Page 15: ...g 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 ...

Page 16: ...overslips 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 ...

Page 17: ...ision A Leica Biosystems Imaging Inc 2019 17 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 ...

Page 18: ...ing 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 ...

Page 19: ...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 barcod...

Page 20: ...r see AutoLoader Specifications on page 57 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 36 for details on placing slides in racks and using the AutoLoader T...

Page 21: ...tch 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 statu...

Page 22: ... Scan Batch Tasks on page 26 Batch View Click the Batch View icon at the top of the rack view to review all slides included in the scan batch in batch view For any slides for which snapshots have been taken or that have been scanned you see the macro image of the slide Features on this window include Status colors give the status of the slides For example green means the slide was scanned and the ...

Page 23: ...single slide view for selected slides Ejects the stage or the rack Captures calibration image Starts the scan Takes a snapshot Selects all slides in all racks Selects all slides that are in scan batch Sets starting slide Selects all slides that failed to scan Excludes all selected slides from scan batch Marks all selected slides for rescanning Removes viewed indicator Automatically sets focus poin...

Page 24: ...ge 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 Refer to Chapter 5 Image Quality Review on page 35 To see this complete list of status colors and their meaning go to the Help menu and select Slide Status Legend Batch Scann...

Page 25: ...or over the scanned slide in rack view or batch view You see the View Slide icon 2 Click this icon to see the slide in the slide view window On the slide view window you can use the tools at the bottom of the window to prepare this slide for rescanning if necessary See Using Snapshots on page 29 for more information on using this window To see the slide in even more detail click the magnifying gla...

Page 26: ...ou took snapshots and click the View Slide icon on one of the slides to view the slides in the slide view window 4 You can fine tune scanning parameters in the slide view window When finished with snapshot review click the Scan button to start scanning the slides See Manually Scanning a Slide on page 28 for more information on using snapshots and the slide view window Scan Batch Tasks Here are som...

Page 27: ...can batch y y To exclude all slides in a rack from the scan batch click the top of the rack to select all slides in the rack then right click and select Exclude selected slides y y To remove a group of selected slides from the current batch place the cursor on a group of selected slides then right click and select Exclude selected slides Select unselect slides y y To select a single slide to mark ...

Page 28: ...ures only available when manually scanning a slide include Creating a calibration image see Calibration on page 31 Auto focusing focus points before the scan see Working with Focus Points on page 30 To place the slide on the scanner stage 1 First eject the slide tray by clicking the Eject Stage button at the bottom of the window Do this to initiate a manual scan even if the stage is already ejecte...

Page 29: ...snapshots Use the zoom slider to zoom into the image click the blue dot to zoom into the entire macro image the red dot to zoom into the maximum scan area the red box and the green dot to zoom into the scan area the green box If you want to Do this Set the scan area The area of the slide that will be scanned is marked by a green box this is limited by the red box the maximum scan area To reset the...

Page 30: ...ide for the scan click in the slide view window Save slide settings If you have changed scanning parameters on this slide you can save the parameters as a slide setting Type a name in the Slide Settings box and click the Save icon You will then be able to apply these settings to selected slides by selecting them from the Slide Settings drop down list Scan z stacks For information on z stack scanni...

Page 31: ...ts If you are manually scanning a slide on the stage you can tell the scanner to automatically focus the focus points before scanning This allows you to test that all focus points can be focused Click the Auto Focus All Focus Points icon Calibration The scanner is calibrated and verified at the factory before shipment No further manual calibration or verification is required by the customer Howeve...

Page 32: ...o dark or displays shadowing the light may need replacing If the calibration image shows tissue move the blue diamond calibration point out of the tissue area and make a new calibration image 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...

Page 33: ...as a slide setting to use in the future on other slides by clicking the Create button See Saving Z Stack Settings as a Slide Setting on page 34 For a visual reminder of how the z stack layers are arranged and for tips on using the controls hover over the Info icon in either the basic or the advanced configuration sections Basic Z Stack Settings Configure the basic z stack scan settings by telling ...

Page 34: ...ck settings require a thorough understanding of the tissue or type of tissue you want to create a z stack for For example if you know that the best detail in the tissue occurs above the best focus layer and if you are not interested in the tissue below the best focus layer place the best focus layer at the bottom of the stack and scan layers above the best focus layer Saving Z Stack Settings as a ...

Page 35: ...ners provide a macro image a low resolution image of the entire slide that also provides a green outline of the scanned image 1 From your MDDS open the scanned images in Aperio ImageScope DX 2 Look at the entire image to see if the entire tissue sample was scanned 3 Adjust the zoom level by using the Zoom tool Click in the thumbnail in the Aperio ImageScope DX window and pan the image All eSlide i...

Page 36: ... by the AutoLoader The AutoLoader for your scanner can be used with 1 inch x 3 inch 2 54 cm x 7 62 cm slides Under no circumstances should you attempt to modify the slide AutoLoader slide tray insert or system software configuration to enable scanning of a different slide format as this may result in damage to your scanner and or slides For detailed specifications on the exact size of slides that ...

Page 37: ... when you insert the rack into the AutoLoader and the coverslip up DO NOT ATTEMPT TO SCAN DAMAGED SLIDES AS DOING SO MAY DAMAGE THE APERIO AT2 DX SCANNER Loading Slides into the AutoLoader 1 In the Console select the rack position you want to use and click the Eject button on that rack this moves that rack position to the front of the carousel where you can remove or load a rack 2 Open the scanner...

Page 38: ...e rack with the slide labels facing towards the rear of the rack and the coverslips up Note The slide racks can be loaded into any position on the AutoLoader This is possible because the scanner automatically senses which AutoLoader positions contain a slide rack However you must use the Console to move the rack position you want to use to load position before removing or replacing a rack Do not t...

Page 39: ...nner access door The slide rack positions are indicated on the Console display and the scanner LCD display The scanner LCD displays Scanner Ready Inspecting the AutoLoader and Racks It is important to keep the AutoLoader rack the AutoLoader compartment and the scanning stage slot the area on the scanning stage onto which the AutoLoader places the slide clean at all times Prior to each AutoLoader r...

Page 40: ...form a Presnap on page 41 Daily Verify display function Open a slide image in Aperio ImageScope DX to verify that the monitors are working properly Verify that there are no flickering or artifacts on the display and no damage to the display Monthly Clean objective See Clean the Objective on page 42 Monthly Set line camera gains See Set Line Camera Gains on page 41 Monthly Clean slide tray on stage...

Page 41: ...esnap window appears and the scanner stage moves to the access position 2 Clean an unused blank slide with no markings 3 Load the blank slide into the slide tray with the coverslip up and label to the front Make sure the slide is inserted so that the front edge is even with the edge of the slide tray 4 In the New Presnap window click OK 5 When the scanner status screen reads Scanner Ready and the ...

Page 42: ...ove artifacts you will need to remove the objective and clean it more thoroughly outside of the scanner To remove the objective place two fingers of one hand under the objective to protect it and using your other hand carefully unthread the objective rotating to the left or counterclockwise if viewing from below without touching the glass lens as you rotate it When the objective is free of the mou...

Page 43: ...y protection and procedures pick up and wipe up the visible pieces of any broken slides Please contact Leica Biosystems Technical Services for advice before operating the scanner Cleaning the Slide Tray on the Stage Gently wipe the slide tray from the top to the bottom with a lint free tissue After initial wipe down final polishing can be done using a micro fiber cloth Only if necessary use a gent...

Page 44: ...der to the scanning stage is precisely positioned This procedure should be done every six months This will be done as part of your annual maintenance visit by Leica Biosystems Technical Services First you will restart the scanner Controller service This initializes the scanner and puts the stage and AutoLoader in the home position 1 Turn the scanner off and back on Press the main power switch on t...

Page 45: ...ng the amplifier cover latch is at the top of the amplifier Pull it toward you to open the cover In this illustration the cover is open Be very careful not to press any buttons on the amplifier other than the Set button PRESSING OTHER BUTTONS ON THE AMPLIFIER COULD PUT THE SCANNER INTO A STATE THAT CAN ONLY BE REMEDIED BY A SERVICE TECHNICIAN VISIT 4 Locate the Set button on the amplifier marked i...

Page 46: ...d If you change the password you must also update the credentials of the ApService service that runs under the Aperio service account or the scanner will not operate Perform the procedures below on the Aperio AT2 DX control station Changing the Aperio Service Account Password To change the password for the Aperio service account 1 Log in as the Aperio service account user The default Aperio servic...

Page 47: ...rvice account password you must also update the credentials for the ApService service that runs under that account Follow these steps to update the services credentials 1 Click the Start button on the Windows task bar 2 In the search box at the bottom of the pane type services msc 3 On the Services window locate ApService 4 Right click on it and select Properties from the context menu ...

Page 48: ...e button 7 On the Select User window go to the Enter the object name to select text box If the Aperio service account user name is not already filled in type it AperioSvc Next click the Check Names button and the full Aperio service account specification is filled in 8 Click OK 9 On the Log On tab enter and confirm the password you used for the Aperio service account in Changing the Aperio Service...

Page 49: ...Quality Control and Maintenance 10 Click Apply You see a warning that the changes won t take effect until you stop and restart the service 11 Click OK on the message box to exit 12 Click the Aperio Service Manager icon and select Restart All from the context menu to restart all services ...

Page 50: ... and says Start Controller Service click the entry to restart it Console or LCD displays Failed to move stage or Check stage locks If the stage is locked you cannot scan Contact Leica Biosystems Technical Services for assistance Trouble scanning a particular slide 1 Is the slide tissue extremely thick or thin 2 Is the slide extremely dark or faint Use a parameter set such as faint 3 Is the label l...

Page 51: ...tor display click on a clear glass area without tissue and verify that location is clear Then move the blue diamond calibration point to that clear area 3 If the calibration image contains coverslip or other defects try the parameter set coverslip to help the scanner ignore edges or defects If the problem persists either select the scan area manually or adjust the area of interest for all slides t...

Page 52: ...ned 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 error message it means that the scanner tried to load a slide from the AutoLoader but a slide is already on the stage In most cases this is the result of an opera...

Page 53: ...ote the label on the pusher assembly Make sure that the dotted lines indicated by the red arrows in the illustration above line up with each other this ensures the pusher is fully retracted Stalled AutoLoader Carousel or Rack Lift If the AutoLoader carousel or rack lift stall during use first look for any obstructions including the rack or slides preventing the axis from moving and clear the obstr...

Page 54: ...r Service Motion Control The Console Motion Control options allow you to move the scanner stage extend it to the stage access position retract it to move the stage back inside the scanner and home the stage move the stage back to its normal position under the objective Go to the Console Tools menu and select Motion Control Then select the action you want to perform Magnification Changer Troublesho...

Page 55: ... AutoLoader shuts down because of improperly prepared slides or improper use you also may need to home the stage To recover from this error 1 Verify the magnification changer is completely pulled out The scanner cannot start with the magnification changer in See Magnification Changer Troubleshooting on page 54 2 Turn the scanner off and back on Press the main power switch on the back of the scanne...

Page 56: ...le power supply rated at 2200VA with power conditioning that protects connected loads from electrical surges and spikes lightning and other power disturbances The UPS allows the scanner to run for an additional 30 minutes giving you time to safely shut it down Transporting or Moving the Aperio AT2 DX If you need to transport the scanner either to move it to a new location or to return it to your d...

Page 57: ... power factor corrected 100vAC 240VAC 50Hz 60Hz 2 amp See AC Power on page 56 for UPS recommendations Monitor Calibrated LCD monitor AutoLoader Specifications The AutoLoader can contain up to 400 1 inch x 3 inch 2 54 cm x 7 62 cm slides and has been designed to work with many commonly available glass microscope slides The dimensions of a slide must be such that each slide fits easily into an AutoL...

Page 58: ...onment 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 Also refer to the table below Feature Details Transportation storage temperature 22 degrees Fahrenheit ...

Page 59: ... should be placed in an area where air circulation is not impeded 5 Biosafety Procedures Please refer to your institution s biosafety policies and procedures regarding the proper handling of tissue and other potentially hazardous materials in connection with the use of this device 6 Water and Moisture Do not use the scanner near water for example near a water bath wash bowl kitchen sink or laundry...

Page 60: ... Any mounting of the scanner needs to follow manufacturer s installation instructions Do not place anything on top of the scanner 16 Moving The scanner should be moved with care Quick stops excessive force and uneven surfaces may cause the product to overturn Removal of the scanner may void the applicable product warranty contact Leica Biosystems Imaging for advice 17 Servicing Refer all servicing...

Page 61: ...manually entering 20 requirements 19 batch view 22 best focus layer 32 C calibration 14 31 image 51 making calibration image 31 camera gains setting 41 Console automatically adding focus points 30 batch view 22 focus points 30 adding 31 automatically focusing 31 deleting 31 moving 31 including slides in batch 21 interactive scan 26 saving slide settings 30 selecting slides 21 setting start slide 3...

Page 62: ...g controller 41 schedule 40 setting camera gains 41 manual scanning 20 28 motion control 54 motion fault 55 N network connection 13 O objective cleaning 42 P preparing slides staining 15 preset scanning parameters 19 presnap 41 51 problems 50 R recalibrating AutoLoader slide in rack sensor 44 regulatory compliance 11 repacking 56 restarting controller service 41 retracting stage 54 S safety instru...

Page 63: ...ftware 58 staining 15 storing 56 T Technical Support 9 tissue preparation 15 training 15 transporting 56 troubleshooting 50 AutoLoader 51 AutoLoader stalled 53 AutoLoader status light 51 magnification changer 54 motion fault 55 slide on stage error 52 U UPS 56 W warning symbols 10 Z z stack scanning advanced options 34 basic options 33 best focus layer 32 introduction 32 slide settings 34 ...

Page 64: ...Aperio AT2 DX User s Guide Revision A Leica Biosystems Imaging Inc 2019 64 Index ...

Page 65: ... waste disposal Caution 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 ho...

Page 66: ...www LeicaBiosystems com Aperio ...

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