Scanscope Cs guide 3h1440

ScanScope CS ’s Guide

Copyright © 2006-2013 Aperio Part Number/Revision: MAN-0030, Revision M Date: 24 April 2013 This document applies to eSlide Manager Release 12 and later. All rights reserved. This document may not be copied in whole or in part or reproduced in any other media without the express written permission of Aperio. Please note that under copyright law, copying includes translation into another language. Please refer to Aperio Copyright Usage Requirements on aperio.com for additional information concerning copyrights, services, products, technologies, and processes described in this document that may be the subject of Aperio Intellectual Property rights and are not licensed hereunder.

Resources For the latest information on Aperio products and services, please visit the Aperio website at: http://www.aperio.com. 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 Aperio or for other advanced instruction. Aperio Field Representatives should be ed immediately for assistance in the event of any instrument malfunction. Installation of hardware should only be performed by a certified Aperio Service Engineer. ImageServer is intended for use with the SVS file format (the native format for eSlides created by scanning glass slides with the ScanScope scanner). Educators will use Aperio software to view and modify eSlides in Composite WebSlide (CWS) format. Trademarks and Patents Aperio and ScanScope are ed trademarks and Genie, ImageScope, Aperio ePathology Solutions, eSlideShare, and eSlide Manager are trademarks of Aperio. All other trade names and trademarks are the property of their respective holders. Aperio 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. Information Headquarters

Europe Office

Asia Office

Aperio

Aperio UK Ltd

Aperio KK

Vista, CA 92081

167 Banbury Road

3-3-17, Surugadai

1360 Park Center Drive United States

Prama House

Summertown

UZ Building 5F

Kanda, Chiyoda-ku

Oxford OX2 7HT

Tokyo, Japan 101-0062

Tel: 866-478-4111 (toll free)

Tel: +44 (0) 1865 339651

Tel: +81-3-3259-5255

Customer Service:

Customer Service:

Customer Service:

Email: [email protected]

Email: [email protected]

United Kingdom

Fax: 760-539-1116

Tel: 866-478-4111 (toll free)

Fax: +44(0) 1865 339301

Tel: +44 (0) 1865 339651

Fax: +81-3-3259-5256

Email: [email protected]

Technical :

Technical :

Technical :

Direct International Tel: 1 (760) 539-1150

Email: [email protected]

Email: [email protected]

US/Canada Tel: 1 (866) 478-3999 (toll free) US/Canada/Worldwide Email: [email protected]

ii | ScanScope CS 's Guide

Direct International Tel: 1 (760) 539-1150

Direct International Tel: 1 (760) 539-1150

Contents 1 | SAFETY AND SPECIFICATIONS.................................................................... 1 If You Need Help .......................................................................................................1 Symbols and Warnings .............................................................................................2 Intended Use...............................................................................................................2 Instrument Warnings ................................................................................................4 Safety Instructions .....................................................................................................4 Installation Specifications .......................................................................................9 Recommended Operating Environment .............................................................9 Work Surface ...........................................................................................................9 AC Power ............................................................................................................... 11 Local Area Network (LAN) ................................................................................. 11 Telephone .............................................................................................................. 11 Stage Locks ............................................................................................................ 11 Power Supply Shipping Block ............................................................................ 11 ScanScope Hardware Specifications .................................................................... 12 Software Specifications .......................................................................................... 13 System Requirements ............................................................................................. 13 Monitor Requirements ......................................................................................... 13 Workstation – Viewing Station ........................................................................... 13 Environment Specifications ................................................................................... 14 Compliance Specifications..................................................................................... 15 Input and Output Connections ............................................................................. 15 ScanScope............................................................................................................... 15 LCD Monitor ......................................................................................................... 16 Stocker-Yale/Techniquip 21DC Illuminator Light Source............................... 16 ScanScope External Interconnections ................................................................. 16 Transporting or Moving the ScanScope .............................................................. 16 Removing and Installing the Power Supply Shipping Block ......................... 17 Locking and Unlocking the Stage ....................................................................... 17 Long Term Storage .................................................................................................. 20 Equipment Maintenance ........................................................................................ 20 Cleaning Objectives .............................................................................................. 20 Light Source Bulb Replacement .......................................................................... 22 AC Line Fuse Replacement ................................................................................. 22

ScanScope CS 's Guide| iii

Contents

Cleaning the ScanScope Casing .......................................................................... 22 Cleaning the ScanScope Interior ......................................................................... 22 2 | SCANSCOPE SYSTEM OVERVIEW ............................................................... 23 Scanning Slides........................................................................................................ 24 Oil-Immersion Scanning Option .......................................................................... 24 Viewing and Sharing eSlides - ImageScope ...................................................... 24 3 | SCANSCOPE STARTUP AND SHUTDOWN ..................................................... 25 System Startup ......................................................................................................... 25 System Shutdown .................................................................................................... 26 4 | SCANNING SLIDES................................................................................ 27 Manual and Automatic Functions ........................................................................ 27 Slide Preparation Tips ............................................................................................ 27 Tissue Preparation ................................................................................................ 27 Slide Preparation .................................................................................................. 28 ScanScope Controls ................................................................................................. 29 Using the Start and Stop Buttons ....................................................................... 29 Single-slide Automatic Scan ................................................................................. 30 What Happens During the Scan?.......................................................................... 30 Compressing and Storing eSlides....................................................................... 31 Multiple Slide Scanning Using the 5-Slide Tray............................................... 31 Oil-Immersion Scanning ........................................................................................ 32 Working with a Magnification Changer ............................................................. 32 Disengaging the Mag Changer ........................................................................... 33 Engaging the Mag Changer ................................................................................ 34 Using the ScanScope Console ............................................................................... 34 Snapshot Review .................................................................................................. 34 2x3 Slide Scanning ................................................................................................ 34 Configuration Options ......................................................................................... 34 5 | CALIBRATION AND VERIFICATION ............................................................. 35 6 | VIEWING ESLIDES WITH IMAGESCOPE ......................................................... 37 Opening and Viewing an eSlide .......................................................................... 37 Navigation................................................................................................................. 39 Changing Viewing Magnification........................................................................ 39 Zoom Navigation.................................................................................................. 40 Immediate Maximum Zoom ............................................................................... 40 For More Information ............................................................................................. 40

iv | ScanScope CS 's Guide

Contents

APPENDIX A | OIL-IMMERSION SCANNING ...................................................... 41 Switching from Dry to Oil Scanning ................................................................... 41 1 – Remove Dry Scan Slide Tray ......................................................................... 41 2 – Configure the ScanScope for Oil Scanning .................................................. 41 3 – Clean the Oil Scan Slide Tray, the Slide (If Coverslipped), and the Objective ................................................................................................................ 42 4 – Load the Slide into the Oil Scan Slide Tray ................................................. 42 5 – Place Oil on the Slide ...................................................................................... 42 Using the ScanScope Console to Scan ................................................................. 43 Starting the Console ............................................................................................. 43 Selecting Magnification and Scan Area ............................................................. 44 Setting Focus Points.............................................................................................. 47 Taking a Calibration Image ................................................................................. 50 Scanning ................................................................................................................. 50 Oil Scanning Tips .................................................................................................. 51 Switching from Oil to Dry Scanning ................................................................... 54 1 – Remove Oil Scan Slide Tray .......................................................................... 54 2 – Clean the Oil Scan Slide Tray, the Slide (If Coverslipped), and the Objective ................................................................................................................ 54 3 – Configure the ScanScope for Dry Scanning ................................................ 54 4 – Load the Slides into the Dry Scan Slide Tray .............................................. 55 5 – Start the Console ............................................................................................. 55 6 – Insert the Prepared Dry Scan Slide Tray ..................................................... 55 7 – Select Magnification Level ............................................................................. 55 8 – Start Dry Scanning .......................................................................................... 55 APPENDIX B | REPLACING THE FIBER-OPTIC ILLUMINATOR LIGHT BULB.................... 57 APPENDIX C | REPLACING THE AC LINE FUSE ................................................... 61 APPENDIX D | RECOVERING FROM A MOTION FAULT .......................................... 63 APPENDIX E | TROUBLESHOOTING................................................................. 65 INDEX................................................................................................... 67

ScanScope CS 's Guide | v

Contents

vi | ScanScope CS 's Guide

1 | Safety and Specifications This manual applies to both the ScanScope CS and the ScanScope CSO models. Differences between the two models are noted throughout.

Please read this chapter before using your ScanScope, and be sure to save these instructions for future reference! The ScanScope® CS and CSO (oil scanning option) slide scanners have been manufactured to the highest quality standards. Following these safety guidelines will protect your unit and provide optimal operation. For an overview of the ScanScope, refer to the next chapter. Note that annual servicing is required to maintain ScanScope performance. The ScanScope scanner is intended to be used to digitize traditional glass microscope slides through a scanning process and to compress and view the digital images (known as eSlides) using Aperio software applications. 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 of slide preparation, processing, storage, and disposal. Use this equipment only for this purpose and in the manner described in this guide.

If You Need Help Refer to “Appendix E |Troubleshooting” on page 65 for troubleshooting tips. For further ScanScope technical , your local Aperio office. Refer to page ii of this manual for information.

ScanScope CS 's Guide | 1

1 |Safety and Specifications

Symbols and Warnings The following symbols are used throughout the documentation to alert you to potential danger in operating the ScanScope. Symbol

Description The exclamation point within an equilateral triangle is intended to

alert you to the presence of important operating and maintenance (servicing) instructions.

Le point d'exclamation dans un triangle équilatéral vise à avertir l'utilisateur qu'il s’agit d’instructions d'utilisation et d'entretien importantes.

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.

Le symbole de l'éclair avec la pointe de flèche dans un triangle équilatéral vise à avertir l'utilisateur que le boîtier du produit

présente une « tension dangereuse » non isolée d’une amplitude suffisante pour constituer un risque d'électrocution.

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.

Le symbole d’une surface plane et de vagues dans un triangle

équilatéral vise à avertir l'utilisateur de la présence de surfaces chaudes qui peuvent ca des brûlures.

Intended Use The ScanScope® System is an automated digital slide creation and viewing device. It is intended for research use only. Not for use in diagnostic procedures. This manual is intended for customers in the United States and other non-European Union areas and reflects the intended use of the ScanScope product manufactured and labeled for your specific geographical region. If you have received the incorrect version of the manual for your geographical location, please do not use this manual. Instead, your Aperio Sales Representative for information on obtaining the correct manual.

2 | ScanScope CS 's Guide

1 |Safety and Specifications

IMPORTANT If the ScanScope 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. Si le ScanScope est utilisé d'une autre manière que celle spécifiée dans cette documentation, la protection assurée par l’appareil risque d’être altérée. AVERTISSEMENT : Cet appareil génère, utilise et peut émettre une énergie de radiofréquences. S’il n’est pas installé et utilisé conformément aux instructions de ce guide, il peut brouiller les communications radio. Cet appareil a été testé et déclaré conforme aux limites des appareils numériques de Classe A (selon la sous-partie B de la section 15 des règlements de la FCC), qui sont destinés assurer une protection raisonnable contre un brouillage préjudiciable lorsque l'appareil est utilisé dans un milieu commercial.

ScanScope CS 's Guide | 3

1 |Safety and Specifications

Instrument Warnings CAUTION MISE EN GARDE RISK OF ELECTRIC SHOCK DO NOT OPEN RISQUE DE CHOC ÉLECTRIQUE

NE PAS OUVRIR WARNING: SHOCK HAZARD - DO NOT OPEN AVERTISSEMENT : RISQUE DE CHOC ÉLECTRIQUE - NE PAS OUVRIR WARNING: SHOCK HAZARD - DO NOT OPEN CAUTION: TO REDUCE THE RISK OF ELECTRIC SHOCK DO NOT REMOVE ANY COVER OR . NO SERVICEABLE PARTS INSIDE. REFER SERVICING TO QUALIFIED SERVICE PERSONNEL.

AVERTISSEMENT : RISQUE D’ÉLECTROCUTION - NE PAS OUVRIR MISE EN GARDE : POUR RÉDUIRE LE RISQUE DE CHOC ÉLECTRIQUE, NE RETIRER AUCUN COUVERCLE OU PANNEAU. NE CONTIENT

AUCUNE PIÈCE RÉPARABLE PAR L'UTILISATEUR. FAIRE APPEL À UN TECHNICIEN QUALIFIÉ POUR TOUT ENTRETIEN.

WARNING: TO REDUCE THE RISK OF FIRE OR ELECTRIC SHOCK, DO NOT EXPOSE THE SCANSCOPE TO RAIN OR MOISTURE.

MISUSE OF ELECTRICAL EQUIPMENT CAN CAUSE ELECTROCUTION, BURNS, FIRES, AND OTHER HAZARDS.

AVERTISSEMENT : POUR RÉDUIRE LES RISQUES D'INCENDIE OU DE

CHOC ÉLECTRIQUE, NE PAS EXPOSER CET APPAREIL À LA PLUIE OU L'HUMIDITÉ.

UN MAUVAIS USAGE D’UN APPAREIL ÉLECTRIQUE PEUT

PROVOQUER L’ÉLECTROCUTION, DES BRÛLURES ET D’AUTRES DANGERS.

Safety Instructions Basic safety precautions should always be taken, including all those listed below. Read All Instructions – All safety and operating instructions must be read before operating the product. Retain All Instructions – All safety and operating instructions must be retained for future reference. Il faut toujours prendre les mesures de sécurité de base, y compris celles énumérées cidessous.

4 | ScanScope CS 's Guide

1 |Safety and Specifications

Lisez toutes les instructions - Vous devez lire toutes les consignes de sécurité et d'utilisation avant d 'utiliser l’appareil. Conservez toutes les instructions - Vous devez conserver toutes les instructions à des fins de consultation ultérieure. 1.

Heed All Warnings – All warnings on the ScanScope and those listed in the operating instructions must be adhered to. Tenez compte des avertissements – Vous devez respecter tous les avertissements à propos du ScanScope ainsi que de ceux indiqués dans les instructions d’utilisation.

2.

Follow All Instructions – All operating and ScanScope usage instructions must be followed. Suivez toutes les instructions – Vous devez suivre toutes les instructions d’utilisation du ScanScope.

3.

Heat – The ScanScope must be situated away from any heat sources such as radiators, heat s, stoves, or other products that produce heat. Chaleur – Le ScanScope doit être placé loin de toutes sources de chaleur telles que les radiateurs, les bouches de chaleur, les cuisinières ou autres appareils produisant de la chaleur.

4.

Ventilation – Slots and openings in the ScanScope are provided for ventilation. They ensure reliable operation of the product, keeping it from overheating. These openings must not be blocked nor covered during operation. Keep air openings free of lint, hair, fluff, etc. This product should not be placed into a rack unless proper ventilation is provided through following the manufacturer’s recommended installation procedures. Ventilation – Le ScanScope est doté de fentes et d’ouvertures de ventilation. Elles assurent le fonctionnement fiable de l'appareil, en l’empêchant de surchauffer. Ces ouvertures ne doivent pas être bloquées, ni couvertes pendant l’utilisation. Gardez les ouvertures libres de charpie, de cheveux, de peluches, etc. Cet appareil ne doit pas être placé dans un bâti à moins qu’une ventilation adéquate ne soit fournie en suivant le mode d’installation recommandé par le fabricant.

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. Procédure de biosécurité – Veuillez vous référer aux politiques et aux procédures de biosécurité de votre établissement relativement à la manipulation adéquate de tissus et autres matières potentiellement dangereuses en lien avec l’utilisation de cet appareil.

6.

Water and Moisture – Do not use the ScanScope near water—for example, near a water bath, wash bowl, kitchen sink, or laundry tub; in a wet basement; or near an open pool of water or the like. If the ScanScope

ScanScope CS 's Guide | 5

1 |Safety and Specifications

becomes wet, unplug it before touching it. Eau et humidité – N’utilisez pas le ScanScope près de l’eau, par exemple, un bain-marie, une cuvette, un évier, une cuve de lessivage, dans un sous-sol humide ou près d’un bassin ouvert. Si le ScanScope est mouillé, débranchez-le avant de le toucher. 7.

Attachments – Do not use any attachments not recommended by the product manufacturer as they may cause hazards. Accessoires – N’utilisez pas d’accessoires non recommandés par le fabricant de l'appareil, car ils peuvent ca un risque.

8.

Power Sources – The ScanScope must be operated from the type of power source indicated on the marking label and in the installation instructions. If you are not sure of the type of power supplied to your facility, consult your local power company. Check that the voltage setting matches the electrical supply voltage. Alimentation – Le ScanScope ne doit être utilisé qu’avec la source d’alimentation spécifiée sur l’étiquette signalétique et les instructions d’installation. En cas de doute sur le type de courant fourni à votre établissement, consultez votre compagnie d'électricité locale. Vérifiez si le réglage de la tension correspond à la tension d’alimentation électrique.

9.

Grounding and Polarization – The ScanScope is equipped with a polarized AC plug with integral safety ground pin. Do not defeat the safety ground in any manner. Mise à la terre et polarisation – Le ScanScope est muni d’une fiche c.a. polarisée à intégré de mise à la terre de sécurité. En aucun cas, ne retirez la mise à la terre de sécurité.

10. Power Cord Protection – Power supply cords must be routed so that they are not likely to be walked on nor pinched by items placed upon or against them. Pay particular attention to the cords at AC wall plugs and convenience receptacles and at the point where the cord enters the ScanScope. Protection du cordon d'alimentation – Les cordons d'alimentation doivent être placés de manière à ce qu'il y ait peu de risque qu'une personne marche dessus ou qu'ils soient coincés par un meuble ou un autre objet. Veillez particulièrement à protéger le cordon près des prises murales c.a., des prises utilitaires et de sa sortie de l'appareil. 11. Lightning – For added protection for this ScanScope during a lightning storm, or when it is left unattended and unused for long periods of time, unplug it from the AC wall outlet. This will prevent damage to the product due to lightning and power line surges. Éclairage – Pour protéger davantage l’appareil, débranchez le cordon du ScanScope de la prise murale c.a. pendant un orage ou s’il est laissé sans surveillance ou qu’il n’est pas utilisé pendant une longue période. Cette mesure empêchera que la foudre ou qu’une surtension cause des dommages à l'appareil.

6 | ScanScope CS 's Guide

1 |Safety and Specifications

12. Power Overloading – Do not overload AC wall outlets, extension cords, or integral convenience outlets as this can result in a fire or electric shock hazard. Surcharge – Ne surchargez pas les prises murales c.a., les rallonges ou les prises utilitaires intégrées car ceci risquerait de provoquer un incendie ou une électrocution. 13. Operating Environment – Observe these basic safety requirements: Milieu de fonctionnement – Respectez ces consignes de sécurité de base :

 Do not operate the ScanScope out of doors. N’utilisez pas le ScanScope à l’extérieur.

 Do not use where aerosol sprays are being used or where oxygen is being istered. Ne l'utilisez pas à proximité d'aérosols ou d’endroits où de l’oxygène est istré.

 Do not let the ScanScope or its cables or accessories come into with surfaces which are too hot to touch. Ne laissez pas le ScanScope ou ses câbles et ses accessoires entre en avec des surfaces qui sont trop chaudes au toucher.

 Do not place anything on top of the ScanScope. Ne placez rien sur le ScanScope. 14. Object and Liquid Entry – Never push objects of any kind into the ScanScope through openings as they may touch dangerous voltage points or short-out parts that could result in a fire or electric shock. Never spill liquid of any kind on the ScanScope. Pénétration d'objets et de liquides – N'introduisez jamais aucun objets par les orifices du ScanScope. Ils pourraient toucher des points sous tension dangereux et court-circuiter des pièces et provoquer ainsi un incendie ou une électrocution. Veillez à ne jamais renverser de liquide dans l'appareil. 15. Accessories – Do not place the ScanScope on an unstable cart, stand, tripod, bracket, or table. The ScanScope may fall, causing serious injury and damage to the product. Any mounting of the ScanScope needs to follow manufacturer’s installation instructions. Do not place anything on top of the ScanScope. Accessoires – Ne placez pas le ScanScope sur un chariot, un socle, un trépied, un ou une table qui n’est pas stable. L'appareil pourrait tomber et provoquer une blessure grave ou être endommagé. Si l'appareil est fixé à un , assurez-vous que les instructions d'installation du fabricant sont respectées. 16. Moving – The ScanScope should be moved with care. Quick stops, excessive force, and uneven surfaces may cause the product to overturn. Removal of the ScanScope may void the applicable product warranty— Aperio for advice. Déplacement – Le ScanScope doit être déplacé avec prudence. Un arrêt brusque, une force excessive ou une surface inégale peuvent faire tomber ScanScope CS 's Guide | 7

1 |Safety and Specifications

l’appareil. Le déplacement du ScanScope peut annuler la garantie – communiquez avec Aperio pour obtenir des conseils. 17. Servicing – Refer all servicing to qualified service personnel. Entretien – Faites appel à un technicien qualifié pour tout entretien. 18. Damage Requiring Service – Unplug the ScanScope from the wall AC outlet and refer servicing to qualified service personnel under the following conditions: Dommage nécessitant un entretien– Débranchez le ScanScope de la prise murale c.a. et faites appel à un technicien qualifié dans les cas suivants :

 When the AC cord or plug is damaged. Le cordon c.a. ou la fiche est endommagé.

 If liquid has been spilled or objects have fallen into the ScanScope. Du liquide a été renversé sur l’appareil ou des objets sont tombés dans l’appareil.

 If the ScanScope has been exposed to rain or water. L’appareil a été exposé à la pluie ou à l’humidité.

 If the ScanScope does not operate normally (when you are following operating instructions). L’appareil ne fonctionne pas normalement (lorsque vous suivez les instructions d’utilisation).

 If the ScanScope has been dropped or damaged in any way. L’appareil est tombé ou est endommagé de quelque façon que ce soit.

 When the ScanScope exhibits a distinct change in performance. This indicates a need for service. L’appareil présente des changements visibles de performances. Cela indique la nécessité d’un entretien. 19. Replacement Parts – When replacement parts are required, be sure the service technician has used replacement parts specified by the manufacturer. Unauthorized substitutions may result in fire, electric shock, or other hazards. Pièces de rechange – Si des pièces doivent être remplacées, assurez-vous que le technicien utilise bien les pièces de rechange prescrites par le fabricant. L'utilisation des pièces non autorisées peut entraîner un risque d'incendie ou de choc électrique, ou d'autres dangers. 20. Operational Check – Upon completion of any repairs to this ScanScope, ask the service technician to perform operation checks to determine that the product is in proper operating condition. Vérification du fonctionnement – Après toute réparation du ScanScope, demandez au technicien d’effectuer les vérifications nécessaires pour s'assurer que l'appareil est en bon état de fonctionnement. 21. Cleaning – Do not use liquid cleaners or aerosol cleaners. Use only a damp cloth for cleaning.

8 | ScanScope CS 's Guide

1 |Safety and Specifications

Installation Specifications CAUTION: Two people are required for lifting the ScanScope. MISE EN GARDE : Il faut deux personnes pour soulever le

ScanScope.

Installation and setup of the ScanScope should only be performed by a trained Aperio Field Service Representative. L'installation et le réglage du ScanScope doivent être effectués uniquement par un représentant qualifié de service sur site d’Aperio.

Recommended Operating Environment Typically, the ScanScope work area should have good lighting and the air should be clean and cool. See “Environment Specifications” on page 14 for details.

Work Surface The work surface must be level to within 1 degree with minimum dimensions of 4 feet (1.2 meters) long by 30 inches (76.2 centimeters) deep. The work surface should be of standard desk or workbench height, must be heavy duty and very stable (no shaking or vibrations) and must be able to easily 75 pounds (34 kilograms). Do not place the ScanScope instrument next to an instrument that vibrates during operation. Cable access either between the work surface and wall or a cable cutout must be provided if the AC power or computer is below the level of the work surface. A minimum clearance of 18 inches is required between the back of the instrument and the nearest facing wall in order to allow for access to the On/Off switch. Figure 1 illustrates the proper ScanScope work surface.

ScanScope CS 's Guide | 9

1 |Safety and Specifications

Figure 1: Front and top views of the ScanScope working area

10 | ScanScope CS 's Guide

1 |Safety and Specifications

AC Power CAUTION: If the power cord supplied with this product does not match the wall plug configuration, do not use. a qualified electrician to obtain the proper cord.

MISE EN GARDE : Si le cordon d'alimentation fourni avec ce produit ne

correspond pas à la configuration de la prise murale, ne l'utilisez pas. ez un électricien qualifié pour obtenir le cordon approprié.

At least one grounded dual AC wall socket (3 conductor) is recommended for a power source. Connected to that is a surge protected 4-6 outlet power strip to be provided in close proximity to the work surface and easily accessible. To protect the ScanScope, Aperio recommends using a UPS (uninterruptible 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 ScanScope to run for an additional 30 minutes, giving you time to safely shut it down.

To protect the ScanScope, Aperio recommends using a UPS (uninterruptible 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 ScanScope to run for an additional 30 minutes, giving you time to safely shut it down. The ScanScope does not require a LAN connection in order to operate. It need only be connected to a LAN if remote access is necessary.

Local Area Network (LAN) A LAN connection with internet access must be provided to allow remote maintenance of the ScanScope over the Internet.

Telephone It is recommended to place a telephone near the ScanScope in order to facilitate communications between technical personnel and the ScanScope operator as needed.

Stage Locks Note that the ScanScope is shipped with the stage locked. After the ScanScope is installed and on its work surface, unlock the stage. See “Locking and Unlocking the Stage” on page 17.

Power Supply Shipping Block The ScanScope is shipped with a shipping block inserted that protects the ScanScope from damage by preventing the power supply from moving during shipment. This will be removed by the Aperio technician who installs your ScanScope, but you will need to re-insert it if you ship the ScanScope. See “Removing and Installing the Power Supply Shipping Block” on page 17.

ScanScope CS 's Guide | 11

1 |Safety and Specifications

ScanScope Hardware Specifications Feature

Details

Input format

1-inch x 3-inch (25 mm x 75 mm) microscope slides 2-inch x 3-inch (5.08 cm x 7.62 cm ) (optional for dry scanning)

Slide loading Scanning region

Manual/Automatic single-slide capacity (for dry scanning, five-slide tray

standard on CS) Dry scanning:

1 x 3″ slides: 26.3 mm (top to bottom edges) x 60 mm (measured from right edge of the slide)

2 x 3″ slides (optional slide tray): 50 mm (top to bottom edges) x 60 mm (measured from right edge of the slide) Oil scanning: 10 x 10 mm Objective lens

Dry scanning: 20x/0.75 NA Plan Apo (40x scanning with 2x optical mag

changer)

Oil scanning: 60x/1.35 NA Plan Apo. Scanning resolution

Dry scanning: 50,000 pixels per inch (0.5 µm per pixel with 20x

objective); 0.25 µm per pixel when scanning at 40x with 2x optical mag changer

Oil scanning: 150,000 pixels per inch (.17 µm per pixel) with 60x objective Scanning method

Line scanning (U.S. Patent 6,711,283)

Tissue finding

Automatic

Focus

Automatic

Scan output

24-bit color contiguous pyramid TIFF, immediately viewable

eSlide file format

Standard pyramid tiled TIFF with JPEG2000 image compression

Network interface

1 gigabit per second Ethernet

Dimensions

Approximately 19 inches (H) x 12.5 inches (W) x 20.5 inches (D) 465 mm (H) x 318 mm (W) x 502 mm (D)

Weight

Approx. 55 lbs (25 kg)

Power

Universal AC input, power factor corrected. 100vAC – 240VAC,

50Hz/60Hz, 2 amp. See “AC Power” on page 11 for UPS recommendations.

Monitor

LCD monitor (see “Monitor Requirements” below)

12 | ScanScope CS 's Guide

1 |Safety and Specifications

Software Specifications Feature

Details

Operating system

Windows XP Professional

Scanning software

ScanScope Console/ScanScope Controller

Viewing software

ImageScope

System Requirements Following the recommendations below will help to ensure that you receive maximum performance from your ScanScope system. For the latest information on system requirements, refer to the document Aperio System Requirements Application Note.

Monitor Requirements Because Aperio eSlides are by design high resolution and information rich, for best results you should use a high quality monitor to view them. Make sure the monitor is at the proper viewing height and in a room with appropriate lighting. We recommend any high quality LCD monitor meeting the following requirements Display Type:

CRT minimum LCD (flat ) recommended

Screen Resolution:

1024(h) x 768(v) pixels minimum 1920 x 1050 or larger recommended

Screen Size:

15” minimum 19” or larger recommended

Color Depth:

24 bit

Brightness:

300 cd/m2 minimum 500 or higher recommended

Contrast Ratio:

500:1 minimum 1000:1 or higher recommended

Workstation – Viewing Station U Speed:

1.5 GHz, 2 GHz or faster recommended

Hard Disk Space

50GB free disk space

Memory:

1GB minimum, 2GB or more recommended

Network Card:

1 Gigabit network card or faster

Video Card:

24-bit color at monitor’s resolution

Operating System:

Windows XP SP3 or Windows 7 (32-bit or 64-bit)

ScanScope CS 's Guide | 13

1 |Safety and Specifications

Environment Specifications The ScanScope is designed to be operated under the following environmental conditions: indoor use, MAINS supply voltage fluctuations of up to ± 10% of 100 - 120 V (Japan /US) and 220 - 240 V (Europe), 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

-22 degrees Fahrenheit to 113 degrees

temperature

Fahrenheit

-30 degrees Celsius to 45 degrees Celsius Transportation/storage humidity

10% - 95%, non-condensing

Maximum operating temperature

65 - 82 degrees Fahrenheit 18 – 27 degrees Celsius

System Heat Dissipation

Typical BTU/hour: 1527

Power Use

Typical watts/hour: 449

Maximum operating humidity

30 – 90%, non-condensing

Maximum elevation

2000 Meters

Routine setup and alignment may be required by Field Service after shipping.

14 | ScanScope CS 's Guide

1 |Safety and Specifications

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 IEC/EN 61010-1: 2001 IEC 61010-2-081: 2001 IEC 61010-2-101: 2002 UL/CSA 61010-1: 2nd ed.:2004 EMC

EMC Directive 2004/108/EC IEC 61326: 2006; Class A FCC Part 15 Sub Part B

Input and Output Connections CAUTION: The RJ-45 connector on the ScanScope computer rear is to be connected to a computer network; it is not

intended to be connected to a telephone system.

MISE EN GARDE : Le connecteur RJ-45 du panneau arrière de

l'ordinateur du ScanScope doit être connecté à un réseau informatique; il n'est pas conçu pour être connecté à un système téléphonique.

ScanScope

 120 volt power cable (to outlet); (Europe: 240 volt)  1 Gigabit Ethernet cable (to Network)  Serial Interface cable (to fiber-optic illuminator)  ScanScope to PC umbilical cable set  Keyboard  Mouse

ScanScope CS 's Guide | 15

1 |Safety and Specifications

LCD Monitor

 120 volt power cable (to outlet); (Europe: 240 volt)  Monitor cable (to ScanScope) Stocker-Yale/Techniquip 21DC Illuminator Light Source 120 volt power cable (to outlet); (Europe: 240 volt).

ScanScope External Interconnections

Transporting or Moving the ScanScope If you need to transport the ScanScope, either to move it to a new location or to return it to your distributor for repair, be sure to pack it in its original packing material and crate, using all packing material that came with it. The packing material and crate have been specifically designed to ensure your ScanScope can be shipped without damage. Before using the ScanScope, unlock the stage and remove the power supply shipping block. Before moving the ScanScope from one work surface to another, lock the stage. (If you are not reshipping the ScanScope, you do not have to reinstall the power supply shipping block.) Before shipping the ScanScope, lock the stage and insert the power supply shipping block. (See the next sections for details.) 16 | ScanScope CS 's Guide

1 |Safety and Specifications

Removing and Installing the Power Supply Shipping Block The power supply shipping block keeps the power supply from moving during shipment and protects the ScanScope from damage. Before you first use the ScanScope, you must remove the power supply shipping block. (This may already have been done for you by an Aperio technician.) Note the tab outside the ScanScope door that reminds you to perform this procedure. Follow the numbered steps printed on the shipping block to remove it. 1.

Open the ScanScope case.

2.

Fold this tab toward you.

3.

Pull the entire shipping

block down so that it clears the that is in front of it.

4.

Pull the shipping block

straight out toward you so that it clears the ScanScope.

To re-install the shipping block before shipping the ScanScope: 1.

Fold the tab on the right back behind the power supply.

2.

Insert the shipping block and slide it up so it sits behind the .

Locking and Unlocking the Stage To prevent damage to the ScanScope, be sure to lock the stage before moving it, even if you are only moving it from one work surface to another. Note that the lock/unlock steps are slightly different depending on whether you are using a ScanScope CS equipped only for dry scanning or a ScanScope CS equipped with the oil scanning option that allows both dry and oil immersion scanning. See the following sections for details.

ScanScope CS 's Guide | 17

1 |Safety and Specifications

Locking and Unlocking the Stage on a ScanScope CS

See the diagram above for the location of the stage locks. To lock the stage: 1.

Switch off power to the ScanScope.

2.

Open the ScanScope access door.

3.

Locate the Z-axis locking plunger to the left of the microscope objective. Rotate the locking plunger lever 180° toward the objective. The plunger will snap into one of the locking holes located on the Z-axis bracket.

4.

Facing the access door, move the stage toward the access door and to the right, aligning the FIRST locking hole on the top stage plate directly below the locking plunger mechanism. Rotate the lever 180° toward the rear of the ScanScope. The plunger will snap into the locking hole on the top stage plate.

To unlock the stage: 1.

Open the ScanScope access door.

2.

Locate the Z-axis locking plunger to the left of the microscope objective. Rotate the locking plunger lever 180° away from the objective until it latches into the unlocked position. The plunger should stay fixed in the unlocked condition, allowing the axis to move freely.

3.

Rotate the X/Y-axis locking plunger lever (near the access door) 180° so that it is pointing toward the front of the ScanScope. The plunger will latch into the unlocked position. The plunger should stay fixed in the unlocked condition, allowing the stage to move freely.

4.

You may now switch on power to the ScanScope.

18 | ScanScope CS 's Guide

1 |Safety and Specifications

Locking and Unlocking the Stage on a ScanScope CS with the Oil Scanning Option

See the diagram above for the location of the stage locks. To lock the stage: 1.

Switch off power to the ScanScope.

2.

Open the ScanScope access door.

3.

Locate the Z-axis locking plunger to the left of the microscope objective. Rotate the locking plunger lever 180° toward the objective. The plunger will snap into one of the locking holes located on the Z-axis bracket.

4.

Facing the access door, move the stage toward the access door and to the right, aligning the SECOND locking hole on the top stage plate directly below the locking plunger mechanism. Rotate the lever 180° toward the rear of the ScanScope. The plunger will snap into the locking hole on the top stage plate.

To unlock the stage: 1.

Open the ScanScope access door.

2.

Locate the Z-axis locking plunger to the left of the microscope objective. Rotate the locking plunger lever 180° away from the objective until it latches into the unlocked position. The plunger should stay fixed in the unlocked condition, allowing the axis to move freely.

3.

Rotate the X/Y-axis locking plunger lever (near the access door) 180° so that it is pointing toward the front of the ScanScope. The plunger will latch into the unlocked position. The plunger should stay fixed in the unlocked condition, allowing the stage to move freely.

4.

You may now switch on power to the ScanScope.

ScanScope CS 's Guide | 19

1 |Safety and Specifications

Long Term Storage If you plan on not using the ScanScope 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, lock the stage (see the previous section), and replace the ScanScope in its original packing material and crate. After uncrating it again, and placing it on a work surface, unlock the stage (see above).

Equipment Maintenance CAUTION: When cleaning and servicing a ScanScope with the access door open, to prevent injury to the operator that can occur when a scan is initiated by a remote operator, first press the main power switch on the back of the ScanScope to the Off (0) position and disconnect the power cord to the ScanScope.

MISE EN GARDE : Avant d’ouvrir la porte d'accès pour le nettoyage ou

l'entretien du ScanScope, appuyez d'abord sur l'interrupteur principal au dos de l'appareil pour le mettre à la position arrêt (0) puis

débranchez le cordon d'alimentation afin d'éviter que l'utilisateur ne soit blessé si une lecture était commencée par un utilisateur à

distance.

Cleaning Objectives 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 Aperio when it is outside of the ScanScope. Because the tip of the objective is more scratch resistant than the interior lens, first try cleaning the objective without removing it from the ScanScope.

Removing the Objective If cleaning the objective in the ScanScope does not fully remove artifacts, you will need to remove the objective and clean it more thoroughly outside of the ScanScope. 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 mount, remove the objective and place it in an objective case to protect it. After you remove the objective, you may see a Console error message that a motion error has occurred—ignore that message for now and continue cleaning the lens. See “Installing the Objective” below for information on recovering from a motion error. Dust the lens surface with compressed air prior to cleaning to remove loose particles. Only use compressed air if the objective has been removed from the ScanScope—never use compressed air inside the ScanScope.

20 | ScanScope CS 's Guide

1 |Safety and Specifications

Cleaning a Dry Scan Objective To avoid the possibility of introducing very fine scratches onto the surface, never drag anything across the lens surface with a high degree of pressure, including lens paper. Clean the lens with a solvent designed for optical surfaces or, in an emergency, absolute ethanol. Avoid other solvents because they might react with optical coatings on the glass. Slightly moisten a Q-tip with lens cleaner or ethanol and very gently wipe it over the lens several times, turning the cotton tip before each . Blot excess solvent with lens tissue and allow the lens to dry thoroughly. Repeat this procedure if necessary. Note that applying immersion oil to a dry objective will possibly destroy the lens as these objectives are optimized optically for use in air and are not sealed against the intrusion of fluids into the lens barrel. For more information on cleaning dry scan objectives, please see: http://www.olympusmicro.com/primer/techniques/fluorescence/troubleshoot.html

Cleaning an Oil Scan Objective To avoid the possibility of introducing very fine scratches onto the surface, never drag anything across the lens surface with a high degree of pressure, including lens paper. Immersion oil is most safely removed using only lens tissue without employing any solvents. Use lens cleaning paper that is designed specifically for use on high quality optics to clean an oil scan objective. Draw a folded piece of lens tissue held under light tension with two hands across the objective front lens to absorb the oil. Repeat with a new area of the tissue. Repeat gentle wiping of the lens surface with as many tissues as required until no oil streaks are seen on the tissue, and discard each tissue immediately to avoid re-using contaminated tissues on the lens. Use plenty of fresh lens tissues. For more information on cleaning oil scan objectives, please see: http://www.zeiss-campus.magnet.fsu.edu/articles/basics/care.html

Installing the Objective To install the objective into the ScanScope after cleaning it, while keeping two fingers under it without touching the glass lens, use your other hand to carefully hold the objective by its sides, seat it in the objective mount, and rotate it to the right (or clockwise if viewing from below) to secure it. Do not cross-thread or over tighten. After you install the objective, the ScanScope Console may display a message that a motion error has occurred. While changing the objective, you may have moved the stage which causes a motion error. Power down the ScanScope and restart the Controller to rehome the stage and return it to a known position. See “Appendix D |Recovering from a Motion Fault” for more information. ScanScope CS 's Guide | 21

1 |Safety and Specifications

Light Source Bulb Replacement The Stocker-Yale/Techniquip 21DC Fiber Optic Illuminator contains a bulb inside the body of the instrument. The bulb will occasionally need to be replaced. For information and instructions on how to replace the bulb, see “Appendix B |Replacing the Fiber-Optic Illuminator Light Bulb” on page 57.

AC Line Fuse Replacement If the rear AC Line fuse of the ScanScope fails, a loss of power to the ScanScope will result. In order to restore power to the instrument, the AC Line fuse should be replaced. For information and instructions on how to replace the fuse, see “Appendix C |Replacing the AC Line Fuse” on page 61.

Cleaning the ScanScope Casing Clean the outer casing of the ScanScope as needed by wiping it with a damp cloth and immediately drying it with a dry cloth. Be sure to clean only the outside of the instrument.

Cleaning the ScanScope Interior In the unlikely event that slides have broken in the ScanScope, use the utmost care in removing glass shards and biological material. Turn off power to the ScanScope and unplug the power cord before placing your hands inside the ScanScope. Using proper safety protection and procedures, pick up and wipe up the visible pieces of any broken slides. Please Aperio Customer Service for advice before operating the ScanScope. Dans le cas peu probable où une lamelle se serait brisée dans le ScanScope, enlevez les morceaux de verre et le matériel biologique avec le plus grand soin. Mettez l’appareil hors tension et débranchez le cordon d’alimentation avant de mettre les mains à l'intérieur de l'appareil. En utilisant les dispositifs de protection appropriés et en suivant les procédures de sécurité pertinentes, ramassez tous les morceaux de lamelles brisées et essuyez les pièces visibles. Veuillez er le service clients d’Aperio pour obtenir des conseils avant d'utiliser le ScanScope.

22 | ScanScope CS 's Guide

2 | ScanScope System Overview The Aperio ScanScope is a microscope slide scanner that digitizes entire slides at high resolution. The ScanScope system comes with a host of software applications that enable you to scan, compress, and view your eSlides. The ScanScope’s automated ultra-fast and high-capacity scanning makes it optimally suited for high throughput environments.

ScanScope CS features include:

 Automatically load and scan a single slide with the touch of a button (or automatically scan up to five slides if you have the five-slide tray).

 Create eSlides, continuously, at an average rate of five minutes per slide.  eSlides are 24-bit color, with giga-pixel resolution  Optional upgrade provides oil-immersion scanning capability. For a discussion of how to use the ScanScope controls, see “ScanScope Controls” on page 29.

ScanScope CS 's Guide | 23

2 |ScanScope System Overview

Scanning Slides The slide scanning process begins with the ScanScope. Microscope slides are loaded onto the ScanScope; you choose specific scan parameters, and the slide is scanned, producing a digital image of the microscope slide. At this point, you can view the slide using ImageScope software. For an introduction to scanning, see “4 |Scanning Slides” on page 27. The ScanScope scanning system includes interactive Console software to allow you to customize your scans and perform special functions. Read on for more on the various components of the ScanScope system.

Oil-Immersion Scanning Option When equipped with the optional oil-immersion scanning upgrade, the ScanScope CS provides exceptionally detailed scans of blood smear, bone marrow, Gram stain, and other slides that are difficult to scan by traditional methods. See “Appendix A |Oil-Immersion Scanning” on page 41 for details on oil scanning with a ScanScope CS.

Viewing and Sharing eSlides - ImageScope After the eSlides have been created, you can make the images available for remote viewing to others via a local area network (LAN) or through an ImageServer. s can also view images through the Internet using eSlide Manager. The primary tool for viewing eSlides is ImageScope, which provides such features as:

 Instant zoom and pan of images.  Annotation of eSlides. For more information on many more of the ImageScope features, and for a quick tour of its operation, see “6 |Viewing eSlides with ImageScope” on page 37.

24 | ScanScope CS 's Guide

3 | ScanScope Startup and Shutdown This chapter contains information on how to turn the ScanScope and the computer it is connected to on and off.

System Startup To start up the ScanScope and its external light source: 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 ScanScope to the On (|) position.

3.

Press the power button on the front of the workstation.

4.

Press the power button on the front of the computer monitor.

5.

When the Microsoft Windows log on screen appears, press Ctrl+Alt+Delete on the keyboard. Type your name and in the appropriate fields.

with the name and provided during ScanScope installation. If your has changed the default (a recommended security practice), your if you do not know the . Be sure the stage is unlocked and that the power supply shipping block is removed or you will not be able to scan a slide (see “Removing and Installing the Power Supply Shipping Block” and “Locking and Unlocking the Stage” on page 17). The ScanScope takes approximately three minutes to initialize and place the stage mechanism in the home position. When the ScanScope has completed these processes, the status screen on the front of the ScanScope reads ScanScope Ready.

ScanScope CS 's Guide | 25

3 |ScanScope Startup and Shutdown

System Shutdown To shut down the ScanScope: 1.

Press the main power switch on the back of the ScanScope to the Off (O) position.

2.

Turn off the ScanScope external light source.

3.

Close all ScanScope software applications and any additional Windows applications that are open.

4.

Click the Windows Start button and select Shut Down.

5.

Select Shutdown from the window and click OK.

6.

Turn off the computer monitor.

26 | ScanScope CS 's Guide

We advise leaving the ScanScope instrument powered on unless it is to be idle for an extended period of time.

4 | Scanning Slides This chapter contains information on scanning slides with a ScanScope. We discuss how to perform a simple automatic scan and discuss scanning concepts. Finally, we talk about additional operations you can perform with the ScanScope Console software. CAUTION: Keep hands clear of the mechanical stage assemblies when the ScanScope is operating.

MISE EN GARDE : Gardez les mains éloignées de l'assemblage mécanique

pendant le fonctionnement du ScanScope.

Manual and Automatic Functions You can use the ScanScope to manually scan a single slide. You can scan up to five slides automatically if your ScanScope has the five-slide tray. You might prefer to use the manual method if you want full control over the scan area and parameters. Automatic scanning provides a high quality scan of the entire tissue sample with a minimum of operator interaction.

Slide Preparation Tips 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, Aperio Technical for assistance. Consult the material safety data sheets for the stains and re-agents you are using, as well as your institution’s bio safety policies and procedures regarding safely handling biological materials. Consultez la fiche signalétique des colorants et des réactifs que vous utilisez, ainsi que les politiques et les procédures en matière de biosécurité de votre établissement pour la manipulation sécuritaire du matériel biologique.

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.

ScanScope CS 's Guide | 27

4 |Scanning Slides

Slide Preparation The preparation of the slide is important for its scan quality and ease of scanning. The slides should be in clean and good condition—no air pockets under the coverslip, no dirt, no fingerprints, no markings, no writing, no extra adhesive, no broken slides, no chips, no scratches, no overhanging coverslip, etc. . Prior to loading slides, please ensure that all slides are fully cured (that is, not “wet”). For best results, all slides scanned should have coverslips. Make sure there is no glue around the edges of a slide that would cause it to stick or catch in the ScanScope stage area. 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. 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.

Keep the glue attaching the coverslip 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. Before scanning the slide, make sure it is very clean. Wipe it with a clean cotton rag (don’t use chemical cleaners).

28 | ScanScope CS 's Guide

4 |Scanning Slides

ScanScope Controls

Using the Start and Stop Buttons If a slide tray is already loaded, pressing the green button has a different effect depending on the state in which the ScanScope was left after the last scan:

 If the slide tray is empty, pressing the green button extends the tray to the access position.

 If the slide tray has a slide loaded and is in scanning position, pressing the green button once will start a scan rather than extending the tray to the access position.

 If the slide tray has a slide loaded and is not in scanning position, pressing the green button will move it to the home position. Pressing the green button again will start the scan.

 Pressing the red button halts the scan process and returns the slide stage to the access position.

ScanScope CS 's Guide | 29

4 |Scanning Slides

If you do not want to start the scan, but wish to extend the tray to replace the slides, open the Console application, go to the Tools menu, and select Configure. Then on the Configure window, go to the Motion Properties tab and click the Extend button.

Single-slide Automatic Scan Although you would normally use the ScanScope Console software to scan, change scanning parameters and perform special functions, we are going to step through a simple automatic scan using just the ScanScope scanner without the Console to illustrate some of the basics of scanning. 1.

Press the green button on the front of the ScanScope to move the slide stage to the slide access position so you can place a slide on the slide tray. (See the illustration above for the location of the green and red buttons and the slide tray access.)

2.

Position the slide into the front-most position in the tray with the coverslip facing up and the slide label oriented to the left.

3.

After you place the slide on the stage, press the ScanScope green button again to retract the stage and start the automatic scan. Pressing the red button halts the scan process and returns the slide stage to the side access position.

What Happens During the Scan? During the automatic scan discussed above, the ScanScope performs the following steps: 1.

Macro Image – Uses the macro camera inside the ScanScope to take a macro image of the entire slide and then the label. This quick snapshot of the slide is associated with the scanned slide and used by various ScanScope software.

2.

Find Macro Focus Value – The macro focus value gives the ScanScope a rough approximation of where the tissue is on the slide, and where the objective has to move to get the tissue in focus. Note that when oil scanning, a slight vibration noise can be heard—this is normal and indicates the ScanScope is measuring the height of the slide glass.

3.

Find Tissue – The tissue finder now tries to find the tissue on the slide more precisely. It looks the slide over and sets the scan area. It sets the blue diamond location (which you can see in the Console), to an area that does not appear to have tissue (background), which helps differentiate tissue from non-tissue during the scan. The blue diamond must be located in the part of the slide that is under the coverslip.

4.

Place Focus Points – The ScanScope now finds focus points. Focus points create a 3D map of your specimen. Each focus point is assigned a value based on the perceived depth of the surface of the specimen at that point.

30 | ScanScope CS 's Guide

Although the quick example in this chapter discusses the basics of scanning, you will want to become familiar with the ScanScope Console, which gives you a way to interact with the ScanScope and customize scanning parameters to your needs. For information on using the Console, refer to the ScanScope

Console ’s Guide.

4 |Scanning Slides

For example, a focus point on the “peak” of the tissue is a lesser number than a focus point in the “valley” of the tissue. Based on the focus point values, the ScanScope determines the range of focus for the piece of tissue. There are times when you may want to use the Console to change the focus points. For example, if a focus point is on an air bubble or on ink writing that is on the coverslip, focus will be off. Or, based on your understanding of the specimen, you may want to remove focus points from areas that are not important. 5.

Calibration – Calibration calculates adjustments for minor illumination differences to ensure that the ScanScope performs consistently to repeatedly scan high-quality images. The ScanScope makes a calibration image of the white background at the location of the blue diamond (which must be positioned at a location that does not appear to have tissue) and then uses the image to obtain a shading correction that will be applied during the scanning process. Calibration then performs white-balancing. The final step of calibration is to measure intensity across the entire calibration image, and then normalizing the calibration image to a predefined value. Not only does this provide uniformity for images made by a single ScanScope, but calibration also ensures images are similar in intensity across multiple ScanScopes.

6.

Scan – When the scan is finished, the scan stripes are stitched together into a single, compressed image and saved to the location you specified in the Console. You can now view the digital image of the slide using the Console or ImageScope.

Compressing and Storing eSlides eSlides are fairly large in of file size, so they need to be compressed in order to store and share the images efficiently. This is accomplished automatically at the completion of the scanning process. The result is a JPEG2000 compressed image in the SVS file format.

Multiple Slide Scanning Using the 5-Slide Tray The ScanScope slide tray allows you to automatically scan five 1” x 3” tissue slides unattended at the touch of a button. All images are compressed as they are being scanned. 1.

Push the ScanScope green button to eject the slide tray out the front of the device.

2.

Place slides into the slide tray with the coverslip up and with the slide labels oriented to the left.

3.

Push the ScanScope green button again to initiate auto scanning.

ScanScope CS 's Guide | 31

4 |Scanning Slides

 Pressing the ScanScope red button while scanning halts the scan process, then moves the slide tray out to the “load” position.

 Pressing the ScanScope green button after a “halt” causes the ScanScope to go to the next slide and continue the scan process.

Oil-Immersion Scanning When equipped with the optional oil-immersion upgrade, a ScanScope CS can be used for oil scanning as well as traditional dry scanning. For information on oil scanning, see Appendix A, “Oil-Immersion Scanning,” on page 41.

Working with a Magnification Changer The ScanScope CS is provided with a built-in optical magnification changer that enables both 20x and 40x dry scanning using a single objective lens. Note that the magnification changer cannot be used with oil scanning on this ScanScope model. Magnification with 20x Plan Apo objective:

 Mag Changer out = 20x  Mag Changer in = 40x You will see on the ScanScope display “Doubler Inserted” when the mag changer is engaged.

32 | ScanScope CS 's Guide

4 |Scanning Slides

Disengaging the Mag Changer To move the mag changer out to disengage it: 1.

Open the ScanScope side door.

Access door

2.

Pull the mag changer out gently until it stops before starting the system.

ScanScope CS 's Guide | 33

4 |Scanning Slides

Engaging the Mag Changer To initialize 40x (with 20x Plan Apo installed), simply push the mag changer in. If you are unable to push it all the way in, perform a manual scan and wait for the macro image to appear—this will lower the objective lens. To return to 20x, simply pull the mag changer out until it stops.

Using the ScanScope Console The Console software provides an interactive scanning experience. You use it to connect to the ScanScope and direct the scanning operation. Depending on the version of Aperio software you are using, the Console may have slightly different features. Please refer to the ScanScope Console ’s Guide for the latest information on using the ScanScope Console. You can use the Console to:

 Perform manual or automatic scans  Set up the scan area  Manually place focus points  Perform a calibration operation  Scan the slide  Change ScanScope configuration Additional procedures you can perform using the Console are discussed below. See the ScanScope Console ’s Guide for details.

Snapshot Review The snapshot feature improves your scanning workflow by allowing you to review and adjust slide snapshot previews before scanning. This is especially useful when scanning slides that are difficult to scan, such as slides that have high background staining.

2x3 Slide Scanning The ScanScope s scanning slides that are 2x3 inches compared to normal 1x3 slides. This option is an additional feature and Aperio provides a separate slide tray which holds two 2x3 slides. 2x3 slides can only be scanned at 20x. To scan 2x3 slides, use the Console to select the 2x3 parameter. To return to scanning 1x3 slides, use the Console to reset the ScanScope to using 1x3 slides.

Configuration Options The Console Configure window contains information and functions for servicing the ScanScope. To access the Configuration window, go to the Console Tools menu and select Configure. 34 | ScanScope CS 's Guide

5 | Calibration and Verification The ScanScope 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 Aperio Technical Services, to make sure the ScanScope is operating correctly. The ScanScope scanner provides automatic calibration and verification every time a slide is scanned by performing prescan calibration during the scan. (See the ScanScope Console 's Guide for more information on the prescan operation.)

ScanScope CS 's Guide | 35

5 |Calibration and Verification

36 | ScanScope CS 's Guide

6 | Viewing eSlides with ImageScope This chapter is a quick introduction to the ImageScope viewing application. For detailed information on your version of ImageScope, refer to the ImageScope ’s Guide.

ImageScope™ is an easy to use tool for viewing eSlides that is available for free from the Aperio web site, www.aperio.com. Image Scope offers much more than simple image viewing capabilities:

 eSlide conferencing provides the ability to share and discuss eSlides in real time in multiple remote locations.

 View multiple eSlides concurrently using synchronized navigation.  Apply image adjustments in real time for contrast, brightness, and gamma.

 Feature-rich annotation:  Multiple drawing tools  Ability to draw areas to be excluded from analysis*  Organize annotations by person or department by using annotation layers

 Link annotations or images to create a viewing sequence

 Instantly pan and zoom to any region of the slide.  Extract a region or selected regions of a eSlide in a variety of formats.

Opening and Viewing an eSlide Just as an example, let’s open a eSlide that is on your computer. Note that you can also open eSlides on your local area network through Microsoft file sharing, or remotely on an Aperio ImageServer. 1.

Click

on the ImageScope toolbar.

2.

On the Open Image window, navigate to the location that contains the image you want to view.

3.

Click the name of the eSlide you want to open and click Open.

The ImageScope window appears (the version you see may differ slightly depending on the version of ImageScope you are using).

ScanScope CS 's Guide | 37

6 |Viewing eSlides with ImageScope

Here are the main elements of the ImageScope viewer window:

 Toolbar – Many of the ImageScope commands and features are available on the toolbar. You can also access many of these features through the ImageScope menus.

 Zoom Slider – You can magnify or shrink the current view.  Filmstrip – The filmstrip shows what slides are open. You can move between eSlides by clicking the slide’s image in the filmstrip.

 Label Window – If a photo of the slide label has been associated with the eSlide, you can see it in the slide label window.

 Thumbnail Window – eSlides are large and often you see only a portion of one in the ImageScope main window. The thumbnail is a view of the complete eSlide.

 Magnifier Window– Move this tool to the area you are interested in to see a magnified view.

38 | ScanScope CS 's Guide

6 |Viewing eSlides with ImageScope

Navigation There are many ways to move around in a eSlide image. Here are the most commonly used methods.

 Panning – Left-click and hold the mouse button down while you drag the cursor across the eSlide. Your cursor turns into a closed fist . Panning moves the slide in the direction you are dragging, allowing you to see more of the slide.

 Scrolling – You can scroll across a eSlide to the right, left, up, or down. As you move your cursor toward the edge of the ImageScope main window, the cursor changes to an arrow: ; click and hold the mouse button down to scroll in that direction. To stop scrolling, release the mouse button.

 Using the Thumbnail Window – Depending on the magnification in use, the main ImageScope window may show only a portion of the slide The thumbnail window shows the entire eSlide. The portion of the eSlide being displayed in the main window is enclosed in a black rectangle in the thumbnail.

 Click in the thumbnail to move the main image to that part of the slide or drag the image in the thumbnail to move to another area of the eSlide.

 Using the Filmstrip –You can open multiple eSlides. To move between multiple eSlides in ImageScope, in the filmstrip click the image of the one you want to see.

 Page Panning – Use the keyboard arrow keys to move an entire screenpage at a time (for example, Shift+Right arrow moves a page to the right; Shift+Left Arrow moves a page to the left, and so on).

 Using the Magnifier Window – Use the magnifier window to show a larger view of a particular portion of the eSlide.

Changing Viewing Magnification In addition to using the magnifier window to show a portion of the eSlide in greater resolution, you can also change the resolution of the entire main window image.

ScanScope CS 's Guide | 39

6 |Viewing eSlides with ImageScope

You can adjust the magnification of the entire display by using the zoom slider.

 Click Fit to set the magnification to 0x and fit the entire eSlide within the main viewing area.

 Click 2x through the maximum magnification setting to zoom in using those magnifications.

 Click the slider and drag it up or down to change the magnification in small increments.

 If your mouse has a scroll wheel, roll the scroll wheel to move the slider. Or, hold down the Control key and press the + key to zoom in; hold down the Control key and press the – key to zoom out.

Zoom Navigation To zoom into a particular area of the eSlide: 1.

Click

on the ImageScope toolbar.

2.

Click in the main image window at the upper-left corner of the area you want to zoom into and left-click, holding the mouse button down, while you draw a rectangle around the area you want to zoom into.

3.

Let go of the mouse button and the main window will be zoomed to that area.

Immediate Maximum Zoom Double-clicking the image in the main window immediately zooms that image to the maximum magnification. Double-click again to return to the most recently used magnification that was not the maximum magnification.

For More Information For detailed information on using ImageScope, see the ImageScope ’s Guide.

40 | ScanScope CS 's Guide

Appendix A | Oil-Immersion Scanning Because of the special characteristics of oil scanning optics and the nature of the tissue being scanned, we do not recommend using automatic scanning when oil scanning. Manually step through the scanning steps using the ScanScope Console rather than using the Console One Touch button or the ScanScope automatic scan buttons. 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.

This appendix discusses how to oil scan on a ScanScope CS equipped with the optional oil scanning upgrade. Note: Always make sure your objective and slides are kept clean and free of immersion oil. If left to dry on your ScanScope equipment and slides, some immersion oils may leave crystalline residue on optical surfaces.

Switching from Dry to Oil Scanning Before you begin oil scanning, there are several steps you must follow to prepare the slide and the ScanScope.

1 – Remove Dry Scan Slide Tray If the dry scan slide tray is not already extended, click Manual Load on the Console Start tab to partially eject it. Pull the dry scan slide tray out of the ScanScope.

2 – Configure the ScanScope for Oil Scanning Open the side access door and: 1.

Protect the mag changer from finger prints by pushing it in.

2.

Flip the oil objective protection lever DOWN for oil scanning.

3.

Being careful not to touch the lens, push the objective up to give you more room to work inside the ScanScope.

4.

Carefully unthread the 20x objective (rotating to the left—or counterclockwise if viewing from below), protecting it by placing two

ScanScope CS 's Guide | 41

Appendix A |Oil-Immersion Scanning

fingers of one hand under it without touching the glass lens as you rotate it with the other hand. When it is free of the mount, remove the objective and place it in an objective case to protect it. 5.

Carefully holding the 60x objective by its sides, seat it in the objective mount, and rotate it to the right (or clockwise if viewing from below) to secure it. Keep two fingers under it without touching the glass lens to protect it. Do not cross-thread or over tighten.

After you change the objective, the ScanScope Console may display the message “A motion error has occurred. Power down the ScanScope and rehome the stage.” By changing the objective, you may have moved the stage with the result that the ScanScope does not know its exact position—rehoming the stage returns it to a known position. After powering down the ScanScope, rehome the stage by going to the Console Tools menu, selecting Configure, clicking on the Motion Properties tab, and then clicking the Home button. For more information, see Appendix D, “Recovering from a Motion Fault” on page 63. 6.

Pull out the mag changer. (You cannot do oil scanning with it inserted.)

3 – Clean the Oil Scan Slide Tray, the Slide (If Coverslipped), and the Objective 1.

Gently wipe excess oil from the top and bottom of the oil scan slide tray using a lint-free tissue. After excess oil is absorbed by the tissue, final polishing can be done using a micro-fiber cloth. Only if necessary, use a gentle solvent such as Windex or xylene to remove any remaining oil residue.

2.

Gently wipe excess oil from the coverslipped slide and the objective using a lint-free tissue. After excess oil is absorbed by the tissue, final polishing can be done using a micro-fiber cloth.

For more information on cleaning objectives, refer to “Cleaning Objectives” on page 20.

4 – Load the Slide into the Oil Scan Slide Tray Load the slide into the oil scan slide tray by snapping the frame in place over the slide. (For information on removing a slide from the tray, see “Removing a Slide from the Oil Scan Slide Tray” on page 53.)

5 – Place Oil on the Slide Place 1-2 drops of Type A oil on the slide in the Area of Interest (AOI) using an eyedropper or other applicator. If you are scanning slides without coverslips, Type B oil is recommended. However, coverslipped slides provide the best images.

42 | ScanScope CS 's Guide

Appendix A |Oil-Immersion Scanning

Using the ScanScope Console to Scan Now that the slide has been prepared and the ScanScope configured for oil scanning, you can begin scanning. This section discusses features of the ScanScope Console that specifically apply to oil scanning. For details on the use of all Console features, see the ScanScope Console ’s Guide.

Starting the Console 1.

If not already running, start the ScanScope Console by double-clicking the ScanScope Console icon on the Windows Desktop (as shown below) or from the Windows Start menu by clicking Start, pointing to All Programs, pointing to ScanScope, and then selecting ScanScope Console.

The first thing the Console does is ask you what ScanScope you want to connect to.

2.

Either type the name of the ScanScope you want to connect to in the Controller Name text box or select one from the drop-down list of ScanScopes that have been recently connected to.

3.

Type the ScanScope name and .

4.

Click Connect.

ScanScope CS 's Guide | 43

Appendix A |Oil-Immersion Scanning

Selecting Magnification and Scan Area 1.

Insert the prepared oil scan slide tray into the front of the ScanScope.

2.

Click Manual Load on the Start tab.

3.

On the New Slide window, optionally type a file name and description.

4.

Click Manual Scan.

44 | ScanScope CS 's Guide

Appendix A |Oil-Immersion Scanning

When the ScanScope loads the slide for oil scanning, a slight vibration noise can be heard—this is normal and indicates that the ScanScope is measuring the height of the slide glass before performing a macro focus.

5.

Click the Console Scan Area tab and if not already selected, select 83 in the Scan Magnification drop-down list. (Although the ScanScope is equipped with a 60x Objective, the ScanScope uses an additional optical element which increases the total optical magnification to 83x.) Note that the magnification changer cannot be used for oil scanning.

6.

Drag the green rectangle to select a very small scan area within the AOI for focus offset calibration. (Small boxes on the right-side of the macro image represent the clips that hold the glass down in the slide tray—you cannot move the scan area over those clips as that area cannot be scanned.)

ScanScope CS 's Guide | 45

Appendix A |Oil-Immersion Scanning

7.

Position the calibration location (blue diamond) by moving it to a clear region and under the oil. (If you are having trouble seeing a clear area, see “Help with Setting the Calibration Point” on page 51.)

46 | ScanScope CS 's Guide

Appendix A |Oil-Immersion Scanning

Setting Focus Points 1.

On the Focus Points tab, click Auto Select. This places points in a rectangular grid (best for oil).

ScanScope CS 's Guide | 47

Appendix A |Oil-Immersion Scanning

2.

Optional – Focusing the focus points. a.

Press Alt+M or go to the View menu and select Video Monitor to open the Video Monitor window.

b.

Resize the Video Monitor window to its smallest size—click on the drop-down list on the lower left corner and select the smallest resolution.

c.

Drag the Video Monitor window so that it is adjacent to the macro image if needed.

d. Right-click anywhere within the AOI and select Perform Macro Focus from the context menu.

that the image in the Video Monitor window is in focus. If there is not enough detail for auto focus, then use the Manual Macro Focus command. 3.

Click the Auto Focus button.

48 | ScanScope CS 's Guide

Appendix A |Oil-Immersion Scanning

The focus points will turn from yellow to green after being focused. If any focus points remain yellow, select them one at a time, reposition the focus point to a different area, right-click, and then select Auto Focus This Point. 4.

Set Focus Offset to 0.0 microns to start. See “Focus Offset Calibration” on page 51 for information on this setting.

ScanScope CS 's Guide | 49

Appendix A |Oil-Immersion Scanning

Taking a Calibration Image The calibration operation calibrates the ScanScope background illumination levels. 1.

Click the Calibrate tab.

2.

Click the Calibrate button. A calibrate image is taken. When the calibrate operation is complete, the calibration image appears in the upper portion of the window. The calibration image should be light gray in color and should not contain tissue. If the calibration image is too dark or displays shadowing, the bulb may need replacing. If the calibration image shows tissue, go back to the Scan Area tab and move the blue diamond calibration point out of the tissue area and make a new calibration image. If you have trouble taking a calibration image, see “Using a Default Calibration Image” on page 52.

Scanning On the Scan tab, click Start Scan to start the scan. As part of your scanning, you will want to perform focus offset calibration (see the next section).

50 | ScanScope CS 's Guide

Appendix A |Oil-Immersion Scanning

As the scan proceeds, the slide graphic indicates “Scanning.”

Oil Scanning Tips Help with Setting the Calibration Point If you are not able to see a clear area to move the calibration point to, type Alt+M to open the Video Monitor window to get a better view.

Focus Offset Calibration Due to the thickness of the specimen and limited depth of field at high magnification, many slides require a focus offset. This is a function of the specimen, and may be different for every slide. Typical offset values are between -0.3 to +0.3 micron, although they may be outside of that range. Best scans are obtained by determining the offset by trial and error. 1.

Select a very small scan area.

2.

Start the Scan with Focus Offset on the Focus Points tab set to 0 microns.

3.

Set Focus Offset to -0.3 microns and repeat the scan.

4.

Set Focus Offset to +0.3 microns and repeat the scan.

5.

Open all three images in ImageScope.

ScanScope CS 's Guide | 51

Appendix A |Oil-Immersion Scanning

a.

Go to the ImageScope Window menu and select Tile Vertical to see all three images side by side.

b.

Visually inspect the images and decide which focus offset is best, or repeat with other offsets if needed. Telling the Images Apart – As the images were created, their file names were created ending in a number—the numbers increment as the files are created. Therefore, the file name of the first image created with Focus Offset of zero has the lowest number, the file name of the image created with Focus Offset of -0.3 has the next highest number, and the file name of the final image created has the highest number.

5.

Based on your inspection of the test scans, select the appropriate Focus Offset value on the Focus Points tab.

6.

Select the desired scan area and perform a scan.

Using a Default Calibration Image Some types of slides used with oil scanning contain very little clear area (for example, blood smear slides or bone marrow slides). In this case, you may not be able to successfully make a calibration image. If you have previously made a good calibration, you may have clicked the Set As Default button to save it as a default calibration image. If you have a default image saved, and the calibration fails, you will be asked if you want to use the default calibration image. Click Yes or No. If you want to use the default calibration image for this scan, select the Use Default check box before you click the Calibration button and ScanScope will use the default calibration image.

52 | ScanScope CS 's Guide

Appendix A |Oil-Immersion Scanning

Image Sharpening Due to thickness of the specimen and limited depth of field at high magnification, most slides scan better with slight image sharpening. We recommend using the Imagefilter 3 parameter set. To use this parameter set: 1.

Go to the Console Tools menu and select Configure.

2.

Click on the ScanScope properties tab of the Configure window.

3.

In the Parameter Set drop-down box, select Imagefilter 3.

You may prefer to turn off sharpening by selecting No Filter while determining the best focus offset, and then selecting Imagefilter 3 for the actual scan.

Removing a Slide from the Oil Scan Slide Tray To remove a slide from the oil scan slide tray: 1.

Lift the slide frame.

2.

While holding back the retaining clip, push the slide to the right and push gently down on the label side. This causes the other side to pop up.

If the slide doesn’t pop up easily (due to oil underneath), don’t push down, as this will break the slide. Instead, use your fingernails to pry up under the label side.

ScanScope CS 's Guide | 53

Appendix A |Oil-Immersion Scanning

Switching from Oil to Dry Scanning This section discusses how to switch back to dry scanning.

1 – Remove Oil Scan Slide Tray If the oil scan slide tray is not already extended, click Manual Load on the Console Start tab to partially eject it. Pull the oil scan slide tray out of the ScanScope.

2 – Clean the Oil Scan Slide Tray, the Slide (If Coverslipped), and the Objective 1.

Gently wipe excess oil from the top and bottom of the oil scan slide tray using a lint-free tissue. After excess oil is absorbed by the tissue, final polishing can be done using a micro-fiber cloth. Only if necessary, use a gentle solvent such as Windex or xylene to remove any remaining oil residue.

2.

Gently wipe excess oil from the coverslipped slide and the objective using a lint-free tissue. After excess oil is absorbed by the tissue, final polishing can be done using a micro-fiber cloth.

For more information on cleaning objectives, refer to “Cleaning Objectives” on page 20.

3 – Configure the ScanScope for Dry Scanning Open the side access door and: 1.

Protect the mag changer from finger prints by pushing it in.

2.

Flip the oil objective protection lever UP for dry scanning.

3.

Push the objective up to give you more room to work inside the ScanScope.

4.

Carefully unthread the 60x objective (rotating to the left—or counterclockwise if viewing from below), protecting it by placing two fingers of one hand under it without touching the glass lens as you rotate

54 | ScanScope CS 's Guide

Appendix A |Oil-Immersion Scanning

it with the other hand. When it is free of the mount, remove the objective and place it in an objective case to protect it. 5.

Carefully holding the 20x objective by its sides, seat it in the objective mount, and rotate it to the right (or clockwise if viewing from below) to secure it. Keep two fingers under it without touching the glass lens to protect it. Do not cross-thread or over tighten.

After you change the objective, the ScanScope Console may display the message “A motion error has occurred. Power down the ScanScope and rehome the stage.” By changing the objective, you may have moved the stage with the result that the ScanScope doe not know its exact position—rehoming the stage returns it to a known position. After powering down the ScanScope, rehome the stage by going to the Console Tools menu, selecting Configure, clicking on the Motion Properties tab, and then clicking the Home button. For more information, see Appendix D, “Recovering from a Motion Fault” on page 63. 6.

Pull out the mag changer.

4 – Load the Slides into the Dry Scan Slide Tray Load the slides into the dry scan slide tray with the labels on the left.

5 – Start the Console If not already running, start the Console and connect to the ScanScope.

6 – Insert the Prepared Dry Scan Slide Tray Insert the dry scan slide tray into the front of the ScanScope.

7 – Select Magnification Level Click the Console Scan Area tab and select 20 in the Scan Magnification dropdown list.

8 – Start Dry Scanning Start dry scanning as usual.

ScanScope CS 's Guide | 55

Appendix A |Oil-Immersion Scanning

56 | ScanScope CS 's Guide

Appendix B | Replacing the Fiber-Optic Illuminator Light Bulb If the calibration stripes on scanned slides begin to turn progressively darker shades of gray, then the light source bulb probably needs to be replaced. This section describes the replacement procedure for the light sources that may be used on your ScanScope. The recommended replacement bulbs for the ScanScope light source are:

 For ScanScope CS used only for dry scanning – General Electric Quartzline Lamp (Model number EKE, 21 volt /150 watts).

 For ScanScope CS equipped with the oil scanning option – Ushio Halogen Projector Lamp (Model number EJV 21V150W). Note that this bulb must be used for oil scanning, but may also be used for dry scanning so you do not have to switch bulbs when switching between oil and dry scanning. These can be purchased online from the following sites:

 www.bulbman.com – USA & Canada  www.bltdirect.co.uk – Europe IMPORTANT Do not touch the bulb with your fingers; wear clean gloves or use a cloth when replacing the bulb. Oil from the skin will reduce the life of the new bulb. If the bulb needs to be cleaned, use a lint free cloth with alcohol.

IMPORTANT Ne touchez pas l'ampoule avec vos doigts; portez des gants propres ou servez-vous d’un chiffon pour remplacer l'ampoule. L’huile de la peau réduit la durée de vie de la nouvelle ampoule. Si l'ampoule doit être nettoyée, utilisez un chiffon non pelucheux et de l'alcool.

The Stocker-Yale/Techniquip illuminator is bench mounted and sits next to the ScanScope. It has a black and white casing and is labeled Model 21DC on the front . 1.

Turn off (O) the illuminator’s power switch (located on the rear ), then unplug the instrument from the power outlet.

3.

Remove the Illuminator light cable by loosening the retaining thumbscrew.

ScanScope CS 's Guide | 57

Appendix B |Replacing the Fiber-Optic Illuminator Light Bulb

4.

Wait one hour to allow the bulb to cool down. WARNING: Hot Surface The halogen bulb becomes hot during use and can cause

burn damage if touched without first allowing for sufficient cool-down time.

AVERTISSEMENT : Surface chaude – L’ampoule halogène devient chaude pendant

l'usage et peut ca une brûlure si on la touche sans la laisser refroidir suffisamment d'abord.

5.

Loosen the two front fasteners located on the lamp access . Remove the lamp module so that the bulb housing is completely exposed.

6.

Pull the bulb up and out of the spring retainer clips.

7.

Remove the ceramic connector from the bulb.

Note: This is a tight connection. Carefully rock the connector back and forth while applying a pulling force. 8.

Plug the new bulb into the ceramic connector.

58 | ScanScope CS 's Guide

Appendix B |Replacing the Fiber-Optic Illuminator Light Bulb

IMPORTANT Do not touch the Fiber-lite bulb with your fingers; wear clean gloves or use a cloth when replacing the bulb. Oil from the skin will reduce the life of the new bulb. 9.

Press the new bulb back into the spring retainer clips until it is completely seated.

10. Push the lamp module back into the frame of the illuminator. 11. Re-tighten the front fasteners, then reinstall the light cable. 12. Plug the illuminator’s power cord back into the power outlet then turn on (|) the main power switch.

ScanScope CS 's Guide | 59

Appendix B |Replacing the Fiber-Optic Illuminator Light Bulb

60 | ScanScope CS 's Guide

Appendix C | Replacing the AC Line Fuse CAUTION: To reduce the risk of electric shock, do not perform any

servicing other than the fuse replacement described below. Refer all servicing to qualified service personnel.

MISE EN GARDE : Pour réduire le risque d'électrocution, n'effectuez

aucun entretien à part le remplacement du fusible décrit plus bas. Confiez tout entretien à un technicien qualifié.

If the rear AC line fuse of the ScanScope fails, a loss of power to the ScanScope will result. In order to restore power to the instrument, the AC line fuse should be replaced. The AC line fuse is located inside the power entry module of the instrument. 13. Make sure that the power switch is in the Off position (O) and that the instrument is unplugged from the power outlet. 14. Unplug the AC cord from the power entry module to access the fuse. 15. Use a small flat blade screwdriver to pry apart the fuse holder from the power entry module. The 5 x 20mm sized fuse is clipped into the fuse holder assembly. 16. Replace the fuse with the following type and rating fuse (also indicated on the rear silkscreen): 250V 2.0A (Fast-Blo) 17. Reinstall the fuse holder into the power entry module and reinsert the power cord. 18. Press the power switch to the On position (|) and the workstation power switch momentarily to the up position. If the fuse immediately fails again, refer servicing to qualified service personnel.

ScanScope CS 's Guide | 61

Appendix C |Replacing the AC Line Fuse

62 | ScanScope CS 's Guide

Appendix D | Recovering from a Motion Fault This appendix discusses what to do when you receive a motion fault error message. If you move the stage by hand or it is otherwise moved in some way other than by the ScanScope motor, a motion fault may occur and the ScanScope Console displays the message: “Critical Notice—A motion error has occurred. Power down the ScanScope and rehome the stage.” This error does not indicate damage to the stage, but simply that the ScanScope may have lost track of the exact position of the stage. To recover from this error: 19. Turn the ScanScope off and back on: 20. Press the main power switch on the back of the ScanScope to the Off position then press it to the On position. 21. Go to the Console Tools menu and select Configure. 22. On the Configure window click the Motion Properties tab. 23. Click the Home button to rehome the stage. Rehoming the stage tells the ScanScope exactly where the stage is.

If you do not recover from this error, the quality of your scans may suffer.

ScanScope CS 's Guide | 63

Appendix D |Recovering from a Motion Fault

64 | ScanScope CS 's Guide

Appendix E | Troubleshooting This appendix contains tips for troubleshooting the most common problems you may encounter with your ScanScope. If the information below does not help you find or fix the problem you are having, for further ScanScope technical your local Aperio office. Refer to page ii of this manual for information. Symptom ScanScope fails to start up or initialize.

Solution 1. 2.

that the power switch at the back of the unit is on.

Click the Aperio Service Manager icon

in the

Windows taskbar and check that the entry for the Controller has a green dot and says “Stop

Controller Service.” If it has a red dot and says

“Start Controller Service,” click the entry to restart it. Console or LCD displays

“Failed to move stage” or “Check stage locks.” Trouble scanning a particular slide.

If the stage is locked, you cannot scan. See the instructions in “Locking and Unlocking the Stage” on page 17. 1.

Is the slide tissue extremely thick or thin? If

manual macro focus does not allow you to bring the tissue into focus, call customer service for assistance.

2.

Is the slide extremely dark or faint? Use manual macro focus or a parameter set such as faint or

gain adjust low. 3.

Is the label large or located inside the area of

interest? Remove the label or adjust the area of interest.

4.

Are there pen marks on the coverslip? Remove

5.

Is there dust or debris on the coverslip or bottom

6.

Are there bubbles under the coverslip? Perform a

7. During the scan, the

Tissue Finder included a non-tissue area in the

the marks or perform a manual scan.

surface? Clean the slide. manual scan.

Is there excess adhesive around edges of the

coverslip? Clean or perform manual scan.

Perform a new presnap with a very clean, blank slide and repeat the manual load.

scan area of interest.

ScanScope CS 's Guide | 65

Appendix E |Troubleshooting

Symptom

Solution

During the scan you are

Try another slide to see if the problem is with the slide.

unable to obtain a macro focus.

Entire image is out of focus.

1.

that the slide is being held flat and not

moving in the tray during scanning (tape down the slide if necessary).

2.

Optic surfaces (such as the objective) may contain finger prints. See “Cleaning Objectives” on page 20 for information on cleaning the objective.

Individual stripes of the

image are poorly focused

but a neighboring stripe is perfect.

Autofocus did not detect

at least four focus points.

This may indicate that the slide is moving during scanning. 1.

that the slide tray is clean.

2.

that the slide is sitting flat and not rocking.

1.

The tissue may be too faint to scan; use the faint

parameter set.

2.

Try performing a new presnap.

Calibration image is

1.

If the calibration image is clear but too dark or too

message “bulb may be

2.

If the calibration image contains considerable

displayed but error

unusable” is displayed.

bright, perform set camera gains.

tissue, while looking at the video monitor display, click on a clear glass area without tissue and

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

ScanScope ignore edges or defects. If problem

persists, either select the scan area manually or adjust the area of interest for all slides to avoid defects. 4.

If the calibration image is very uneven, the slide is sitting flat. Repeat with another slide. An uneven calibration may also indicate optical

misalignment due to mishandling which requires a service visit or factory repair. Scan quality is not good.

It may be that a motion fault occurred and was not

recovered from. See Appendix D, “Recovering from a Motion Fault” for assistance.

66 | ScanScope CS 's Guide

Index

AC line fuse replacement, 22, 61 AC power, 11 bulb, light source, 57 calibration, 36, 50 cleaning case, 22 cleaning objective, 21 compression, 31 connecting to ScanScope, 43 connections, 15 Console, 34 2 x 3 slides, 34 configuration, 34 connecting to ScanScope, 43 oil scanning, 43 snapshot review, 34 controls, 30 doubler, 32 environment specifications, 14 ergnomics, 10 eSlide compression, 31 creating, 31 sharing, 24 viewing, 24, 37 FCC compliance, 15 fiber-optic bulb replacement, 22, 57 focus points, 30 automatically focusing, 49 hardware specifications, 12 ImageScope features, 37 navigating filmstrip, 39 page panning, 39 panning, 39 scrolling, 39 thumbnail window, 39 toolbar, 38 window magnifier window, 39 thumbnail window, 39

zoom toolbar, 39 input/output connections, 15 installation specifications, 9 LAN, 11 light source,bulb replacement, 57 live video monitor, 48 macro focus value, 30 macro image, 30 mag changer, 32 control, 30 maintenance, 22, 57 AC line fuse replacement, 22, 61 cleaning case, 22 fiber-optic bulb replacement, 22, 57 monitor requirements, 13 motion fault, 63 network connection, 11 objective, cleaning, 21 oil scanning, 32, 41 preparation, 41, 54 power supply shipping block, 17 problems, 65 regulatory compliance, 15 repacking, 16 safety instructions, 4 scanning, 24, 27 2x3 slides, 34 automatic, 27 calibration, 50 focus points, 30 introduction, 30 macro image, 30 manual, 27 multiple slides, 31 oil-immersion, 43 snapshot review, 34 tissue finder, 30 ScanScope, 23 calibration, 36 configuration, 34 ScanScope CS 's Guide | 67

Index

Console, 34 controls, 29, 30 overview, 23 shutdown, 26 startup, 25 storing, 20 transporting, 16 slide preparation tips, 27 slide tray access, 30 software specifications, 13 specifications connections LCD monitor, 16 ScanScope, 15 Stocker-Yale/Techniquip 21DC Illuminator light source, 16 environment, 14 hardware, 12

68 | ScanScope CS 's Guide

monitor requirements, 13 regulatory compliance, 15 software, 13 stage locks, 18, 19 start and stop buttons, 29, 30 Stocker-Yale/Techniquip 21DC Illuminator, 57 storing, 20 Technical , 1 tissue finder, 30 transporting, 16 troubleshooting, 65 UPS, 11 viewing workstation requirements, 13 warning symbols, 2 work surface, 9 working area configuration, 10

ScanScope CS 's Guide | 69

ScanScope CS ’s Guide MAN-0030, Revision M