ScanScope CS UserGuide

ScanScope CS
Users 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.
User 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 contacted 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 registered 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.
Contact 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: info@aperio.com
Email: europeinfo@aperio.com
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: asiainfo@aperio.com
Technical Support:
Technical Support:
Technical Support:
Direct International Tel: 1 (760) 539-1150
Email: europesupport@aperio.com
Email: asiasupport@aperio.com
US/Canada Tel: 1 (866) 478-3999 (toll free)

US/Canada/Worldwide Email:
support@aperio.com
ii | ScanScope CS User's Guide
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 User'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 User'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 User's Guide | v
Contents
vi | ScanScope CS User'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 support 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 support, contact your local Aperio office. Refer to
page ii of this manual for contact information.
ScanScope CS User'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 quilatral vise avertir

l'utilisateur qu'il sagit dinstructions 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 products enclosure that may be of

sufficient magnitude to constitute a risk of electric shock to
persons.
Le symbole de l'clair avec la pointe de flche dans un triangle

quilatral vise avertir l'utilisateur que le botier du produit
prsente une tension dangereuse non isole dune amplitude

suffisante pour constituer un risque d'lectrocution.
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 dune surface plane et de vagues dans un triangle
quilatral vise avertir l'utilisateur de la prsence de surfaces

chaudes qui peuvent causer des brlures.
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, contact your Aperio Sales Representative for information on
obtaining the correct manual.
2 | ScanScope CS User's Guide
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 utilis d'une autre manire que celle spcifie dans cette
documentation, la protection assure par lappareil risque dtre altre.
AVERTISSEMENT : Cet appareil gnre, utilise et peut mettre une nergie de
radiofrquences. Sil nest pas install et utilis conformment aux instructions de ce
guide, il peut brouiller les communications radio. Cet appareil a t test et dclar
conforme aux limites des appareils numriques de Classe A (selon la sous-partie B de la
section 15 des rglements de la FCC), qui sont destins assurer une protection
raisonnable contre un brouillage prjudiciable lorsque l'appareil est utilis dans un
milieu commercial.
Instrument Warnings
CAUTION
MISE EN GARDE
RISK OF ELECTRIC SHOCK
DO NOT OPEN
RISQUE DE CHOC
LECTRIQUE
NE PAS OUVRIR
WARNING: SHOCK HAZARD - DO NOT OPEN
AVERTISSEMENT : RISQUE DE CHOC LECTRIQUE - NE PAS OUVRIR
WARNING: SHOCK HAZARD - DO NOT OPEN
CAUTION: TO REDUCE THE RISK OF ELECTRIC SHOCK DO NOT
REMOVE ANY COVER OR PANEL. NO USER SERVICEABLE PARTS
INSIDE. REFER SERVICING TO QUALIFIED SERVICE PERSONNEL.
AVERTISSEMENT : RISQUE DLECTROCUTION - NE PAS OUVRIR

MISE EN GARDE : POUR RDUIRE LE RISQUE DE CHOC LECTRIQUE,
NE RETIRER AUCUN COUVERCLE OU PANNEAU. NE CONTIENT
AUCUNE PICE RPARABLE PAR L'UTILISATEUR. FAIRE APPEL UN

TECHNICIEN QUALIFI 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 RDUIRE LES RISQUES D'INCENDIE OU DE
CHOC LECTRIQUE, NE PAS EXPOSER CET APPAREIL LA PLUIE OU

L'HUMIDIT.
UN MAUVAIS USAGE DUN APPAREIL LECTRIQUE PEUT
PROVOQUER LLECTROCUTION, DES BRLURES ET DAUTRES

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 scurit de base, y compris celles numres cidessous.
Lisez toutes les instructions - Vous devez lire toutes les consignes de scurit et
d'utilisation avant d 'utiliser lappareil.
Conservez toutes les instructions - Vous devez conserver toutes les instructions
des fins de consultation ultrieure.
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 propos du ScanScope ainsi que de ceux indiqus dans les
instructions dutilisation.
2.
Follow All Instructions All operating and ScanScope usage

instructions must be followed.
Suivez toutes les instructions Vous devez suivre toutes les instructions
dutilisation du ScanScope.
3.
Heat The ScanScope must be situated away from any heat sources such
as radiators, heat registers, stoves, or other products that produce heat.
Chaleur Le ScanScope doit tre plac loin de toutes sources de chaleur telles
que les radiateurs, les bouches de chaleur, les cuisinires 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 manufacturers recommended
installation procedures.
Ventilation Le ScanScope est dot de fentes et douvertures de ventilation.
Elles assurent le fonctionnement fiable de l'appareil, en lempchant de
surchauffer. Ces ouvertures ne doivent pas tre bloques, ni couvertes pendant
lutilisation. Gardez les ouvertures libres de charpie, de cheveux, de peluches,
etc. Cet appareil ne doit pas tre plac dans un bti moins quune ventilation
adquate ne soit fournie en suivant le mode dinstallation recommand par le
fabricant.
5.
Biosafety Procedures Please refer to your institutions biosafety

policies and procedures regarding the proper handling of tissue and
other potentially hazardous materials in connection with the use of this
device.
Procdure de bioscurit Veuillez vous rfrer aux politiques et aux
procdures de bioscurit de votre tablissement relativement la manipulation
adquate de tissus et autres matires potentiellement dangereuses en lien avec
lutilisation de cet appareil.
6.
Water and Moisture Do not use the ScanScope near waterfor

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
becomes wet, unplug it before touching it.

Eau et humidit Nutilisez pas le ScanScope prs de leau, par exemple, un
bain-marie, une cuvette, un vier, une cuve de lessivage, dans un sous-sol
humide ou prs dun bassin ouvert. Si le ScanScope est mouill, dbranchez-le
avant de le toucher.
7.
Attachments Do not use any attachments not recommended by the

product manufacturer as they may cause hazards.
Accessoires Nutilisez pas daccessoires non recommands par le fabricant de
l'appareil, car ils peuvent causer 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 tre utilis quavec la source
dalimentation spcifie sur ltiquette signaltique et les instructions
dinstallation. En cas de doute sur le type de courant fourni votre
tablissement, consultez votre compagnie d'lectricit locale. Vrifiez si le
rglage de la tension correspond la tension dalimentation lectrique.
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 la terre et polarisation Le ScanScope est muni dune fiche c.a.
polarise contact intgr de mise la terre de scurit. En aucun cas, ne retirez
la mise la terre de scurit.
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
tre placs de manire ce qu'il y ait peu de risque qu'une personne marche
dessus ou qu'ils soient coincs par un meuble ou un autre objet. Veillez
particulirement protger le cordon prs 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.
clairage Pour protger davantage lappareil, dbranchez le cordon du
ScanScope de la prise murale c.a. pendant un orage ou sil est laiss sans
surveillance ou quil nest pas utilis pendant une longue priode. Cette mesure
empchera que la foudre ou quune surtension cause des dommages l'appareil.
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 intgres car ceci risquerait de provoquer un incendie ou une
lectrocution.
13. Operating Environment Observe these basic safety requirements:
Milieu de fonctionnement Respectez ces consignes de scurit de base :
Do not operate the ScanScope out of doors. Nutilisez pas le ScanScope

lextrieur.
Do not use where aerosol sprays are being used or where oxygen is
being administered. Ne l'utilisez pas proximit d'arosols ou dendroits
o de loxygne est administr.
Do not let the ScanScope or its cables or accessories come into

contact with surfaces which are too hot to touch. Ne laissez pas le
ScanScope ou ses cbles et ses accessoires entre en contact 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.
Pntration 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 pices et provoquer ainsi un incendie ou une
lectrocution. Veillez 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 manufacturers installation instructions. Do not place anything on
top of the ScanScope.
Accessoires Ne placez pas le ScanScope sur un chariot, un socle, un trpied,
un support ou une table qui nest pas stable. L'appareil pourrait tomber et
provoquer une blessure grave ou tre endommag. Si l'appareil est fix un
support, assurez-vous que les instructions d'installation du fabricant sont
respectes.
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
contact Aperio for advice.
Dplacement Le ScanScope doit tre dplac avec prudence. Un arrt
brusque, une force excessive ou une surface ingale peuvent faire tomber
lappareil. Le dplacement 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 un technicien qualifi 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 ncessitant un entretien Dbranchez le ScanScope de la prise
murale c.a. et faites appel un technicien qualifi dans les cas suivants :
When the AC cord or plug is damaged. Le cordon c.a. ou la fiche est

endommag.
If liquid has been spilled or objects have fallen into the ScanScope.
Du liquide a t renvers sur lappareil ou des objets sont tombs dans
lappareil.
If the ScanScope has been exposed to rain or water. Lappareil a t

expos la pluie ou lhumidit.
If the ScanScope does not operate normally (when you are following
operating instructions). Lappareil ne fonctionne pas normalement
(lorsque vous suivez les instructions dutilisation).
If the ScanScope has been dropped or damaged in any way.

Lappareil est tomb ou est endommag de quelque faon que ce soit.
When the ScanScope exhibits a distinct change in performance. This

indicates a need for service. Lappareil prsente des changements visibles
de performances. Cela indique la ncessit dun 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.
Pices de rechange Si des pices doivent tre remplaces, assurez-vous que le
technicien utilise bien les pices de rechange prescrites par le fabricant.
L'utilisation des pices non autorises peut entraner un risque d'incendie ou de
choc lectrique, 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.
Vrification du fonctionnement Aprs toute rparation du ScanScope,
demandez au technicien deffectuer les vrifications ncessaires pour s'assurer
que l'appareil est en bon tat de fonctionnement.
21. Cleaning Do not use liquid cleaners or aerosol cleaners. Use only a
damp cloth for cleaning.
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 rglage du ScanScope doivent
tre effectus uniquement par un reprsentant qualifi de service sur site dAperio.
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 support 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.
Figure 1: Front and top views of the ScanScope working area
AC Power
CAUTION: If the power cord supplied with this product does not match
the wall plug configuration, do not use. Contact a qualified electrician
to obtain the proper cord.
MISE EN GARDE : Si le cordon d'alimentation fourni avec ce produit ne
correspond pas la configuration de la prise murale, ne l'utilisez pas.

Contactez un lectricien qualifi pour obtenir le cordon appropri.
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 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 m per pixel with 20x
objective); 0.25 m per pixel when scanning at 40x with 2x optical mag
changer
Oil scanning: 150,000 pixels per inch (.17 m 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)
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 panel) 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

CPU 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 monitors resolution
Operating System:
Windows XP SP3 or Windows 7 (32-bit or 64-bit)
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.
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
panel 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 arrire de
l'ordinateur du ScanScope doit tre connect un rseau

informatique; il n'est pas conu pour tre connect un
systme tlphonique.
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
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.)
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 support 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 support.
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.
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.
2.
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.
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.
3.
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.
2.
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.
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 douvrir la porte d'accs pour le nettoyage ou
l'entretien du ScanScope, appuyez d'abord sur l'interrupteur principal

au dos de l'appareil pour le mettre la position arrt (0) puis
dbranchez le cordon d'alimentation afin d'viter que l'utilisateur ne

soit bless si une lecture tait commence par un utilisateur
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
occurredignore 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
ScanScopenever use compressed air inside the ScanScope.
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 pass. 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.
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 panel 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 contact Aperio Customer Service
for advice before operating the ScanScope.
Dans le cas peu probable o une lamelle se serait brise dans le ScanScope, enlevez les
morceaux de verre et le matriel biologique avec le plus grand soin. Mettez lappareil hors
tension et dbranchez le cordon dalimentation avant de mettre les mains l'intrieur de
l'appareil. En utilisant les dispositifs de protection appropris et en suivant les
procdures de scurit pertinentes, ramassez tous les morceaux de lamelles brises et
essuyez les pices visibles. Veuillez contacter le service clients dAperio pour obtenir des
conseils avant d'utiliser le ScanScope.
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 ScanScopes 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.
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. Users 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.
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 panel of the workstation.
4.
Press the power button on the front panel of the computer monitor.
5.
When the Microsoft Windows log on screen appears, press

Ctrl+Alt+Delete on the keyboard. Type your user name and password in
the appropriate fields.
Log in with the user name and password provided during ScanScope
installation. If your administrator has changed the default password (a
recommended security practice), contact your administrator if you do not know
the password.
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 panel of the ScanScope reads ScanScope
Ready.
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.
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 loignes de l'assemblage mcanique
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, contact Aperio Technical
Support for assistance.
Consult the material safety data sheets for the stains and re-agents you are using,
as well as your institutions bio safety policies and procedures regarding safely
handling biological materials.
Consultez la fiche signaltique des colorants et des ractifs que vous utilisez, ainsi que les
politiques et les procdures en matire de bioscurit de votre tablissement pour la
manipulation scuritaire du matriel 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.
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 conditionno 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 (dont use chemical cleaners).
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.
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 heardthis 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.
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 Users
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 terms 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.
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.
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.
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 appearthis 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 Users 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 Users 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 supports 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.
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 User's Guide for more information on the prescan
operation.)
5 |Calibration and Verification
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 Users 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, lets 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).
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 slides 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.
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.
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 Users 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 leftor

counterclockwise if viewing from below), protecting it by placing two
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 positionrehoming 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
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.
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 Users 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 login user name and password.
4.
Click Connect.
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.
When the ScanScope

loads the slide for
oil scanning, a slight
vibration noise can
be heardthis 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 trayyou
cannot move the scan area over those clips as that area cannot be
scanned.)
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.)
Setting Focus Points

1.
On the Focus Points tab, click Auto Select. This places points in a
rectangular grid (best for oil).
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 sizeclick 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.
Verify 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.
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.
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).
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.
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 numberthe 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.
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 doesnt pop up easily (due to oil underneath), dont push down, as
this will break the slide. Instead, use your fingernails to pry up under the label
side.
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
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
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 leftor

counterclockwise if viewing from below), protecting it by placing two
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 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 positionrehoming 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.
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 dun
chiffon pour remplacer l'ampoule. Lhuile de la peau rduit la dure de vie de la nouvelle
ampoule. Si l'ampoule doit tre nettoye, 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 panel.
1.
Turn off (O) the illuminators power switch (located on the rear panel),
then unplug the instrument from the power outlet.
3.
Remove the Illuminator light cable by loosening the retaining

thumbscrew.
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 Lampoule halogne devient chaude pendant
l'usage et peut causer une brlure si on la touche sans la laisser refroidir

suffisamment d'abord.
5.
Loosen the two front panel fasteners located on the lamp access panel.
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.
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 panel fasteners, then reinstall the light cable.
12. Plug the illuminators power cord back into the power outlet then turn
on (|) the main power switch.
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 rduire le risque d'lectrocution, n'effectuez
aucun entretien part le remplacement du fusible dcrit plus bas.

Confiez tout entretien un technicien qualifi.
If the rear panel 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 panel 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.
Appendix C |Replacing the AC Line Fuse
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 NoticeA 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.
Appendix D |Recovering from a Motion Fault
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 support contact your local Aperio office.
Refer to page ii of this manual for contact information.
Symptom
ScanScope fails to start up
or initialize.
Solution
1.
2.
Verify 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.
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.
Verify 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.
Verify that the slide tray is clean.
2.
Verify 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
verify that location is clear. Then move the blue

diamond (calibration point) to that clear area.
3.
If the calibration image contains coverslip or other

defects, try the parameter set coverslip to help
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, verify 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.
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
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
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 Support, 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 Users Guide

MAN-0030, Revision M

ScanScope CS UserGuide

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ScanScope CS

Copyright 2006-2013 Aperio

167 Banbury Road

1360 Park Center Drive

Oxford OX2 7HT

Tokyo, Japan 101-0062

Tel: 866-478-4111 (toll free)

Tel: +44 (0) 1865 339651

Tel: 866-478-4111 (toll free)

Fax: +44(0) 1865 339301

Tel: +44 (0) 1865 339651

Direct International Tel: 1 (760) 539-1150

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

ii | ScanScope CS User's Guide

Direct International Tel: 1 (760) 539-1150

Direct International Tel: 1 (760) 539-1150

ScanScope CS User's Guide| iii

Cleaning the ScanScope Casing .......................................................................... 22

iv | ScanScope CS User's Guide

APPENDIX A | OIL-IMMERSION SCANNING ...................................................... 41

ScanScope CS User's Guide | v

vi | ScanScope CS User's Guide

1 | Safety and Specifications

If You Need Help

ScanScope CS User's Guide | 1

1 |Safety and Specifications

Symbols and Warnings

alert you to the presence of important operating and maintenance

Le point d'exclamation dans un triangle quilatral vise avertir

The lightning flash with arrowhead symbol within an equilateral

dangerous voltage within the products enclosure that may be of

Le symbole de l'clair avec la pointe de flche dans un triangle

prsente une tension dangereuse non isole dune amplitude

The flat surface with waves symbol within an equilateral triangle is

cause burn damage.

Le symbole dune surface plane et de vagues dans un triangle

quilatral vise avertir l'utilisateur de la prsence de surfaces

2 | ScanScope CS User's Guide

1 |Safety and Specifications

ScanScope CS User's Guide | 3

1 |Safety and Specifications

AVERTISSEMENT : RISQUE DLECTROCUTION - NE PAS OUVRIR

AUCUNE PICE RPARABLE PAR L'UTILISATEUR. FAIRE APPEL UN

WARNING: TO REDUCE THE RISK OF FIRE OR ELECTRIC SHOCK, DO

MISUSE OF ELECTRICAL EQUIPMENT CAN CAUSE ELECTROCUTION,

AVERTISSEMENT : POUR RDUIRE LES RISQUES D'INCENDIE OU DE

CHOC LECTRIQUE, NE PAS EXPOSER CET APPAREIL LA PLUIE OU

UN MAUVAIS USAGE DUN APPAREIL LECTRIQUE PEUT

PROVOQUER LLECTROCUTION, DES BRLURES ET DAUTRES

4 | ScanScope CS User's Guide

1 |Safety and Specifications

Follow All Instructions All operating and ScanScope usage

Ventilation Slots and openings in the ScanScope are provided for

Biosafety Procedures Please refer to your institutions biosafety

Water and Moisture Do not use the ScanScope near waterfor

ScanScope CS User's Guide | 5

1 |Safety and Specifications

becomes wet, unplug it before touching it.

Attachments Do not use any attachments not recommended by the

Power Sources The ScanScope must be operated from the type of

Grounding and Polarization The ScanScope is equipped with a

6 | ScanScope CS User's Guide

1 |Safety and Specifications

12. Power Overloading Do not overload AC wall outlets, extension cords,