ScanScope FL UserGuide PDF

Aperio FL Console
Users Guide
MAN-0160, Revision C | 17 October 2013
Aperio FL Console Users Guide

This document applies to eSlide Manager Release 12 and later.
Copyright Notice
Copyright 2007-2013 Leica Biosystems Imaging, Inc. All rights reserved.
Customer Resources
For the latest information on Leica Biosystems Aperio ePathology products and services, please visit www.LeicaBiosystems.com/ePathology.
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 Leica Biosystems Imaging or for other advanced instruction. Leica
Biosystems Imaging Field Representatives should be contacted immediately for assistance in the event of any instrument malfunction. Installation
of hardware should only be performed by a certified Leica Biosystems Imaging Service Engineer.
ImageServer is intended for use with the SVS file format (the native format for eSlides created by scanning glass slides with the scanner).
Educators will use Aperio ePathology 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 Leica Biosystems Imaging, Inc. All other trade names and trademarks are the property of their respective holders.
Aperio ePathology 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.
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Aperio FL Console Users Guide, Revision C Leica Biosystems Imaging, Inc. 2013
Contents
1 Introduction to Scanning Slides...................................................................................... 6
What Happens During a Scan...............................................................................................................6

Compressing and Storing eSlides......................................................................................................7
Using the Aperio FL Console................................................................................................................8
For More Information.........................................................................................................................8
Additional Manuals........................................................................................................................8
2 Getting Started.................................................................................................................. 9
Prerequisites....................................................................................................................................9
Monitor Requirements....................................................................................................................9
Starting the Console........................................................................................................................10
What If the Scanner Is Not Connected to eSlide Manager?.................................................................... 11
Console Continue/Retry Window................................................................................................. 11
Selecting the Scanning Data Group..................................................................................................... 11
The Console Main Window................................................................................................................12
Viewing Slide Status........................................................................................................................15
Slide Operations Menu.....................................................................................................................17
Selecting Multiple Slides...............................................................................................................18
Slide Settings.............................................................................................................................19
Assigning a Parameter Set to a Group of Slides..................................................................................20
About Global Parameter Sets..........................................................................................................21
Error Handling................................................................................................................................22
3 Scanning Slides.............................................................................................................. 24
Connecting to the Aperio FL...............................................................................................................24
Loading Slides................................................................................................................................24
Automatic File Names...................................................................................................................27
Viewing Options..............................................................................................................................28
Setting up the Scan Area..................................................................................................................29
Channel Selection...........................................................................................................................31
Adding a Channel........................................................................................................................32
Channel Focus Offset Settings.....................................................................................................33
Changing Channel Scan Order.........................................................................................................33
Contents
Editing Dye Display Colors.............................................................................................................33

Setting Channel Exposure Time.......................................................................................................34
Placing Focus Points.........................................................................................................................37
Repositioning, Removing or Adding Focus Points.................................................................................38
Focusing the Focus Points..............................................................................................................39
Focus Offset (Optional)..................................................................................................................41
Additional Focusing Tools..............................................................................................................41
Performing a Calibration...................................................................................................................43
Setting and Using a Default Calibration Image....................................................................................44
Calibration Reports......................................................................................................................45
Scanning the Slide...........................................................................................................................45
Judging Scan Quality.......................................................................................................................48
Scan Quality Tips.........................................................................................................................49
4 Snapshot Review............................................................................................................ 50
Getting Snapshots...........................................................................................................................50
Reviewing Snapshots.......................................................................................................................53
Locked Snapshots........................................................................................................................54
Scanning After Snapshots Are Reviewed..............................................................................................55
5 Configuration Options.................................................................................................... 57
Image Properties.............................................................................................................................57
Motion Properties............................................................................................................................58
Macro Move...............................................................................................................................58
Stage Move................................................................................................................................58
Stage Options.............................................................................................................................58
ScanScope Properties.......................................................................................................................59
Properties..................................................................................................................................59
Compression...........................................................................................................................62
Overwriting a Parameter Set Property...............................................................................................62
Parameter Sets...........................................................................................................................63
Parameter Sets Override Console Options......................................................................................63
Slide Settings.............................................................................................................................63
Area of Interest ..............................................................................................................................63
Defining Dyes.................................................................................................................................64
Defining a Filter Wheel Configuration...................................................................................................65
Defining a New Filter....................................................................................................................66
Removing or Moving a Filter...........................................................................................................67
Defining a Filter Cube Configuration.....................................................................................................67
Defining a New Filter Cube............................................................................................................69
Contents
Moving or Removing a Filter Cube...................................................................................................70
6 2x3 Slide Scanning......................................................................................................... 71
Selecting 2x3 Slides.........................................................................................................................71

Resetting to 1x3 Slides.....................................................................................................................71
7 Working with a Magnification Changer......................................................................... 72

A Troubleshooting.............................................................................................................. 73
Optimizing Fluorescence Scans...........................................................................................................73

Choosing the Best Filters and Filter Cubes.........................................................................................73
Evaluating Macro Images..............................................................................................................73
Correcting Striped Images..............................................................................................................74
Thick Tissues..............................................................................................................................74
Focus Point Fading.......................................................................................................................74
Mounting Medium Selection..........................................................................................................74
Counterstains.............................................................................................................................74
Troubleshooting Tips........................................................................................................................75
B Barcode Support............................................................................................................. 77
Barcode Support.............................................................................................................................77
Optical Character Recognition (OCR)....................................................................................................77
Prerequisites and Limitations..........................................................................................................77
Installing Barcode and OCR Support.....................................................................................................78
Barcode/OCR Options.......................................................................................................................78
eSlide Manager Barcode/OCR Support.................................................................................................80
Index...................................................................................................................................... 81
Symbols................................................................................................................................ 85
Introduction to Scanning
Slides
This chapter introduces scanning on the Aperio FL.

The Aperio FL creates whole-slide images by scanning slides stained with multiple fluorochromes. For details on using the
Aperio FL, such as instructions on changing excitation filters, refer to the Aperio FL Users Guide.
Using the Console software to scan puts all of the scanning parameters under your control, enabling you to make decisions
about each of the scanning steps.
CAUTION: Keep hands clear of the mechanical stage assemblies when the scanner is operating.
MISE EN GARDE: Gardez les mains loignes de lassemblage mcanique et du disque porte-filtres
motoris et du barillet pendant le fonctionnement du numriseur.
What Happens During a Scan

Before we discuss using the Console, lets discuss the basic steps of scanning.
1. Install the filter set that is appropriate for the fluorochromes used to stain your slides. This includes inserting
excitation filters in the filter wheel and installing one or more filter cubes in the filter cube turret. (See the Aperio FL
Users Guide.)
2. Start the Console.
3. If the dyes you are using are not already defined in the Console and if the scanner is not using the standard set
of excitation filters in the filter wheel and filter cubes in the cube turret, you need to configure these items in the
Console now. (SeeChapter 5: Configuration Options on page 57 for details.) Note that the scanner ships
with a basic filter set installed that is already defined in the Console.
4. Open the Console and click the Manual Load button on the first tab of the Console to move the slide stage to the
slide access position so you can place one or more slides on it.
5. Position the slides into the tray with the coverslips facing up and the slide labels oriented to the left.
6. Insert the slide tray into the scanner.
7. The macro camera inside the scanner takes macro images of each entire slide and then each slide label.
8. After you place the slides in the tray, go through the scan setup steps discussed in Chapter 3: Scanning
Slides on page 24 to get ready to scan:
a. Set up the scan area by selecting the tissue area.
Chapter1: Introduction to Scanning Slides
b. Position the blue diamond calibration point on a background area that does not appear to have tissue.
Calibration helps differentiate tissue from non-tissue and provides a flatfield correction for the camera. The
blue diamond calibration point must be located in the part of the slide that is under the coverslip. See Setting
up the Scan Area on page 29 for more on the calibration point.
c. Select the channels to tell the scanner what dyes (fluorochromes) are used for the sample and what filters to
use for those dyes.
d. Determine and apply the exposure times for each channel.
e. Place focus points (at least four) on various areas of the tissue. 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. 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 scanner determines the range of focus for the piece
of tissue, and adjusts the scanner objective while scanning to ensure the highest possible quality scan. See
Placing Focus Points on page 37 for more information on setting, moving, and adjusting focus points.
f. Perform calibration. Calibrating scans a small region near the blue diamond calibration point and uses this
image to obtain a shading correction image for the tissue. See Performing a Calibration on page 43 for
more information on calibrating.
9. Click the Start Scan button on the Console Scan tab.
When the scan is finished, the scan stripes for each channel are stitched together into a single, compressed image
and saved to your ImageServer or other location specified using the Console. You can now view the digital image of
the slide using the Console, ImageScope, or through eSlide Manager.
Note that pressing the red button on the front of the scanner halts the scan process and returns the slide stage to
the slide access position.
Images acquired on the Aperio FL using the quad multi-bandpass filter cube should be perfectly registered. Images acquired
using single-bandpass filter cubes or images imported from other sources may require registration changes so that the
channels are aligned correctly. For information on adjusting image registration, see the ImageScope Users Guide.
Compressing and Storing eSlides

Because eSlides are fairly large in terms of file size, 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. By default, the scanner creates an
eSlide using the SVS file format using compression type 2 (JPEG).
You can use the Console configuration options to set the compression type and the file format to which the eSlide will be
saved. See Compression on page 62 for more information.
Chapter1: Introduction to Scanning Slides
Using the Aperio FL Console

The Console software provides an interactive scanning experience. You use it to connect to the scanner and direct the
scanning operation.
You can use the Console to:
`` Set all scan parameters.
`` Perform the scan.
`` Change the scanner configuration.
In addition to standard scanning features, the Console has a Snapshot Review workflow tool that saves time and provides
results tailored to your slides. See Snapshot Review on page 50 for details.
For More Information

For information on:
See:
Installing and starting the Console software
Chapter 2: Getting Started on page 9
Manual scanning using the Console to personally control

each scanning step
Chapter 3: Scanning Slides on page 24
Using snapshot review to speed up your scanning workflow
Chapter 4: Snapshot Review on page 50
Configuring the scanner using the Console
Chapter 5: Configuration Options on page 57
Configuring the scanner to use 2 x 3 slides
Chapter 6: 2x3 Slide Scanning on page 71
Magnification changer/doubler
Chapter 7: Working with a Magnification Changer on

page 72
Correcting possible scanning problems
Appendix A: Troubleshooting on page 73
Additional Manuals
For information on:
See:
Using the Aperio FL to create fluorescent eSlides
Aperio FL Users Guide
Using eSlide Manager to manage and view your eSlides
eSlide Manager Operators Guide
Using ImageScope to view and adjust eSlides
ImageScope Users Guide
Getting Started
This chapter introduces the Console and contains information on basic concepts and features.
Prerequisites
The Aperio FL Console software is installed on the scanner control workstation by Leica Biosystems Imaging Technical
Services. If you wish to install the Console software on additional workstations, please contact Leica Biosystems Imaging
Technical Services for assistance.
Monitor Requirements
Because 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 minimum requirements:
Display Type:
LCD (flat panel)
Screen Resolution:
1680(h) x 1050(v) pixels
Screen Size:
24-inch
Color Depth:
24-bit
Brightness:
300 cd/m2
Contrast Ratio:
500:1
Chapter2: Getting Started
Starting the Console

1. Start the Aperio FL Console by double-clicking the ScanScope Console icon on the Windows Desktop (as shown
below) or from the Windows Start menu by going to All Programs > ScanScope > ScanScope Console.
The first thing the Console does is ask you what scanner you want to connect to.
The Console passes along your login credentials if you open an eSlide from within the
Console by using another application (for example, by using the View Slide button to open the
eSlide in ImageScope), so you will not need to log in again to the new application.
2. Either type the name of the scanner you want to connect to in the Controller Name text box or select one from
the drop-down list of scanners that have been recently connected to.
3. Type your user name and password (the same user name and password you use to log into eSlide Manager). Your
eSlide Manager login must be assigned a user role that allows scanning.
4. Click OK.
10
What If the Scanner Is Not Connected to eSlide Manager?

If this scanner has not been configured to use a DataServer on your Digital Slide Repository (DSR), or if the DataServer is
down, you can leave the user name and password fields blank, and will still be allowed to use the Consolein this case,
however, any eSlides created will not be cataloged in eSlide Manager, but will be saved locally.
If the scanner is temporarily disconnected from eSlide Manager and you save images locally, later
you can manually move them to the image directory where eSlide Manager stores its images. Please
contact Leica Biosystems Imaging Technical Services for assistance.
Console Continue/Retry Window

If the network connection to the DSRDigital Slide Repositorywhere the scanner Controller normally saves scanned
images is lost, the Console displays a window that gives you several choices:
`` Retry the connection
`` Save images locally
If you continue the scan, the scanned image is not cataloged by eSlide Manager, but it is saved on the scanner itself or, if
another location is defined as the local image share, in that location.
Selecting the Scanning Data Group

By default, scanned images will be cataloged in eSlide Manager in the Default data group. However, the scanner operator
can choose which data group his or her eSlides will be added to by logging into eSlide Manager, going to the eSlide
Manager Administrative menu, selecting My Settings, and choosing the data group to add the scanned images to from the
Data Group for Scanning drop-down list:
11
The Console Main Window

Once you have selected an Aperio FL and connected to it, you see a window that looks something like the illustration below.
The graphic on the Start tab differs depending on whether slides have already been scanned.
12
The graphic may show that slides have already been scanned. An arrow indicates which slide in the tray is selected for
scanning.
13
If slides are already loaded in the scanner and have already been scanned, the Scan tab may be selected instead of the
Start tab and the window may look something like this:
14
Viewing Slide Status

The Start tab tray graphic displays color codes reflecting the state of the slide. Some of these color codes relate to the
snapshot feature (see Chapter 4: Snapshot Review on page 50).
Here are the color codes that can appear on the Start tab tray graphic:
Category
Snapshots
Slide State
Color Code
Needs Snapshot A slide is in the queue to

get a snapshot, but the snapshot has not yet
been made.
White with blue diagonal lines
Has Snapshot A snapshot was made of

this slide and it is available to be visited and
reviewed.
Light blue
Visited A snapshot was made of this slide and Dark blue

the snapshot has been reviewed.
Scanning
Failed Snapshot Scanner attempted to get a

snapshot of this slide but the snapshot failed.
White with red diagonal lines
Locked Another Console user is reviewing

this slides snapshot at this time, so you cannot
make changes to it.
Yellow with black diagonal lines
Scanning This slide is being scanned.
Yellow with the word

SCANNING
Scanned The slide was scanned and the

scanner was able to focus the tissue.
Green
15
Category
Rack Contents
Slide State
Color Code
Review The slide was scanned but the

scanner may not have been able to focus the
tissue.
Orange
Failed Scanner attempted to scan this slide,

but the scan failed.
Red
Unknown The state of this tray position is

Gray
unknown. It may contain a slide, but if so a
snapshot has not been made of it nor has it been
scanned
Empty No slide is in this tray location.
White
The scanning status colors displayed on the Console Start tab graphic indicate how well the scanner was able to focus the
tissue on the slide. Although a well-focused slide is likely to result in a better image than a poorly-focused slide, status
colors should not be interpreted as an absolute indicator of image quality.
Instead, they should be used as a diagnostic tool alerting you to possible problems with a scan. Regardless of the scan
status color displayed by the Console, all slides should be reviewed for acceptable image quality.
For information on the colors that indicate scan quality and for tips on improving your scans, see Judging Scan Quality on
page 48.
You can also determine the status of a specific slide by holding your cursor over the slide in the Start tab graphic:
16
Slide Operations Menu

The scanner Console displays a graphic representing all slide positions on the tray. Right clicking the mouse on any
individual position displays a menu of operations that act on that individual slide or the entire tray. (See the next section for
information on selecting multiple slides to affect groups of slides with a single command.) The arrow on the left hand side
of the tray indicates the current slide.
`` Get Snapshot and Review Snapshot These commands relate to the snapshot review feature. See Chapter
4: Snapshot Review on page 50.
`` Save Slide Settings This command lets you quickly save a variety of settings (such as fluorochromes and
exposure times) that can be applied to multiple slides. See Slide Settings on page 19 for details.
`` Apply Slide Settings You can apply a saved slide setting to a group of slides. SeeSlide Settings on page
19 for details.
`` Assign Parameter Set You can apply a scanning parameter set to one or more slides. See Assigning a
Parameter Set to a Group of Slides on page 20.
`` Set Current Slide This command directs the scanner to start the next scan operation with this position and
continue scanning through all remaining tray positions then continue through the remaining tray positions in a
normal fashion. If a slide is currently being scanned, the scan will be completed before moving to the new current
slide position.
`` Rescan Slide Select this command to cause the scanner to rescan the slide after the current set of slides have
been completed.
`` Remove Slide Selecting this command will mark that tray position as empty. The Console automatically detects
empty positions and skips the empty slots while continuing scanning. You can save some time by manually marking
the empty slide positions so that the scanner does not go through the mechanical process of determining that they
are empty. You can also use this command if you want to leave the slide in the tray but dont want to scan it.
17
`` Replace Slide Selecting this command will mark the slide position in the tray as occupied by a replacement
slide and ready for scanning during the next slide session.
`` Replace Rack Selecting this command will mark the entire tray as being replaced and ready for scanning during
the next slide session. If you lift out the tray, the tray status is reset just as if you used this command.
`` Clear Rack Marks every position in the tray as empty. Even if slides are loaded into the tray, they will be
skipped during scanning.
`` View Compressed Image If a compressed image is available, this command will open the scanned image file
in the ImageScope viewer.
`` View Uncompressed Image If an uncompressed image is available, this command will open the assembled
uncompressed image stripes in the ImageScope viewer.
Selecting Multiple Slides

You can affect multiple slides with a single command from the context menu when more than one slide is selected. To select
entire trays, click Select Rack on the tray graphic.
The illustration below shows the Select Rack box for the slide tray graphic:
You can also select specific slides using standard Windows techniques:
`` Click on one slide. Press and hold down the Shift key and click on another slide in the same tray to select a
contiguous group of slides.
`` Click on one slide. Press and hold down the Control key while you select non-contiguous slides.
`` Select multiple non-contiguous slides using the Control key, and then hold down the Shift and the Control keys to
select a contiguous group of slides without unselecting the previously selected slides.
18
Slide Settings
Parameter sets (discussed in the next section) apply to overall scanner settings. Slide settings on the other hand, define
slide-specific settings such as channel configurations and exposure settings.
After saving slide settings, you can apply the same settings to multiple slides. For example, if you have a set of slides from
the same block in which the tissue area is the same, you can set the scan area on one slide, save the slide settings, and
then apply the settings to an entire group of slides.
To create a slide setting:
1. Right-click on a slide in the Start tab graphic and select Save Slide Settings. The Add Slide Settings window
displays:
2. Select the settings for that slide that you want to save. For example, if all slides use the same channel
configurations, select Channels and Exposure Settings.
3. Type a name for the slide setting in the Setting Name box.
4. Click Save.
19
To apply a slide setting:

1. Select one or more slide positions in the start graphic and select Apply Slide Settings, then select the specific
setting you saved from the menu:
2. To remove a slide setting from a slide tray position, select that position, right-click, select Apply Slide Settings
and select None.
Assigning a Parameter Set to a Group of Slides

You can set scanning parameters for a group of slides by selecting multiple slides on the Console Start tab graphic and then
right-clicking while the cursor is on one of the selected slides. From the context menu, select Assign Parameter Set and
select the parameter set you want to use:
20
In the example above, slides 3, 4, and 5 are selected (the black border indicates they are selected), so the parameter set
selected applies just to them.
Parameter sets are optimized to handle special situations. For an explanation of the different parameter sets available, see
Chapter 5: Configuration Options on page 57. Remember to set the parameter set to None when you are finished
scanning.
You can also use the Save Slide Settings and Apply Slide Settings commands to define and apply your own set of
parameters.
See Reviewing Snapshots on page 53 for information on setting a parameter set or slide setting for a single slide in the
Review Snapshots window.
About Global Parameter Sets

There are three ways to apply a parameter set to slides:
1. From the Console Configuration window Selecting a parameter set here applies the parameter set to all
slides that dont currently have a parameter set applied. This is considered a global parameter set.
2. From the Console Start tab Right-clicking when one or more slides have been selected displays a context
menu from which you can select Assign Parameter Set and then choose a parameter set. From this menu you can
also select Global ParmSet and None.
21
3. From Snapshot Review Selecting a parameter set here applies the parameter set only to the slide selected for
snapshot review and overrides global parameter settings.
Global ParmSet and None behave differently: selecting Global ParmSet returns the slide to using whatever global parameter
set has been applied, while None overrides any global parameter set, causing the global parameter set to be ignored for the
selected slides.
Note that one exception to this is the 2x3 parameter set; a snapshot review parameter set cannot override the fact that a
2x3 slide is being reviewed, but can override other settings such as compression.
Error Handling
Because a great deal of slide scanning is automated, if an error occurs during scanning, rather than halting the scanning
process the scanner logs the error and continues scanning. After the scan is complete, you can review the error log to see if
any errors occurred and then take action to repair any errors.
To view the error log, go to the View menu and select Error Messages. The Error Messages window appears:
22
Click Clear List to reset the log or Close to exit.
23
Scanning Slides
This chapter discusses how to scan a single slide.

Lets assume the scanner does not have slides loaded. If it is not already running, start the Console software as discussed in
the previous chapter.
Connecting to the Aperio FL

When you start the Console, it asks you to log in (for details, see Starting the Console on page 10):
At any time you can bring up this window (for example, if your scanning session times out and you need to log in again or if
you want to switch to another scanner), by going to the Console ScanScope menu and selecting Connect.
Loading Slides
1. On the main Console window, click Manual Load.
The scanner slide tray is extended to provide access for slide loading.
2. Position slides into the tray with the coverslips on top and the slide labels oriented to the left. Ensure that the
slides are flat.
3. For the current slide, type the slide name in the File Name box and slide title in the Description box (both are
optional). (A large black arrow indicates which slide is the current slide. See the next page for an illustration.) If
you do not supply a file name, the scanner provides one.
24
Chapter3: Scanning Slides
To automatically assign a file name based on the slides barcode, see Automatic File
Names on page 27.
4. Click Manual Scan to perform a scan.

5. The slide is positioned under the macro camera and a macro image is created for display on the screen. The Scan
Area tab is automatically selected after the macro image is captured.
Note the following features:
`` The viewing options allow you to optimize the viewing window for the element you want to see. See Viewing
Options on page 28 for more information.
`` The blue diamond calibration point should be located on black background that does not contain cells or other
material. See Setting up the Scan Area on page 29 for information on moving the calibration point.
`` The green rectangle identifies the scan area. See Setting up the Scan Area on page 29 for information on
selecting the scan area.
`` The red rectangle identifies the maximum Area of Interest (AOI), which is the area in which the scan area is
located. See Setting up the Scan Area on page 29.
25
26
Automatic File Names

For identification purposes, it is sometimes convenient to have slide data encoded as part of the eSlide file name. For
example, you might want a barcode ID from a glass slides label to be part of the scanned images file name.
Below is a list of the special tags that you can specify in the file name which will get replaced by the actual data when
the file is saved to the disk. You can combine one or more tags along with static text in a file name. The tags must be
surrounded by curly braces. For example:
{ImageID}Barcode{BarCodeID}
Tag
Replaced with
{ImageID}
Slides image ID from eSlide Manager
{BarcodeID}
Barcode ID (if present)
{Rack}
The scanner tray the slide is in
{Slide}
The slide position in the tray
{Parmset}
The slides parameter set (if set)
You can also use the Console Configure window (see Chapter 5: Configuration Options on page 57) to set the file
name format permanently by using the ImageFilenameFormat property. The default value for that property is {ImageId}
simply replace it with your choice of the tags listed above, remembering to use the { } symbols. For example:
27
Viewing Options
You can easily zoom the viewing window to the Area of Interest (AOI), full macro image, or the scan area by using the
controls at the upper left of the screen:
These controls are also available on other Console tabs.

To use these controls:
`` Click
next to Zoom to collapse the menu. Click
to expand it again.
`` Click Macro to show the entire macro image.

`` Click AOI to show the Area of Interest (AOI).
28
`` Click Scan Area to zoom to the scan area.

(The choices in this menu depend on the Console tab you are onif not appropriate for that tab, a menu choice may not be
shown or the menu may not be shown.)
Setting up the Scan Area

1. Select the magnification level from the Scan Magnification list to match the objective lens installed on your
system (for example, 20 for 20x).
A simulated 10x scanning mode using 20x objective is also available. This mode uses a 20x objective at a faster
scanning rate to create a 10x scan.
If using the magnification changer (doubler), see Chapter 7: Working with a Magnification Changer on page
72.
2. Clear the Use Narrow Stripes check box to scan in wide stripes (1640 pixels wide) or select the Use Narrow
Stripes check box to scan in narrow stripes (992 pixels wide). Scanning wide stripes speeds up the scan. The
disadvantage of using wide stripes is that on uneven tissue, less tissue is focused. Narrow stripes provide better
focus with poorly prepared slides.
3. Select the tissue area to be scanned by adjusting the green selection rectangle using the following methods.
29
a. Adjust the green selection rectangle area and location by clicking on the rectangle and dragging the
appropriate adjustment handles.
b. Alternatively, adjust the rectangle by entering area and position coordinates into the entry boxes located in the
Scan Area window. The Left field indicates the number of millimeters the selection rectangle is positioned
from the left edge of the slide viewing area. The Top field indicates the number of millimeters the selection
rectangle is positioned from the top edge of the slide viewing area. The Width and Height fields indicate the
width and height, respectively, of the selection rectangle (in millimeters).
The scan area must be within the Area of Interestyou cannot drag the scan area outside of the Area of
Interest.
4. Position the blue calibration point
symbol to an area that does not contain tissue (either inside or outside of the
scan area selection rectangle). It is crucial that the blue diamond not be located on tissue to achieve proper flatfield
(shading) correction.
30
Channel Selection
Click the Channel Selection tab to view or define channels appropriate for the current glass slide.
Channels define the following:

`` What fluorochromes are present on the slide
`` Order in which the channels will be scanned
`` Filter cube to be used for each channel
`` Excitation filter to be used for each channel
`` Exposure time to be used for each channel
`` Focus offset to be used for each channel
You can also add and delete channels and edit the display color for each channel.
31
Adding a Channel
To add a channel:
1. Click Add Channel.
2. On the new channel line (shown in red on the Channel Selection tab), in the Dye column click Select a dye and
pick the dye to use from the list.
There are a number of things you can do on this dye list:

`` If you have a long list of dyes, you can go to a specific dye by typing the first characters of the dye name.
`` To define a new dye, select New Dye from the list. (For information on defining new dyes, see Defining
Dyes on page 64.)
`` To see information on the dye, right-click on the dye name and select View Details.
3. In the Filter Cube column, click Select a filter and select the filter cube to use from the list. (To define new filter
cubes, see Defining a Filter Cube Configuration on page 67.)
4. In the Excitation Filter column, click Select a filter and select the excitation filter to use (the filter in the scanner
filter wheel). (To define the filters contained in the filter wheel, see Defining a Filter Wheel Configuration on page
65.) Note that if you have defined a single-band filter cube in Step #3, you will not be permitted to assign an
excitation filter.
5. To set the exposure time for this channel, right-click in the specimen image and from the context menu select
Adjust Exposure and then select the channel:
32
6. If you prefer to enter the exposure time manually, you may do so by typing it in the Exposure column of the channel
table or using the arrows in the Exposure column. For details on automatically setting exposure, see Setting
Channel Exposure Time on page 34.
Channel Focus Offset Settings
Sometimes one channel has a slightly different focal plane than the first (reference) channel. This channel may require
a focus offset. To set a focus offset, type the value in the Focus Offset column. This value is relative to the registration
channel (the first channel listed on this window).
Multiple focus offset settings are available in the Console, and they are additive: Focus offset settings set by using the
global slide settings are added to the per-slide focus offset settings on the Focus tab (if any), which are added to the
channel focus offset settings on the Channel Selection tab (if any).
Changing Channel Scan Order

To change the order in which channels are scanned, click a channel to select it and use the up- and down-arrows to move it
up or down in the order.
Editing Dye Display Colors

To fine-tune the color to be used to display a channel, click Edit Display Colors.
33
7. Select a dye from the list on the left.

8. On the right, choose the color to be used to display that dye by using the slider control, entering new RGB values,
or clicking on a color.
9. When you are satisfied with the change, click Save.
This color selection is temporary for this channel configuration; if you remove a dye from this channel configuration and then
add it back in again, its color reverts to its original definition. (However, images scanned using this channel configuration are
permanently saved with the colors defined on this window.)
If you want to save these dye colors to use again, save the channel configuration on the slide settings.
Setting Channel Exposure Time

To set the exposure times to use for all channels:
34
1. Right-click on the macro image, select Adjust Exposure and then select an individual channel or All Channels.
2. If you have not already set exposure times, before finding the exposure time for the first channel, the scanner first
performs a macro focus and the Console then opens a window that shows the automatic exposure adjustment for
that channel at the spot you selected.
35
3. The histogram at the bottom of the image shows the distribution of pixels for different intensity values. You can
see this distribution either on a linear or logarithmic scale by selecting the appropriate control on this window.
a. If you want to use this exposure, click Accept Exposure.
b. If you want to fine-tune the exposure, use the slider control on the left. As you move it up and down, the image
changes to reflect the change and the Reset Exposure and Check Exposure buttons are enabled. Note that
the updated image is an approximation of the new exposure. To verify it, you must use the Check Exposure
button.
c. To set the exposure back to the suggested value, click Reset Exposure.
d. If you have changed the exposure, you must click Check Exposure so that the Console can test this exposure.
When it is finished, click Accept Exposure if you are satisfied with the image.
The pixels shown in the histogram at the bottom of the exposure window should not extend into the red region. In
the example below, the red pixels in the image are saturated, indicating that this exposure time may result in an
image that is overexposed.
36
Placing Focus Points

With fluorescence scanning, focus points must be placed manually on the macro image. Note that a minimum of four focus
points is required or scanning will not proceed.
1. Click the Focus Points tab. A macro image of the scan area appears in the upper portion of the screen.
The focus points you set appear as small yellow squares. If any of the focus points are positioned in clear areas of
the slide, you will need to delete them or reposition them away from the clear areas and into areas that contain
tissue. You can also add or remove focus points as needed. Larger scan areas should contain more focus points and
smaller scan areas should contain fewer focus points.
37
Repositioning, Removing or Adding Focus Points

When you click a focus point to select it, the focus point becomes bigger to distinguish it from the other focus points.
Selected focus point
`` To reposition a focus point, left-click it and then drag it to the desired location or select the focus point and use
the Move controls:
`` To remove a focus point, right-click it and then click Delete This Point from the context menu. To remove all
focus points, click Delete All Focus Points.
`` To add a focus point, double-click the new position or right-click the mouse in the desired location and select Add
Focus Point Here from the context menu. The context menu is slightly different if you right-click on a focus point
(as above) or right-click an empty position (below):
38
Focusing the Focus Points

When the video monitor window is open, light from the light source is hitting the sample. Dont leave
the video window open for long periods of time or you risk photo bleaching your sample.
1. Press the Alt and M keys or go to the View menu and select Video Monitor to open the Video Monitor window.
2. Resize the Video Monitor so it is wider than it is tall.
3. Drag the Video Monitor window so that it is adjacent to the macro image if needed.
4. Right-click one of the focus points and select Auto Focus This Point from the context menu.
Verify that the image in the Video Monitor window is in focus. The image you see is a direct feed from the line camera, a
series of stripes from the first channel. (All other channels are focused with respect to the first channel.) You want to see a
sharp image of the stripes. If the image is not sharp, use the focus sliders below the macro image to bring the image into
focus. Also, see Additional Focusing Tools on page 41 for more methods of focusing.
Note that the appearance of the stripes in the video window will vary depending on the tissue. If there are no stripes, then
your cursor is not on tissue or cells.
39
5. Click the Auto Focus button.

The focus points 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, rightclick, and then select Auto Focus This Point.
40
Focus Offset (Optional)

Focus offset is a function of the specimen, and may be different for every slide. Typical offset values are between -0.3 to
+0.3 microns, although they may be outside of that range.
The Focus Offset resets to zero when you load a new slide as this value is for a single slide only. For information on how
different focus offsets in the Console interact, see Channel Focus Offset Settings on page 33.
Additional Focusing Tools

In addition to the Auto Focus button, the Console provides these focusing tools:
`` Use the Focus slider to fine-tune the focus of the currently selected focus point (the currently selected focus point
is larger than the others). View the video monitor window to see the focus.
Moving the slider up moves the scanner objective up; moving the slider down moves the
objective down.
41
`` You can also use the focus point context menu by right-clicking on a focus point:
`` Right-click on a focus point and select Manual Macro Focus from the context menu.
A Manual Macro Focus window appears on which you can use a coarse and fine sliders to fine-tune the focus of
the image in the video monitor window:
42
`` Right-click on a focus point and select Clear All Focus Values from the context menu to reset all focus points to
their default value of 100. You will then need to use the Auto Focus button or manually focus the points before
performing a calibration.
Performing a Calibration
The Calibration operation acquires a shading correction image for each channel.
1. Click the Calibrate tab.
2. Click the Calibrate button.
A calibration image is acquired for each channel. When the calibration operation is complete, the calibration images
appears in the upper portion of the window. The calibration images should be relatively uniform from left to right with no
artifacts. (The illustration below shows three typical calibration images. The images will look different if you are using 20x
or 40x narrow stripes.)
43
The calibration image for the first channel is displayed at the top with the other channels following in order. In the example
below, three channels have been defined.
The three calibration images may show different levels of darkness depending on the level of background fluorescence in
different channels, and this is not a problem. However, ideally each image should be even with no debris or artifacts, and
evenly shaded (not lighter or darker on one side than on the other).
If the calibration images display artifacts, go back to the Scan Area tab and move the blue diamond calibration point to
another location and make a new calibration image. Or you may want to use a default calibration image (see the next
section).
Setting and Using a Default Calibration Image

Some slides contain very little black area. In this case, you may not be able to successfully make a calibration image.
If you have previously made a good calibration image, you may save it as a default image by clicking the Set As Default
button. If you have a default image saved, and a subsequent calibration fails, you will be asked if you want to use the
default image. Click Yes or No.
44
If you want to use the default calibration image for this scan only, select the Use Default check box and click the Calibrate
button:
To use a default calibration image for a group of slides:

`` Create a slide setting for a slide with the Use Default Calibration check box selected on the Add Slide Setting
window, and then apply that slide setting to the group of slides.
`` Or you can globally apply a slide setting that uses the default calibration image to all scans.
For more information about using a default calibration image, see Slide Settings on page 19.
Calibration Reports
As part of their regulatory compliance process, some laboratories and clinics require a written record of equipment
calibration. The scanner calibrates itself each time you scan a slide and sends the calibration information to eSlide Manager
where you can access a complete report of calibrations. See the eSlide Manager Administrators Guide for details.
Scanning the Slide

After setting all of the scan parameters on the preceding tabs, you can go to the Scan tab to start the scan.
45
1. Click the Scan tab.
2. Click the Start Scan button.

The slide scanning process begins. If you have not already pre-focused them, the focus points turn from yellow to
green as the focus points are focused ahead of the scan.
46
Each channel is scanned separately in the same location (if you have three channels configured, then you see
the same stripe scanned three times, each time displayed in the color assigned to the fluorochrome used for that
channel).
The number of stripes in the scan is displayed during the scanning process. This number is based on the size of the
area to be scanned and whether the scan is in wide or narrow stripes.
3. After scanning is completed, click the View Slide button to preview the image (using ImageScope), to check the
quality of scan and focus. (See the next section for information on scan quality.)
At this point, the image is compressed in the SVS file format (or whatever file format or compression type you have
selected using the Console configuration optionssee Compression on page 62 for information on setting
different compression types).
All images are automatically saved and the scan information is logged into eSlide Manager after scanning is
complete.
47
Judging Scan Quality

After the slide is scanned, the graphic on the Scan tab gives you an indication of the success of the scan. The slide tray or
rack graphic will display a color for each slide scanned.
The scanning status colors displayed on the Console Start tab graphic indicate how well the scanner was able to focus the
tissue on the slide. Although a well-focused slide is likely to result in a better image than a poorly-focused slide, status
colors should not be interpreted as an absolute indicator of image quality.
Instead, they should be used as a diagnostic tool alerting you to possible problems with a scan. Regardless of the scan
status color displayed by the Console, all slides should be reviewed for acceptable image quality.
The status of each slide is represented on the Start tab as follows:
Green
Successful Focus
Red
Failed Scan
Orange
Review Scan for Quality
Gray
Status is unknown
Yellow
In Progress
White
Empty
For example, the status display below indicates that the slide in position 2 of the slide tray was scanned with good focus.
We recommend reviewing all eSlides for quality, including those marked as Successful.
Additional status colors relate to the snapshot review feature. See Viewing Slide Status on page 3 for a complete list of
status colors.
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Scan Quality Tips

Here are some things to look for when reviewing an eSlide for scan quality. A good quality scan:
`` Does not have visible seams between stripes
`` Has stripes that are evenly illuminated (that is, one edge of the stripe is not consistently darker than the other)
`` Is uniformly in focus with no blurry areas
For help in correcting possible scanning problems, refer to Appendix A: Troubleshooting on page 73.
49
Snapshot Review
This chapter discusses using snapshot review to improve your slide-scanning workflow.
Operators can manually perform all of the pre-scan steps on one slide at a time.
In some cases, workflow is improved if the operator first views the snapshots of the slides, manually sets the scan areas,
sets focus points, chooses parameter sets, and so on, before scanning. The advantages of doing so are:
`` Smaller scan areas can be preselected by the operator, reducing the amount of time needed to scan the slides.
`` Snapshots of slides that are difficult to scan, such as slides containing high background staining, can be adjusted
before scanning, yielding better results.
`` Re-scans are reduced as the operator reviews the slide snapshots before the slides are scanned, spotting and
correcting potential problems before scanning.
`` If after review some scans are found to be of poor quality, snapshots of those slides can be reviewed and adjusted
to correct the problem before scanning those slides again.
For fluorescence scanning, snapshot review works best when all the slides use the same fluorochrome/filter combinations.
That way, you can create a single slide setting for the slides, apply that setting to all your slides, then use the snapshot
feature to set your scan areas, focus points, and so on.
Here is a summary of how snapshot review works (more details are below):
1. Load the slides you want to scan.
2. Choose a subset (or choose all) of the slides and tell the scanner to take snapshots of those slides.
3. Review the snapshots before scanning to set scan areas, focus points, scanning parameters, slide settings, and so
on.
4. After reviewing and adjusting all the snapshots, start scanning the slides.
Getting Snapshots
To get a snapshot, select one or more slides on the tray graphic on the Start tab of the console. (For information on how to
select more than one slide at a time, see Selecting Multiple Slides on page 18.)
After you have selected one or more slides, right-click with the cursor on one of the selected slides and select Get
Snapshot (or Get Snapshots if more than one slide is selected) from the context menu:
50
Chapter4: Snapshot Review
As the scanner gets the snapshots, a status window indicates progress:
51
While the slide is in the snapshot queue, the status color of the slide turns to white with blue diagonal lines. After the
snapshot is finished, the slide status color turns to light blue.
After it has been reviewed, the status color turns to dark blue. See the table below for all snapshot review status colors.
Here are all the slide status colors that apply to snapshot review:
Slide State
Color Code
Needs Snapshot A slide is in the queue to get a

snapshot, but the snapshot has not yet been made.
White with blue diagonal lines
Has Snapshot A snapshot was made of this slide and

it is available to be visited and reviewed.
Light blue
Visited A snapshot was made of this slide and the

snapshot has been reviewed.
Dark blue
Failed Snapshot Scanner attempted to get a

snapshot of this slide but the snapshot failed.
White with red diagonal lines
Locked Another Console user is reviewing this slides

snapshot at this time, so you cannot make changes to it.
Yellow with black diagonal lines
(See Viewing Slide Status on page 15 for information on all slide status colors.)
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Reviewing Snapshots
After snapshots have been made, select one or more slides on the Console Start tab graphic that display the light blue
status color and right-click while your cursor is over one of the selected slides. Select Review Snapshot (or Review
Snapshots if multiple slides are selected) from the context menu. The Review Snapshots window appears:
Features of this window include:

`` Viewing Controls By selecting AOI in the viewing controls on the top left, you can see the initial scan area and
then drag the boundaries of the scan area to select a new scan area. By selecting Scan Area you can zoom into the
scan areathis viewing mode is useful when placing focus points by hand. See Viewing Options on page 28
for details on using these controls.
`` Standard Scan Controls On this window you can select many of the same options you would select if you were
manually scanning a single slide, but you are presetting these options prior to the scan. (See Viewing Options on
page 28 for details on scan area, focus points, parameter sets, and other scanning parameters.)
If you leave the file name blank, the scanner will assign a unique file name to the scanned image. If you rescan this
slide using the same file name, the scanner will add a number to the file name to differentiate it from the previous
scan (for example, myfilename-001.svs).
Note that you can set scanning parameters for just this slide, or on the Start tab you can apply a parameter set or
slide settings to a group of slidessee Assigning a Parameter Set to a Group of Slides on page 20 or Slide
Settings on page 19.
`` Color-coded Border The border of the image portion of the Review Snapshots window reflects the status of
the slide. For example, if the border is green, that slide has been successfully scanned. The sample above shows
a light blue border, which indicates that the slide snapshot has not yet been saved with review changes. (Once
snapshot review changes are committed, the border becomes dark blue.) See Getting Snapshots on page 50
for a discussion of the snapshot status color codes.
`` Multiple Snapshot Navigation If you are working on a group of snapshots, the Review Snapshots window
contains Back/Next buttons so you can easily go from one snapshot to the next.
`` Dont Scan If while reviewing this snapshot you decide you dont want to scan this slide, clicking Dont Scan
removes it from the scan queue.
53
`` Revert While you are making changes on the Review Snapshots window, the Revert button is enabled. Clicking
revert reverses all of the uncommitted changes you have made during this session.
If you make a change that changes a setting directly on the scanner, that change is considered committed and
cannot be reversed. For example, clicking Next commits all changes, so if you return to the slide by clicking Back,
the Revert button is disabled because the previous changes cannot be reversed.
The best way to understand this is to use the Review Snapshots window and to try the Revert button to see its
effect.
Locked Snapshots
If you try to review a snapshot that someone else is currently reviewing, the review screen has a yellow and black border
letting you know that the snapshot is lockedwhile you can look at the snapshot, you wont be able to change its settings:
54
If you look at the Start tab, the yellow/black status color tells you which snapshots are being reviewed and are therefore
locked:
Scanning After Snapshots Are Reviewed

To start scanning after reviewing the snapshots, click One Touch on the main Console window. The scanning will begin
with whichever slide is the current slide and proceed through the rest of the slides in the slide tray (whether or not
snapshots have been taken of those slides).
55
The currently selected slide has a large arrow next to it:
To set another slide as the current slide, right-click on the new slide and select Set Current Slide from the context menu.
56
Configuration Options
The Console Configure window allows you to view and change scanner settings.
To open the Configure window, go to the Tools menu and select Configure.
Image Properties
The Image Properties tab displays information about the current slide:
`` File Name The file name assigned to the slide by the person who scanned the slide.
`` Description The description may include details of the experiment or scanning conditions.
`` Update Changes the slide name and slide title to the values you type in the File Name and Description text
boxes. When rescanning a slide you may enter a new file name or description, but must click Update to commit the
changes.
`` Slide File Path The location of the slide image of the last scanned slide.
`` Scan Time The amount of time it took to scan the last slide and the area of the scan.
57
Chapter5: Configuration Options
Motion Properties
The Motion Properties tab contains options for moving the stage.
Macro Move
`` MC Move button Using macro camera coordinates, move the camera to the location specified by the x and y
values.
Stage Move
`` Stage Move Using stage coordinates, move the stage to the location specified by the x and y values.
`` Nudge by Moves the stage by the constant amount specified in the Nudge by box every time one of the four
nudge buttons is selected.
Stage Options
`` Extend Extends the stage to accept a slide.
`` Retract Retracts the stage.
`` Home Runs the stage homing procedure. Also puts the filter cubes and filter wheel in the home position.
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ScanScope Properties
The ScanScope Properties tab allows you to change options and view settings for the scanner.
Properties
1. To view a property setting, enter the Name and click Get.
2. To modify a property setting, enter the Name and a new Value and click Update.
Many of these properties are factory settings that should not be changed in the field. In fact, mixing these
settings improperly can have serious consequencesplease contact Leica Biosystems Imaging Technical
Services for advice if you are not sure how to use these properties.
Properties and parameter sets are stored in the controller.xml file, but we advise you to use the Console configuration
options to select/change them instead of editing the xml file directly.
59
Here are some of the properties that you may wish to change or that Technical Support may advise you to change if they are
assisting you in troubleshooting a problem:
Property
Description
CacheSlideSettings
Saves the macro image of the slide in the tray. To enable, set to True.
CompressionQuality
Controls the JPEG and JPEG2000 compression quality. We recommend a value larger
than 20 and no more than 80. A quality factor of 30 typically results in acceptable image
quality at 30:1 compression (JPEG2000) or 15:1 compression (JPEG).
CompressionType
Settings: 0=None, 1=LZW, 2=SVS with JPEG, 5=SVS with JPEG2000 using Kakadu
library, 10=CWS, 12=JP2. See Compression on page 62 for more information.
DoCompression
Creates the file using the type of compression specified in CompressionType. For
example, if SVS is selected as the compression type, this parameter converts the file to
an .SVS file.
DoFastAlign
If set to true, takes advantage of Release 8 higher performance alignment. Performance

benefits vary depending on the model of the scanner.
DoLabelCapture
Controls whether a label image should be captured during macro image processing.
DoWrite
Controls whether the scanner should write raw stripes to disk.
DSRFailureResponse
Controls what happens if the scanner is not able to save the scanned image to eSlide
Manager because the connection to the DSR has failed. The two options are: 1) ask the
user if he wants to continue the scan saving the image locally or stop the scan (Ask)
or 2) continue the scan and save it locally without asking the user (Continue).
FiberLightIntensity
Adjust the intensity of the scanner light from 0 to 100
FileShare
The name of the Microsoft file share that points to the Stripes directory.
FocusOffset
Fine-tunes autofocus; in microns.
GoodFocusThreshold
The contrast number used to reject a bad focus point.
ImageLocation
The location where compressed slides are stored. Typically a network address.
ImageLocationByDate
If set to True, all compressed slides will be stored in ImageLocation in a folder with the
current date.
ImageServerPort
Specifies which port is used by the ImageServer.
ImageServerURL
The ImageServer name.
LCDPort
Specifies which port is used by the LCD display.
MacroAoiBottomPix
This number establishes the Area of Interest in which the search for tissue will occur.
This is the bottom coordinate where 0,0 is the upper left corner.
MacroAoiLeftPix
This is the left coordinate where 0,0 is the upper left corner.
MacroAoiRightPix
This is the right coordinate where 0,0 is the upper left corner.
MacroAoiTopPix
This is the top coordinate where 0,0 is the upper left corner.
60
Property
Description
MacroFocusPointRadius
Used by the tissue finder routines to control the number of focus points placed on
tissue.
MacroMaxNumberFocusPoints
tissue.
MacroMinNumberFocusPoints
tissue.
MacroNoiseErosionNumber
tissue.
MacroSpatialSigmaThreshold
tissue.
MacroUseBimodalNoiseReject
tissue.
MacroUseColorOnly
tissue.
MacroWhiteSigmaThreshold
tissue.
PrescanDistance
PrescanDistance controls how far in millimeters the scanner scans when capturing a
calibration image. The default value is 1 millimeter. If you are having trouble getting a
good calibration image, increase to improve quality of the calibration image (but it takes
longer to get the image).
PrescanVelocityMultiplier
Decreasing this value can improve calibration images, but it takes longer to get the
image. Increasing this value can speed up calibration at the expense of image quality.
For slides with artifacts in the background (for example, slides prepared with tape
transfer), increasing this value can exaggerate those artifacts. If you are having trouble
getting a good calibration image, try setting this to 2 or 1 to improve the quality of the
calibration image.
QuickSnapAfterHome
If set to true, then the controller will take snapshots of all the slides in the tray after
starting up (homing). This can be useful when combined with the CacheSlideSettings
property. After the machine starts up, you see all the macro images in the Console. This
is only useful for scanners that use a multi-slide tray.
SaturationAdjust
Affects the Consoles video monitor. A value of 1 means do nothing; a value greater
than 1 makes colors richer; a value less than 1 makes colors duller.
SkipBlankStripes
Skips areas of the slide where there is no tissue. To enable set to True.
StripeLocation
The location where raw stripes are stored. Typically C:\Stripes.
TempImageLocation
If ImageLocation is unreachable, this location will be used temporarily. This must define
a valid disk path.
VSRPort
Specifies the TCP/IP port used by the DataServer.
VSRServer
Specifies the name of the DataServer.
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Compression
By default, the scanner creates an eSlide using the SVS file format using compression type 2 (JPEG). You can use the
CompressionType to set the compression and file type for the image:
Setting
0
1
10
12
Compression
File Format
None Output file is a raw TIFF file with no compression.

LZW Compressed TIFF file with lossless Lempel-Ziv Welch
compression. This typically results in a compression ratio of 2:13:1.
JPEG Lossy compression using arithmetic encoding. You may
specify image quality using CompressionQuality (20-90). Output
is an SVS (TIFF) file. Compression ratios are in the range 15:120:1.
JPEG2000/Kakadu - Lossy compression using wavelets,
implemented by the Kakadu image library. You may specify the
target compression ratio using CompressionQuality (20-90).
Output is an SVS file. Compression ratios are in the range 20:125:1.
JPEG Lossy compression using arithmetic encoding. Output is a
JFIF file. Compression ratios are in the range 15:1-20:1. NOTE: it
is not possible to scan directly to this format, but it can be output
from DSS and ImageScope
CWS Lossy compression using arithmetic encoding. You may
specify the target image quality using CompressionQuality (2090). Output is a Composite WebSlide (directory). Compression
ratios are in the range 15:1-20:1.
JPEG2000/Kakadu Lossy compression using wavelets,
implemented by Kakadu Image Library. You may specify the
target image quality using CompressionQuality (20-90). Output is
a JP2 file. Compression ratios are in the range 20:1-25:1.
Extension
TIFF
TIFF
.TIF
.TIF
TIFF
.SVS
TIFF
.SVS
JFIF
.JPG
CWS directory
containing
multiple JFIF files
(directory)
JP2
.JP2
Please be aware that if you set compression type to 0 (uncompressed), you can potentially create an image file greater than
4GB, which Windows may not be able to open. If you have a need for uncompressed images, but they are too large for you
to use, contact Leica Biosystems Imaging Technical Services for alternative methods of creating uncompressed files that will
be easier to use.
Overwriting a Parameter Set Property

By default, you cannot change a property when it is contained in the currently applied parameter set. Selecting the
Overwrite Parmset check box allows you to change a property even if it is in the parameter set. Note that this option
allows you to overwrite just the property in the parameter set that you are changing, but does not disable any other property
in the parameter set.
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Parameter Sets
Parameter sets are predefined settings which have been provided for scanning certain types of tissue. By default, the
parameter set is None.
1. To change the parameter set, click on the arrow to the right of the Parameter Set box. You will see a list of
available parameter sets.
2. Select a parameter set from the list and wait for the Configure panel to update.
Here are some of the most commonly used parameter sets:
Parameter Set
Description
2 x 3 Support
This parameter set is covered in Chapter 6: 2x3 Slide Scanning on page 71.
None
The default set.
When you have completed scanning with a parameter set, reset it back to None; leaving a parameter set active will cause
all future scans to be performed with the selected parameter set. Note that the Brightfield Alignment parameter sets are
used during the manufacturing process and should not be used in the field. You may define your own parameter sets
please contact Leica Biosystems Imaging Technical Services for assistance.
Parameter Sets Override Console Options
If a Console option setting is required for a particular parameter set, choosing that parameter will automatically override the
existing option settings.
Slide Settings
Choosing a slide setting from the Slide Settings drop-down box applies those settings to all slides in the slide tray. See
Slide Settings on page 19 for more.
Area of Interest
This window allows you to reposition the Area of Interest (AOI) by moving the red rectangle to suit your slide layout.
Note that the AOI does not indicate which area of the slide will be scanned, but rather which area will be considered for
scanning. The actual scan area must be a subregion within the AOI.
63
In most cases you will get better results not using this feature, but instead performing a manual scan to let the Console set
the AOI.
Defining Dyes
On the Dyes tab you see the list of dyes currently defined for this scanner.
To search for a dye, begin typing the name of a dye in the Available Dyes search box. For example, to go to the first
occurrence of Alexa in the example above, type a in the search box.
You can also use the New Dye and Delete Dye buttons to define and delete dyes.
64
To define a new dye:

1. Click New Dye. You see the New Dye window.
2. Type the name of the dye you want to define and type the information about the dye (peak excitation and peak
emission values).
A color is automatically chosen based on that dyes peak emission wavelength. Select the display color for the dye
by entering an RGB value, using the slider to select a color, or clicking on a color box in the color display.
3. Click Save.
Defining a Filter Wheel Configuration

On the Filter Wheel tab you can see the list of all filters defined on this scanner. For installed filters, you see where they are
installed on the filter wheel inside the scanner. This configuration MUST match the physical installation of the filters in the
scanner. (For instructions on physically installing the filters in the scanner filter wheel, see the Aperio FL Users Guide.)
The filter wheel configuration also must be in sync with your filter cube configuration. For example, if you are using a filter
cube that contains both an emission and an excitation filter, you will need to leave one position of your filter wheel empty so
that the excitation filter in the filter cube will be used.
65
Defining a New Filter

To define a new filter:
1. Click New Filter to see the New Filter window.
2. Type the name of the filter (you might want to use its catalog number as its name), and band configuration
information.
3. Click Save.
66
Removing or Moving a Filter

To add a filter to the wheel configuration after you have defined it, simply drag it onto the filter wheel map.
To move a filter on the wheel map, drag it to its new position on the wheel map.
To remove a filter from the filter wheel map, right-click it in the filter table and select Delete Filter.
You can also move or delete filters by clicking the down-arrow next to the filter in the Position column and selecting a
position number (or to remove it, selecting None).
Defining a Filter Cube Configuration

On the Cube Turret tab you can see the list of all filter cubes defined on the Aperio FL and where they are installed on the
filter cube turret. This definition MUST match the physical installation of the filter cubes. (For instructions on physically
installing the filter cubes in the scanner, see the Aperio FL Users Guide.)
67
Multi-bandpass cubes will have a + symbol next to the position number. Click the + symbol to see all emission bands
included in the filter cube definition.
To see information on all emission bands included in this filter cube, click the filter cube on the map. For example:
Tip: To remove a filter cube, add a filter cube to an empty position, or change a filter cube in the scanner, you must move the
appropriate cube position in the turret to the loading position. To do this, select the filter cube position number in the Move
the filter number into load position drop-down list or double-click the position on the cube turret map shown on this tab.
68
Defining a New Filter Cube

To define a new filter cube:
1. Click New Cube to see the New Filter Cube window.
2. Type the name of the filter cube. You can use any name you like, such as dye name, catalog number, or description.
3. Define the emission and/or excitation filters included in this configuration. (For a multi-bandpass cube, click Add
Band to add a band.)
4. Click Save.
To add a filter to the wheel configuration after you have defined it, simply drag it onto the filter wheel map.
69
Moving or Removing a Filter Cube

To move a filter cube on the cube turret map, drag it to its new position on the map.
To delete a filter cube, right-click it in the filter cube table and select Delete Filter. To remove it from the cube turret map,
drag it away from the map.
You can also move or delete filters by clicking the down-arrow next to the filter in the Position column and selecting a
position number (or to remove it, selecting None).
70
2x3 Slide Scanning
The Aperio FL supports scanning slides that are 2x3 inches in addition to normal 1x3 slides. This option is an additional
feature and Aperio provides a separate slide tray which holds two 2x3 slides.
The settings required for 2x3 scanning are held as a Parameter Set within the Console.
Selecting 2x3 Slides

1. To change to the 2x3 parameter set, go to the Tools menu and select Configure. Do not select the parameter from
the slide context menu on the Start tab graphic.
2. Click the ScanScope Properties tab.
3. Select the 2x3 Support parameter set from the Parameter Set drop-down list. Wait for the update to complete.
When the update is completed you will see that 2x3 Support is selected in the Parameter Set box.
The Start screen will display the tray for 2x3 slides as shown below. The parameter set makes all the necessary
adjustments for you and will automatically set Narrow Stripes.
4. Scan as you normally do, but using the 2x3 slide-tray.
Resetting to 1x3 Slides

To return to scanning 1x3 slides:
1. Go to the Tools menu and select Configure to open the Configure window.
2. Click the ScanScope Properties tab.
3. Select None from the Parameter Set drop down list.
Wait for the screen to update to show the None parameter set selected. The console has been reset to scan 1x3
slides.
71
Working with a Magnification

Changer
The ScanScope FL is provided with a built-in optical magnification changer (also known as a mag changer) that enables
scanning with different magnification using a single objective lens.
Magnification - for scanning with 20x Objective:
yyMagnification changer out = 20x
yyMagnification changer in = 40x
You will see on the ScanScope LCD system display that the mag changer is in. Pull gently until it stops before starting the
system.
To use the mag changer:
1. Push the mag changer in. If you are unable to push it all the way in, perform a manual scan and wait for the
macro image to appear; this will lower the objective lens.
The Console will automatically recognize the mag changer (doubler). The magnification will change and the bottom
left hand corner will show Scanner Ready, Doubler Inserted.
2. To return to the previous magnification, simply pull the mag changer out as far as it will go. The Console will return
to the original magnification.
72
Troubleshooting
This appendix contains tips for troubleshooting the most common problems you may encounter with your
scanner.
If the information below does not help you find or fix the problem you are having, for further technical support contact Leica
Biosystems Imaging Technical Services. Refer to page ii of this manual for contact information. Also, see Troubleshooting
Tips on page 75 for more troubleshooting information.
Optimizing Fluorescence Scans

This section contains some tips on optimizing the scans you make with the Aperio FL. We discuss some of the potential
problems that can occur and how to correct them.
Choosing the Best Filters and Filter Cubes

When you set up a scan, you must choose the appropriate filters for each fluorochrome:
`` For a multi-band filter cube, make sure you select both the filter cube and the appropriate excitation filter.
`` For a single-band filter cube, dont select an excitation filter.
`` If you select the wrong excitation filter for a cube, you may not get an accurate staining pattern for a fluorochrome.
Most fluorochromes can be viewed with one or more cubes (single-band or multi-band). However, some filters are better
matched to a particular fluorochrome or are preferred because they show less background or bleed-through. Use the filters
that you would use on a fluorescence microscope if possible. Note that filters must be mounted in the Olympus filter blocks
(BMF version, preferably of the zero-shift type if single-band filters).
Evaluating Macro Images

The quality of the macro image affects how easy it is to see where the tissue is located on the slide and depends on many
things:
`` Debris, oil, fingerprints, or wipe marks on the slide or cover slip.
`` Thickness of the tissue (thicker sections have whiter and more dense macro images than thinner ones). See Thick
Tissues on page 74 for more information.
`` Thin sections and cell preps may not even produce a visible macro imageyou may need to outline the scan area
with a marker pen prior to scanning. Note that the Aperio FL is designed for scanning tissue, not cells.
`` If the mirror in the scanner is not clean, this may affect the macro image.
73
AppendixA: Troubleshooting
Correcting Striped Images

Striped images may result from:
`` Poor calibration images for shading/flatfield correction due to:
yy Background debris from tissue transfer tape
yy Debris on top of the tissue/cells or cover slip
yy Pap pen residue
yy Tilted cover slips from uneven mounting or oversized cover slips
yy Thick tissues where focal planes vary from stripe to stripe
`` Long exposure times in one or more channels
Thick Tissues
Thick tissues are difficult to scan. The Aperio FL is optimized for scans of samples less than 25. Although thicker samples
may be scanned, focus problems may occur.
Focus in thick tissues varies widely across the tissueit sometimes helps to scan using the Narrow Stripes setting.
Focus Point Fading

When exposure times are long, the intensity of the Aperio FL light source can cause regional photobleaching in a circular
pattern due to the frequency of focus point checks in the focus channel (e.g., DAPI). (Advanced users can adjust the
frequency of focus point checks in the Aperio FL Controller .xml file. The default is 180 seconds; you can try setting it to 240
seconds). Focus point fading more often occurs on older slides or when DAPI is present in the mounting medium.
Mounting Medium Selection

The mounting medium can be aqueous or resin-based. Resin-based products harden, but some of them can be dissolved if a
slide has to be re-stained. An antifade reagent should be used to retard photobleaching. Some antifade reagents include:
`` ProLong Gold Highly recommended, particularly for Alexa Fluor dyes (both are Invitrogen productssee http://
www.Invitrogen.com).
`` ProLong Pre-dated ProLong Gold (Invitrogen productsee http://www.Invitrogen.com).
`` Vectashield Hard Set Mounting Medium (Vector productsee http://www.VectorLabs.com).
`` DABCO Usually homemade or you can purchase from Sigma (http://www.SigmaAldrich.com) or other vendors.
Counterstains
DAPI is a popular counterstain that makes it easy to focus on the tissue because it stains the nuclei. DAPI may be included
in the mounting medium, but this may result in more background fluorescence. Therefore, some researchers prefer to stain
the slides with DAPI, then rinse off the excess dye before adding mounting medium and a cover slip.
74
Troubleshooting Tips
Symptom
Solution
Scanner fails to start up or initialize.
Verify that the power switch at the back of the unit is on and that the external
light is on.
Console or LCD displays Failed to

move stage or Check stage locks.
If the stage is locked, you cannot scan. Contact Leica Biosystems Imaging
Technical Services for assistance.
Trouble scanning a particular slide.
1. Is the slide tissue unusually thick or thin? Try performing a manual macro
focus.
2. Is the label large or located inside the area of interest? Remove the label or
adjust the area of interest.
During the scan you are unable to

obtain a macro focus.
1. Try another slide to see if the problem is with the slide. Ensure that the
slide is not upside down in the slide tray. Move focus points to ensure that
tissue or cells are present for focusing.
2. Try performing a manual macro focus.
3. Unusually thick or thin slides may require adjustment of the macro focus
limits.
4. Another reason for not being able to obtain a macro focus is that the
exposure time for a channel is too short to give the scanner enough time
to find the macro focustry increasing the exposure time of the first
channel.
Entire image is out of focus.
Verify that the slide is being held flat and not moving in the tray during scanning
(tape down the slide if necessary).
Individual stripes of the image are

This may indicate that the slide is moving during scanning.
poorly focused but a neighboring stripe 1. Verify that the slide tray is clean.
is perfect.
2. Verify that the slide is sitting flat and not rocking.
3. A very thick tissue section may show a focus problem between stripes.
4. Air bubbles or debris under a focus point may affect regional focus thereby
throwing off the focus of a particular stripe.
Autofocus did not detect at least four
focus points.
1. Assign additional focus points or move the focus points and repeat the
process.
2. Manually focus the focus points using the video monitor.
75
Symptom
Calibration image or slide images are
not even or one side of each stripe is
less focused than the other side.
Solution
1. Calibration is probably of poor quality.
2. Ensure that there are no labels or debris on the underside of the slide. Slide
must be flat.
3. Calibration is critical to fluorescence scanningyou may need to use a
default calibration image. See Performing a Calibration on page 43 for
details.)
4. Repeat with another slide. An uneven calibration may also indicate optical
misalignment. This usually requires a service visit or factory repair.
Striped images (focus is good but the

image has stripes)
1. Note whether exposure times for any of the channels is long (for example,
greater than .500 ms) and try adjusting them.
2. Use a default calibration image. (See Performing a Calibration on page
43 for details.)
3. Scan using narrow stripes.
Scan quality is not good.
76
It may be that a motion fault occurred and was not recovered from. See the
Aperio FL Users Guide for information about recovering from a motion fault.
Barcode Support
Glass slide labels often contain barcodes that contain information about the slide (for example, patient
name, case number, stain, etc.).
For licensed barcode types, the Aperio FL automatically reads the barcode on a glass slide label and saves the barcode
string with the eSlide. Human-readable text can also be read from the slide label using the Aperio optical character
recognition feature.
A one-time installation of a license enables support for all barcode types or OCR option for which you have purchased
support. (Customers who have previously purchased support for barcode types automatically receive support for the
previously purchased barcode types when they purchase a license for the new barcode types.)
Barcode Support
The Aperio FL supports the following barcodes: 2D DataMatrix, Interleaved (ID) 2 of 5, Code 39, Code 128, and QR Codes (a
two-dimensional matrix barcode that is common in Japan where it is the most popular type of two-dimensional barcode).
To purchase support for one or more barcode types, contact your Leica Biosystems Imaging representative, who will email
you a license string to decode the barcode types you have purchased support for.
Once the license string is installed, the scanner will automatically switch between licensed barcode types with no operator
intervention necessary when you scan slides that contain those types of barcodes.
Optical Character Recognition (OCR)

When an OCR license is installed that enables optical character recognition (OCR), printed human-readable text can be read
from the glass slide label and saved with the eSlide.
Prerequisites and Limitations

`` English text only is supported.
`` If the OCR decoder is not able to decipher a character, a ? character is added after it.
`` Printed text is supported, but hand-written text is not.
`` Minimum size supported is 40 pixels for a capital letter.
`` There should be at least 2 pixels separating lines so that a descender from one line (as in the case of a g) does
not touch an ascender (for example, in characters such as A, t, and h) from the following line.
Leica Biosystems recommends that sample slides with OCR data be sent to Leica Biosystems Imaging Technical Services for
evaluation before you purchase OCR support.
77
AppendixB: Barcode Support
Installing Barcode and OCR Support

Here is how to install the license string you receive from Leica Biosystems Imaging:
1. Go to the Tools menu and select Configure.
2. Click the ScanScope Properties tab:
3. In the Name field, type BarcodeLicense and click Get to view the current setting.
4. In the Value field, type the license string you received.
5. Click Update.
Barcode/OCR Options
To provide support for marginal barcodes that may not meet specifications, the Aperio FL Console provides several
properties to help with the decoding of those barcodes. If you find you are using these properties frequently for your
particular barcodes, you may want to save them as a parameter set to make them easy to call up for your scanning.
78
Property
Description
Values
Barcode Types
Supported
BarcodeUseShortMargin
The specification for each

type of barcode defines
how much empty space is
required around the barcode
symbol. If the barcodes you
are using do not meet this
requirement (for example,
one edge of the barcode
is too close to the edge of
the label), use this property
to tell the scanner to not
require a margin.
True or False
BarcodePartialMinLength
Defines how many

characters are in this
barcode. Normally used for
partial barcodes, but can
also be useful when a full
barcode is mistaken for a
partial barcode because of
noise on the edge.
0 to disable, >0 to enable.

ID 2 of 5, Code 39, Code 128
Value should not be larger
than the character length of
the barcode you are trying to
decode.
BarcodeImproveBounds
Improves readability when

the edge of the barcode
contains noise (also slows
processing).
True or False
BarcodeChecksum
If the barcode contains a

checksum character, handles
the checksum as indicated
by the property value.
Disable; Check (looks for

checksum and appends it
to the end of the barcode
string); Strip (looks for
checksum character and
strips it from the barcode
string.
ID 2 of 5, Code 39
79
Property
Description
Values
Barcode Types
Supported
BarcodeC39FullASCII
Normally Code 39 barcodes True or False (default)

can contain only uppercase
English letters, numbers,
space, dollar sign, percent
sign, plus symbol, hyphen
and a slash. With this
property enabled, Code
39 barcodes can contain
lowercase letters and any
other character you can type
on a keyboard.
Code 39
BarcodeDMSymbolSize
Can help improve the

decoding of small
DataMatrix barcodes. This
should not be enabled
unless you have small
barcodes and are having
trouble decoding them.
Default = Normal.
Normal, Small, Smallest
DataMatrix
True or False
ID 2 of 5, DataMatrix, Code
39, Code 128
BarcodeImproveLowContrast Can help decoding barcodes

when there is little
separation in color/intensity
between the barcode and
the background.
Default = false.
eSlide Manager Barcode/OCR Support

Although the scanner automatically saves the barcode value or text into the eSlide Manager barcode field for the image, to
configure and parse the data from a barcode and populate appropriate data table fields in eSlide Manager may require some
custom work by Leica Biosystems Imaging. Contact Leica Biosystems Imaging Technical Services for assistance.
80
Index
A
Aperio FL Console. See Console
Area of Interest, AOI 25, 63
automatic file names 27
B
barcode support 77
C
calibration 7, 43, 44
default image 44
report 45
calibration point 25
channel exposure time 34
channel selection 31
compression 7, 62
configuration
image properties 57
motion properties 58
options 57
ScanScope properties 59
connect to scanner 10, 24
Console 8
Area of Interest (AOI) 28
connect to the scanner 10
global parameter 21
group parameters 20
installing 10
logging in 10, 24
macro image 28
main window 12
manual scanning 24
none parameter 21
scan area 28
scanning 55
slide status colors 15, 48
snapshots
getting 50
locked 54
reviewing 50, 53
starting 10
Start tab 12
status graphic 12
continue/retry when DSR connection lost 11
controller properties 60
D
data group, selecting 11
default calibration image 44
digital slide
file name 24
from barcode 27
doubler 72
dye
defining 64
setting display color 65
E
error
handling 22
log 22
eSlide
compression 7
creating 7
data group 11
eSlide Manager 7
exposure time, channel 34
81
Index
F
filter cube
defining 67
deleting 70
moving 70
filter wheel
defining 65
deleting a filter 67
moving a filter 67
fluorochromes
dye 32
focus offset
additive offsets 33
per channel 33
per slide 41
focus points
adding, repositioning, moving 38
automatically focusing 41
manually focusing 42
placing 37
focus slider 41
assigning to snapshots 53
global 21
overwriting property 62
problems 73
R
regulatory compliance, calibration reports 45
narrow stripes 29
saving images locally 11

scan area 25
scanner, connect to 24
scanning 6, 46
2x3 slides 71
errors 22
introduction 6
narrow/wide stripes 29
placing focus points 37
prescan 43
quality 48
tips 49
ScanScope properties 59
selecting scan data group 11
slide settings 20, 63
applying 20
creating 19
slide status
colors 15, 48
viewing 15
snapshots
getting 50
reviewing 50, 52
slide status colors 52
status graphic 12
symbols
product label 85
users guide 85
J
judging scan quality 48
L
live video monitor 39
loading slides 24
logging in 10, 24
M
magnification changer, using 72
manuals, list of 8
OCR support 77
P
parameter sets
assigning to multiple slides 20
82
troubleshooting 73
U
uncompressed files 62
Index
V
viewing scanned image 47
W
wide stripes 29
83
Index
84
Symbols
The following symbols may appear on your product label or in this users guide:
Manufacturer
Date of manufacture (year - month - day)
European Union Authorized Representative
In vitro diagnostic device
Serial number
Relative humidity range
Storage temperature range
Electronic and electrical equipment waste disposal

The exclamation point within an equilateral triangle is intended to alert you to the presence of important operating
and maintenance (servicing) instructions.
Le point dexclamation dans un triangle quilatral vise avertir lutilisateur quil sagit dinstructions dutilisation
et dentretien 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 lclair avec la pointe de flche dans un triangle quilatral vise avertir lutilisateur que le botier
du produit prsente une tension dangereuse non isole dune amplitude suffisante pour constituer un risque
dlectrocution.
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 lutilisateur de la prsence
de surfaces chaudes qui peuvent causer des brlures.
The UV lamp within an equilateral triangle is intended to alert you to the presence of UV light within the
products enclosure that may be of sufficient magnitude to constitute a risk to the operator.
La lampe UV dans un triangle quilatral vise avertir lutilisateur de la prsence de rayonnement
UV dans le botier du produit qui peut tre dune amplitude suffisante pour constituer un risque pour
lutilisateur.
85
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Aperio FL Console

MAN-0160, Revision C | 17 October 2013

Aperio FL Console Users Guide

Trademarks and Patents

Contact Information Leica Biosystems Imaging, Inc.

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

US/Canada Tel: +1 (866) 478-4111 (toll free)

Tel: +1 (866) 478-4111 (toll free)

European Union Authorized Representative

What Happens During a Scan...............................................................................................................6

Editing Dye Display Colors.............................................................................................................33

Moving or Removing a Filter Cube...................................................................................................70

6 2x3 Slide Scanning......................................................................................................... 71

Selecting 2x3 Slides.........................................................................................................................71

7 Working with a Magnification Changer......................................................................... 72

Optimizing Fluorescence Scans...........................................................................................................73

This chapter introduces scanning on the Aperio FL.

What Happens During a Scan

Chapter1: Introduction to Scanning Slides

Compressing and Storing eSlides

Chapter1: Introduction to Scanning Slides

Using the Aperio FL Console

For More Information

Installing and starting the Console software

Chapter 2: Getting Started on page 9

Manual scanning using the Console to personally control

Chapter 3: Scanning Slides on page 24

Using snapshot review to speed up your scanning workflow

Chapter 4: Snapshot Review on page 50

Configuring the scanner using the Console

Chapter 5: Configuration Options on page 57

Configuring the scanner to use 2 x 3 slides

Chapter 6: 2x3 Slide Scanning on page 71

Chapter 7: Working with a Magnification Changer on

Correcting possible scanning problems

Appendix A: Troubleshooting on page 73

Using the Aperio FL to create fluorescent eSlides

Aperio FL Users Guide

Using eSlide Manager to manage and view your eSlides

eSlide Manager Operators Guide

Using ImageScope to view and adjust eSlides

ImageScope Users Guide

LCD (flat panel)

1680(h) x 1050(v) pixels

Chapter2: Getting Started

Starting the Console

Chapter2: Getting Started

What If the Scanner Is Not Connected to eSlide Manager?

Console Continue/Retry Window

Selecting the Scanning Data Group

Chapter2: Getting Started

The Console Main Window

Chapter2: Getting Started

Chapter2: Getting Started

Chapter2: Getting Started

Viewing Slide Status

Needs Snapshot A slide is in the queue to

White with blue diagonal lines

Has Snapshot A snapshot was made of

Visited A snapshot was made of this slide and Dark blue

Failed Snapshot Scanner attempted to get a

White with red diagonal lines