Roche iScan HT RUO User manual

VENTANA Image Viewer User Guide

Version 3.1.4

INTENTIONALLY BLANK

VENTANA Image Viewer User Guide

Ventana Medical Systems, Inc.

Part No.: PL-000132-EN Rev. B

VENTANA Image Viewer User Guide

COPYRIGHT

VENTANA, the VENTANA logo, VANTAGE and VIRTUOSO are trademarks of Roche. All other trademarks are the property of their

respective owners.

The VENTANA Image Viewer software is protected by contract law, copyright laws, and international treaties.

The VENTANA Image Viewer software is licensed for use between Ventana Medical Systems, Inc. and a licensee, and only users

authorized there under are permitted to access and use the software. Unauthorized use and distribution may result in civil and criminal

penalties.

Open Source and Commercial Software

The VENTANA Image Viewer software might contain components or modules that are Open Source or Commercial Software programs.

For copyright and other notices and licensing information regarding such Software programs included with the VENTANA Image

Viewer software please see the Appendix A of the reference guide and the product on-line help pages included with the product.

The product and the VENTANA Image Viewer as a whole may form a regulated device in accordance with the applicable laws - please

refer to the reference guide and the labeling for details. Please note that the respective authorization in accordance with the applicable

laws lapse in case of any unauthorized changes to the VENTANA Image Viewer software.

GOVERNMENT LIMITED AND RESTRICTED RIGHTS LEGEND

If this product is licensed for use by the United States or for use in the performance of a United States government prime contract or

subcontract, you agree that this product is delivered as: (i)”commercial computer software” as defined in DFARS 252.227-7013, Rights

in Technical Data - Noncommercial Items (Oct. 1988), DFARS 252.227-7014 Rights in Noncommercial Computer Software and

Noncommercial Computer Software Documentation (Jun. 1995), and DFARS 252.211-7015 Technical Data Commercial Items (May

1991); (ii) as a “commercial item” as defined in FAR 2.101; or (iii) as “restricted computer software” as defined in FAR 52.227-19,

Commercial Computer Software ― Restricted Rights (Jun. 1987); whichever is applicable. The use, duplication, and disclosure of this

product by the Department of Defense shall be subject to the terms and conditions set forth in the accompanying license agreement as

provided in DFARS 227.7202 (Oct. 1998). All other use, duplication and disclosure of this product and documentation by the United

States shall be subject to the terms and conditions set forth in the accompanying license agreement and the restrictions contained in

subsection (c) of FAR 52.227-19, Commercial Computer Software ― Restricted Rights (Jun. 1987), or FAR 52.227-14, Rights in Data

― General Alternative III (Jun. 1987).

Other product and company names mentioned herein are the trademarks of their respective owners.

Contact

Ventana Medical Systems, Inc.

a Member of the Roche Group

1910 E. Innovation Park Drive

Tucson, AZ 85755

USA

+1 520 887 2155

+1 800 227 2155 (USA)



www.ventana.com

Roche Diagnostics GmbH 

Sandhofer Strasse 116

D-68305 Mannheim

Germany

Part No.: PL-000132-EN Rev. B v

About the VENTANA Image Viewer Software

Welcome!

VENTANA Image Viewer software is bundled as part of the VENTANA iScan scanning system.

The VENTANA Image Viewer software allows you to examine, study, and annotate images stored

locally or remotely. The VENTANA Image Viewer software can be run in parallel with VENTANA

iScan scanning software, allowing for the switching back and forth between the two applications, or

it can be run in a stand-alone (independent) mode from the desktop.

The major features are:

• The VENTANA Image Viewer software application

This Guide Includes Instructions to:

• Use the VENTANA Image Viewer software to view digital-scanned slides locally or remotely.

Who Should Read This Guide?

• Pathologists and/or Technologists using the VENTANA Image Viewer software to view digital

images of slides

What’s in this Guide?

Related Document

For additional information, see the VENTANA Viewer Reference Guide

(PL-000112)

.

VENTANA Image Viewer Features “1: VENTANA Image Viewer Software” on page 1

vi Ventana Medical Systems, Inc. -- A Member of the Roche Group

About the VENTANA Image Viewer Software VENTANA Image Viewer User Guide

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Part No.: PL-000132-EN Rev. B vii

Table of Contents

About the VENTANA Image Viewer Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v

Welcome! . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v

This Guide Includes Instructions to: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v

Who Should Read This Guide? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v

What’s in this Guide? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v

Related Document . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v

Table of Contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

1: VENTANA Image Viewer Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Image Viewer Console . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Main Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Magnification Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Magnification Tooltips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Thumbnail Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Setting Up Image Server. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Starting Up VENTANA Image Viewer software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

View Information about the Image Viewer software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Open and View Online Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Configure General Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Open Local Image. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Open Remote Image from Image Management Service (IMS). . . . . . . . . . . . . . . . . . . . . . 6

Open Remote Image from Image Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

View Layered Volume Scans (Z-Stacking) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Open Recent Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Move Tool Bars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Arrange Multiple Images in Cascade Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Arrange Multiple Images in Tile Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Enhance Images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Show/Hide Thumbnail Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Track Areas of Interest Visited . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Highlight Areas of Interest Visited . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Measure Areas of Interest. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Display Measurements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Draw Annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Change Annotation Color . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Create and Display Text Annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

View Text Annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Modify or Delete Text Annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Save Annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Export Annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Create a Counter. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Reset Counter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19

Remove (Delete) Counter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Edit Counter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Export Count Annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Import Count Annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Merge Count Annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Close Images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21

Shut Down the VENTANA Image Viewer Software Console . . . . . . . . . . . . . . . . . . . . . . 22

viii Ventana Medical Systems, Inc. -- A Member of the Roche Group

Table of Contents VENTANA Image Viewer User Guide

Image Viewer Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23

Tool Bar Button Reference Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45

Part No.: PL-000132-EN Rev. B 1

1: VENTANA Image Viewer Software

VENTANA Image Viewer software can be run in parallel with VENTANA iScan scanners, allowing

for the switching back and forth between the two applications, or it can be run in a stand-alone

(independent) mode.

NOTE: In order to use the VENTANA Image Viewer software to view remote images, you may

have to modify settings in your Image Server configuration file. For more information,

see “Setting Up Image Server” on page 4.

Image Viewer Console

The VENTANA Image Viewer software console is the primary work bench of the viewing system

(See Figure 1). From here, you can open, view, edit, send, transmit, and share digital images.

Figure 1. VENTANA Image Viewer software Console

NOTE: The default magnification is 20X. The 60X and 80X digital zoom buttons are activated

and available only for images scanned at 40X.

Tool Bars

Magnification Tool

Thumbnail Window

Status Bar

Main Window

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Main Window

The Main Window (See Figure 2) displays the selected image.

NOTE: An image is opened at the magnification it was scanned at.

After an image is opened, you can change the magnification of the image as well as the brightness,

contrast, sharpness, and color balance of the image.

Figure 2. VENTANA Image Viewer software Main Window

Magnification Tool

The Magnification Tool (See Figure 3) is located in the upper left corner of the Main Window. Using

this tool, you can change the magnification of an image (using digital zoom).

Figure 3. Magnification Tool

NOTE: Digital zoom is performed electronically on the original scanned image and does not

utilize the optics of the scanner or increase optical resolution.

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Magnification Tooltips

When changing the magnification, tooltips (mouse-over hover boxes) appear displaying the current

level of magnification (See Figure 4).

Figure 4. Magnification Tooltips

Thumbnail Window

The Thumbnail window (See Figure 5), located in the upper right corner of the Main window,

displays a complete view of the image that is currently opened. This window includes a focus box

that outlines the area of interest corresponding to the part of the imaged displayed in the Main

Window. The Focus box is a navigation tool that can be grabbed and moved on the Thumbnail

window to adjust the position of the image in the Main window.

Figure 5. Thumbnail Window and Focus Box with Default Red Border

Main Tool Bar

Figure 6. Main Tool Bar Buttons Available When an Image is Open

Magnification Tool Bar

Figure 7. Magnification Tool Bar Buttons Available When an Image is Open

NOTE: The default magnification is 20X. The 80X button is activated and available only for

images scanned at 40X.

Focus Box

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Annotation Tool Bar

Figure 8. Annotation Tool Bar Buttons Available When an Image is Open

NOTE: Some of the annotation tools are inactive and grayed out and unavailable until at least one

annotation is drawn.

Setting Up Image Server

If possible, use the default settings. If not, follow the steps below to configure your VENTANA

Image Viewer software to view remote images.

1. Navigate to the folder where the Image Server is installed on your system.

2. Open the Image Server.bat file:

BioImageServer -d -port 85 -wd C:\Jp2Images -cd C:\DirTemp -time 360000 -clients 5 -

max_rate 5242880 -max_chunk 52428800 -cache 104857600 -initial_timeout 120 -restrict -

completion_timeout 1800 -connection_threads 4 -record

3. Edit the following settings to reflect the values for your system:

NOTE: In order to use the VENTANA Image Viewer software to view remote images, you may

have to modify settings in your Image Server configuration file.

Starting Up VENTANA Image Viewer software

You can start up the VENTANA Image Viewer software from the Windows Desktop or an iScan

scanner.

Starting up from the Windows Desktop

1. Double-click the VENTANA Image Viewer software icon. (See Figure 9)

The VENTANA Image Viewer software console is opened up on the Windows desktop (See

Figure 10).

You can also start up the VENTANA Image Viewer software from the Windows Desktop by

clicking Start



All Programs



VENTANA Image Viewer software. When the VENTANA

Image Viewer software console is started from the desktop, no image is displayed.

Figure 9. VENTANA Image Viewer software Desktop Icon

port 85 Change this to the port number on your system on which the Image Server is going

to run; for example, change

-port 85 to -port 53

.

-wd C:\Jp2Images Change this to the directory on your system that is going to hold the images; for

example, change

-wd C:\Jp2Images to -wd C:\JrsPhotos

.

-cd C:\DirTemp Change this to the temporary directory on your system that is going to hold the

images; for example, change

-cd C:\DirTemp to -cd C:\JrsTempPhotos

.

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Part No.: PL-000132-EN Rev. B 5

Starting up from the Scanner Console

Follow the instructions in the iScan scanner user guide for using the VENTANA Image Viewer

software with the scanner.

The image is opened on the Windows Desktop in the Main Window of the VENTANA Image Viewer

software console (See Figure 10).

An image is opened, by default, at 20X magnification, unless the magnification is changed before

an image is opened.

When the VENTANA Image Viewer software console is started from the scanner, an image and a

thumbnail view of the image are displayed in the main window. At this point, all menus and buttons

are active and available for use.

NOTE: Some Annotation Tools are inactive and grayed out and unavailable until at least one

annotation is drawn.

Figure 10. VENTANA Image Viewer software Console after Startup from Scanner (Image Open)

View Information about the Image Viewer software

1. Click Help



About VENTANA Image Viewer software.

The About VENTANA Image Viewer software Window is opened.

Open and View Online Help

1. Click Help



Online Help.

The Online Help system is opened on the console.

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Configure General Settings

1. Click Options



Settings.

The General Settings Window is opened.

The default parameters for the Image Viewer software are displayed.

These parameters can be changed to suit your needs or preferences:

Open Local Image

1. Click File



Open Local Image.

The Open Local Image dialog box is opened.

2. Navigate to the folder containing the image.

3. Click the name of the image in the list, then click

Open

.

The image is opened in the Main Window of the Image Viewer software.

After an image is opened, you can work with it using the VENTANA Image Viewer software

menus, buttons, and tools.

Open Remote Image from Image Management Service (IMS)

1. Click File



Open Remote Image.

The Open Remote Image dialog box is opened.

2. Enter the hostname for the computer where your Image Management Service (IMS) is

configured.

3. Enter your port number.

IMS is generally hosted on port 85. If you are unable to establish a connection with your IMS

using port 85, please contact your system administrator to find out your IMS port number.

4. Click

Connect

.

The folders containing images available for viewing at that location are listed.

5. Click a folder.

Magnification Available magnifications: 80X, 60X, 40X, 20X,10X, 4X, 2X, 1X. An image is

opened at the selected magnification. The default is 20X. The 80X and 60X

buttons are activated and available only for images scanned at 40X.

Thumbnail Focus Box Border Color: The default is red.

To change the color:

Click the Thumbnail Focus Box Border Color box: The Color Window is

opened.

Select a Basic Color, then click OK: The selected color is used for the Focus

Box Border.

You can create colors as well: Click Define Custom Colors; Create a color; Click

Add to Custom Colors; Click the Custom Color; Click OK. The Custom color is

used for the Focus Box Border.

Area Measurement Unit Area of a drawn annotation (shape) displayed in pixels, microns, or millimeters.

Continuous Pan Speed Speed of Continuous Pan Navigation tool. Scale: Low to High.

Annotations Tooltip Tooltip text annotations can be displayed when the cursor is placed on or over

annotation.

Mouse Wheel Custom magnification setting: Scroll Down - Zoom In, or Scroll Down - Zoom

Out.

Scaling Scale mouse motion sensitivity to magnification: Low - High.

AOI Display Select this option to display scanned AOI.

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The images in the selected folder are listed.

6. Click an image.

A copy of the image is posted in the Preview Pane of the window.

7. Click

Open

.

The image opens in the Main Window of the VENTANA Image Viewer software.

NOTE: In order to use the VENTANA Image Viewer software to view remote images, you may

have to modify settings in your Image Management Service configuration

Open Remote Image from Image Server

1. Click File



Open Remote Image.

The Open Remote Image dialog box is opened.

2. Enter the server name and port number.

3. Click

Connect

. The folders containing images available for viewing at that location are listed.

4. Click a folder.

5. The images in the selected folder are listed.

6. Click an image. A copy of the image is posted in the Preview Pane of the window.

7. Click

Open

. The image opens in the Main Window of the Image Viewer software.

NOTE: In order to use the VENTANA Image Viewer software to view remote images, you may

have to modify settings in your Image Server configuration file. For more information,

see “Setting Up Image Server” on page 4.

View Layered Volume Scans (Z-Stacking)

Slide images scanned as multi-layered volume scans in the iScan scanner can be viewed by layer

using the following procedure:

1. Click File



Open Remote or Local Volume Scanned Image.

2. Enter the server name and port number for remote images or navigate to the folder containing

the local image.

3. Click

Connect

for remote images.

The folders containing images available for viewing at that location are listed.

4. For local images click the name of the image in the list, then click

Open

.

The image is opened in the Main Window of the Image Viewer software.

Volume scanned images are indicated by the layer tool (See Figure 11)

that appears to the right of

the magnification tool on the Image Viewer console. Toggling the layer tool either up or down moves

between the layers of the volume scan. The amount of layers is specified in the iScan scanner before

scanning.

Figure 11. Volume Scan Layer Tool

Layer Tool

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Volume Scan Tooltips

When toggling between layers of a volume scan, tooltips (mouse-over hover boxes) appear

displaying the current layer of the image (See Figure 12).

Figure 12. Volume Scan Tooltips

In the following example, the volume scan consists of 3 layers; Layer 0 (See Figure 13), Layer 1

(See Figure 14), and Layer -1 (See Figure 15). By default, the volume scanned image is opened at

Layer 0. Toggling through the other layers brings different planes of the scan into focus for enhanced

evaluations.

Figure 13. Volume Scan Viewed at Layer 0

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Figure 14. Volume Scan Viewed at Layer 1

Figure 15. Volume Scan Viewed at Layer -1

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Open Recent Image

1. Click File



<Previously Opened Image>.

The image is opened in the Main Window on the VENTANA Image Viewer software console.

Move Tool Bars

1. Place the cursor on the left border of the bar.

2. Click and hold down the left mouse button.

The tool bar window is grabbed.

3. Move the tool bar to another position on the console or in the Main window.

4. Release the mouse button.

The tool bar is moved.

Arrange Multiple Images in Cascade Format

1. Click Window



Cascade.

Multiple images overlap each other, with visible title bars (See Figure 16).

Figure 16. Cascade Windows View

NOTE: The Thumbnail corresponds to the selected (active) image which has a window border

highlighted in blue.

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Arrange Multiple Images in Tile Format

1. Click Window



Tile.

Multiple images are arranged in rows, like tiles, with visible title bars (See Figure 17).

Figure 17. Tile Windows View

NOTE: The Thumbnail corresponds to the selected (active) image which has a window border

highlighted in blue.

Enhance Images

1. Click the Image Enhancements button: The Image Enhancement Window opens on the console.

2. Click the Brightness/Contrast/Sharpness tab.

3. Adjust the Brightness of the image on the console: Enter an integer between -100 and +100 in

the Brightness box, or drag the Slider Bar.

4. Adjust the Contrast of the image on the console: Enter an integer between -100 and +100 in the

Contrast box, or drag the Slider Bar.

5. Adjust the Sharpness of the image on the console: Enter an integer between -100 and +100 in

the Sharpness box, or drag the Slider Bar.

6. Click the Color Balance Tab.

7. Adjust the Cyan-Red Balance of the image on the console: Enter an integer between -100 and

+100 in the Cyan-Red box, or drag the Slider Bar.

8. Adjust the Magenta-Green Balance of the image on the console: Enter an integer between -100

and +100 in the Magenta-Green box, or drag the Slider Bar.

9. Adjust the Yellow-Blue Balance of the image on the console: Enter an integer between -100

and +100 in the Yellow-Blue box, or drag the Slider Bar.

10. Click

OK

.

The window is closed.

NOTE: If you want to use the enhancements for every image, click the Save As Default button.

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Show/Hide Thumbnail Window

1. Click View



Windows



Thumbnail.

The Thumbnail window is shown/hidden.

Track Areas of Interest Visited

1. Click View



Windows



Highlights.

The Highlight/Tracking Window is opened on the console.

2. Click the Track Visited box.

3. Click the Show box for every level of magnification.

Every area of interest visited at each level of magnification is tracked.

The percentage of the image visited at each level of magnification is displayed in the Visited

column.

Figure 18. Areas of Interest Visited and Highlighted at all available magnifications.

Highlight Areas of Interest Visited

1. Click View Windows



Highlights.

The Highlight/Tracking Window is opened on the console.

2. Click the Highlight Visited box.

3. Click the Show box for every level of magnification.

Every area of interest visited at each level of magnification is highlighted in the color

corresponding to the level of magnification (for example, 10X is green, 20X is dark blue and

4X is yellow) (See Figure 19).

Figure 19. Areas of Interest Visited and Highlighted at 10X, 20X and 4X

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