Spectrum/Spectrum Plus. Operator s Guide

Transcription

1 Spectrum/Spectrum Plus Operator s Guide

2 Copyright 2007 Aperio Technologies, Inc. Part Number/Revision: MAN 0045, Revision B Date: December 3, 2007 This document applies to software versions Release 9.0 and later. All rights reserved. This document may not be copied in whole or in part or reproduced in any other media without the express written permission of Aperio Technologies, Inc. Please note that under copyright law, copying includes translation into another language. User Resources For the latest information on Aperio Technologies products and services, please visit the Aperio Technologies website at: Disclaimers This manual is not a substitute for the detailed operator training provided by Aperio Technologies, Inc., or for other advanced instruction. Aperio Technologies Field Representatives should be contacted immediately for assistance in the event of any instrument malfunction. Installation of hardware should only be performed by a certified Aperio Technologies Service Engineer. ImageServer is intended for use with the SVS file format (the native format for digital slides created by scanning glass slides with the ScanScope scanner). Educators will use Aperio software to view and modify digital slides in Composite WebSlide (CWS) format. Aperio products are FDA cleared for specific clinical applications, and are intended for research use for other applications. Trademarks and Patents ScanScope is a registered trademark and ImageServer, TMALab, ImageScope, and Spectrum are trademarks of Aperio Technologies, Inc. All other trade names and trademarks are the property of their respective holders. Aperio products are protected by U.S. Patents: 6,711,283; 6,917,696; 7,035,478; and 7,116,440; and licensed under one or more of the following U.S. Patents: 6,101,265; 6,272,235; 6,522,774; 6,775,402; 6,396,941; 6,674,881; 6,226,392; 6,404,906; 6,674,884; and 6,466,690. Contact Information Headquarters: Aperio Technologies, Inc Vantage Court Vista, CA United States European Office: Aperio 3 The Sanctuary Eden Office Park Ham Green Bristol BS20 0DD, UK United States of America Tel: (toll free) Fax: Customer Service Tel: (toll free) Technical Support Tel: (toll free) support@aperio.com Europe Tel: +44 (0) Fax: +44(0) Customer Service Tel: +44 (0) Technical Support Tel: +44 (0) europesupport@aperio.com ii Spectrum/Spectrum Plus Operator s Guide

3 Contents CHAPTER 1 - SPECTRUM OVERVIEW... 1 Spectrum and Spectrum Plus...1 What Spectrum and Spectrum Plus Have in Common...2 About This Guide...2 For More Information...3 CHAPTER 2 - LOGGING IN... 5 Start Spectrum and Log In...5 If Your Session Times Out...6 Changing Your Password (Spectrum Plus)...6 If You Want to Change Your Password...6 If You See a Reminder to Change Your Password...7 If Your Account Is Locked...7 CHAPTER 3 - A TOUR OF SPECTRUM S MAIN PAGE... 9 The Main Page...9 The Page Menu Bar...10 Changing the Spectrum Page Font Size...10 General Spectrum Tips...11 Status and Error Messages...11 Monitor Requirements...12 CHAPTER 4 - WORKING WITH SPECTRUM DATA How Spectrum Organizes Data...13 Data Groups...14 General Data Table Functionality...14 Viewing Your Data in Lists and Folders...15 List View...15 Folder View...17 Multi Level Folder View...18 Using Barcodes...19 Auto Complete Feature...20 Case Data Table...20 Case List Commands...22 Using the Case Information Page...22 Deleting Cases...23 Removing Slides and Specimens from a Case...23 Adding New Cases...25 Specimen Data Table...26 Specimen List Commands...26 Digital Slide Data Table...27 Digital Slides List Commands...28 Spectrum/Spectrum Plus Operator s Guide iii

4 Contents CHAPTER 5 - ADDING SLIDES TO SPECIMENS AND CASES...31 Typical Workflow...31 Adding a New Case...32 Adding a Specimen to a Case...33 Adding a Specimen That Already Exists in Spectrum...33 Creating a New Specimen...34 Adding a Gross Image to the Specimen...34 Adding Slides to the Specimen (in a Case)...36 Adding Existing Digital Slides to the Specimen...36 Adding a New Slide to the Specimen...37 Adding an Image to a Digital Slide...38 Creating Slides from Images in a Server Folder or SubFolder...39 CHAPTER 6 - VIEWING IMAGES...41 The View Images Command...41 Tips on Viewing Images...41 Automatic Image Viewing...43 Disabling Automatic Image Viewing...44 ImageScope Toolbar Quick Reference...45 CHAPTER 7 - EXPORTING DATA...47 Exporting Digital Slide Data...48 CHAPTER 8 - ADDING DOCUMENTS TO DATA...51 CHAPTER 9 - SEARCHING SPECTRUM DATA...53 Selecting Search Parameters...54 The Contains Search Parameter...56 The Between Search Parameter...57 CHAPTER 10 - ANALYZING IMAGES...59 Aperio Algorithms...59 Analyzing Digital Slides in Spectrum...60 Batch Analyzing Slides with a Macro...60 Viewing Digital Slide Analysis History...62 Viewing the Analysis Job Queue...62 Canceling Analysis Jobs...63 APPENDIX A - CREATING A WORKSPACE (DASHBOARD)...65 Opening an Existing Workspace...67 Other Dashboard Features...67 APPENDIX B - MANAGING APERIO SERVICES...69 Accessing the Aperio Service Manager...69 INDEX...71 iv Spectrum/Spectrum Plus Operator s Guide

5 1 Spectrum Overview This chapter introduces Spectrum and Spectrum Plus. Spectrum delivers an effective digital pathology information management system that treats high resolution digital slides that can be viewed, managed, and analyzed * as an integrated element in pathology workflow. Spectrum displays information in context, with gross (macro) images, digital slide images, reports, case histories, and other associated documents and images cross linked and concurrently viewable. Spectrum facilitates instant archival and intelligent retrieval of histo pathological data in a searchable, context sensitive manner. Pathologists and histologists are able to work through an entire case without having to get up to track down case information or to wait for glass slides to be delivered. They can work remotely and collaboratively, initiating automated image analyses * and viewing the results, all within Spectrum. Spectrum and Spectrum Plus Two versions of Spectrum provide different sets of features. Both versions are centered around the digital slide. When you scan a microscope slide using the ScanScope scanner, the resulting digital slide is automatically added to the Spectrum database. Spectrum Plus is intended for larger organizations that need user security and may have complex data organization requirements. Spectrum, on the other hand, is intended for organizations that want something simpler to set up and use. Spectrum Plus provides: Unlimited number of users Advanced user password security features Ability to restrict user access to specific data Data table hierarchies configurable for your type of organization (clinical, research, or educational). Using the data table hierarchies, you can associate many digital slides to a specimen and many specimens to a case or project. When a glass microscope slide is scanned by a ScanScope scanner, a 2D DataMatrix, 1D 2 of 5, Code 39, or Code 128 barcode on the slide label can be decoded to automatically fill in data fields in Spectrum Plus. Spectrum/Spectrum Plus Operator s Guide 1

6 Chapter 1 Spectrum Overview Decoding other types of barcodes requires some custom work, so contact Aperio Professional Services for assistance. See Using Barcodes on page 19 for more. For customers who do not need all of the features that Spectrum Plus offers, Spectrum provides: Single user support with guest login. (The guest user is available only with research and educational configurations, not the clinical configuration.) Simplified data table, a single digital slide list What Spectrum and Spectrum Plus Have in Common Spectrum Plus and Spectrum share many features: Feature Spectrum Web-based user interface Search capabilities Remote telepathology (TelePath Live feature) Digital slide table Digital slide conferencing Customize site look (colors and logo) Customize data table titles and fields Security features (user name, passwords, data group access) Multi-user Manage specimen gross images Hierarchies of data tables Auto-fill data tables with barcode data Spectrum Plus About This Guide This guide is intended for Spectrum operators who need to know how to use Spectrum or Spectrum Plus after it has been installed and set up. For administrative information on how to set up Spectrum, refer to the Spectrum/Spectrum Plus Administrator s Guide. 2 Spectrum/Spectrum Plus Operator s Guide

7 Chapter 1 Spectrum Overview For More Information For information on accomplishing specific tasks, see: Task See Spectrum Spectrum Plus Logging into Spectrum Start Spectrum and Log In on page 5 Changing your password Changing Your Password on page 6 Resetting your account If Your Account Is Locked on page 7 Changing the font size displayed on the Spectrum page Changing the Spectrum Page Font Size on page 10 Viewing your data Viewing Your Data in Lists and Folders on page 15 Chapter 6, Viewing Images on page 41 Using data tables Chapter 4, Working with Spectrum Data on page 13 Creating a new case Adding a New Case on page 32 Adding specimens to a case Adding a Specimen to a Case on page 33 Adding digital slides to a case Adding a Digital Slide to a Case on page 36 Creating Slides from Images in a Server Folder or Subfolder on page 39 Creating a specimen Creating a New Specimen on page 34 Adding gross images to a specimen Adding a Gross Image to the Specimen on page 34 Creating a digital slide Adding a New Slide to the Specimen on page 37 Adding images to a digital slide Adding an Image to a Digital Slide on page 38 Exporting data Chapter 7, Exporting Data on page 47 Adding documents to a case Chapter 8, Adding documents to data on page 51 Searching for specific cases, specimens, or digital slides Chapter 9, Searching Spectrum Data on page 53 Analyzing * digital slides Chapter 10, Analyzing Images on page 59 Spectrum/Spectrum Plus Operator s Guide 3

8 Chapter 1 Spectrum Overview Task See Spectrum Spectrum Plus Setting up and saving a desktop view of Spectrum and other applications Appendix A, Creating a Workspace (Dashboard) on page 65 Starting and stopping Aperio services Appendix B, Managing Aperio Services on page 69 * Aperio s image analysis algorithms are FDA cleared for specific clinical applications, and are intended for research use for other applications. This application is not approved or cleared by the FDA for clinical use. 4 Spectrum/Spectrum Plus Operator s Guide

9 2 Logging In Before you can use Spectrum, you must first log in. Start Spectrum and Log In 1. Open your Internet browser and in the address box type the URL of the Spectrum web site. You can get this address from the person who installed Spectrum on your organization s network. The Login page appears:: 2. Enter the user name and password given to you by the Spectrum administrator. Remember that all user names and passwords are case sensitive, so be careful to use the correct combination of upper and lower case characters. 3. Click User Login. If you do not have a user name, click Guest Login to log in as a guest user. (The guest user is available only with research and educational configurations, not the clinical configuration.) Spectrum/Spectrum Plus Operator s Guide 5

10 Chapter 2 Logging In If Your Session Times Out If while using Spectrum you see the following message: Your session has timed out and you will need to log in again. If this happens frequently, ask your Spectrum administrator to make the session timeout period longer. Changing Your Password (Spectrum Plus) You may want to change your password occasionally for security reasons. Or, your administrator may require that you change you password after a specific number of days. If You Want to Change Your Password 1. Go to the Administrative menu in the top menu bar of the Spectrum page. 2. Click My Settings. The User Details page appears: If your password must be a specific length or contain special characters, you will see a reminder next to the New Password box as in the above example. 3. Type your new password in the New Password box and then retype it in the box below. 4. Click Save. 6 Spectrum/Spectrum Plus Operator s Guide

11 Chapter 2 Logging In If You See a Reminder to Change Your Password If your password has expired or if for some other reason the Spectrum administrator wants you to change your password, you will see this message when you try to log in: If your password must be a specific length or contain special characters, you will see a reminder next to the New Password box as in the above example. 1. Type your new password in the New Password box and then retype it in the box below. 2. Click Save. If Your Account Is Locked If you see the following message when you log in: Your account has been locked. Ask the Spectrum administrator to unlock your account. Spectrum/Spectrum Plus Operator s Guide 7

12 Chapter 2 Logging In 8 Spectrum/Spectrum Plus Operator s Guide

13 3 A Tour of Spectrum s Main Page This chapter gives a brief tour of the Spectrum main page. Logo The Main Page When you log into Spectrum, you see the main Spectrum page: Menu Bar Data Table The exact appearance of this page depends on how Spectrum was configured when it was installed and on whether you are using Spectrum or Spectrum Plus. For example, if you are using Spectrum instead of Spectrum Plus, only the Digital Slides table and menu appears on the page, not Cases or Specimens. Or, if Spectrum Plus was configured for Research instead of Clinical use, the top level data category is Projects instead of Cases. For information on the different types of Spectrum Plus configurations available, see How Spectrum Organizes Data on page 13. The main features of this page include: Data Tables You use the data tables displayed on the Spectrum main page to access the information and images stored in Spectrum. Spectrum/Spectrum Plus Operator s Guide 9

14 Chapter 3 A Tour of Spectrum s Main Page Menu Bar The commands on the menu bar at the top of the page provide many of the same features as the data tables. Additional commands that help you use special Spectrum features are also available. See the next section for information. Logo Click the Spectrum logo whenever you want to return to the main Spectrum page. The Page Menu Bar The Spectrum main page contains a menu bar that contains frequently used commands: The first menu/menus provide access to your data (in this case, Cases, Specimens, and Digital Slides). If you are using Spectrum, you see only the Digital Slides data menu. Additional data table menus are displayed for Spectrum Plus the specific data tables you see depend on how Spectrum Plus is configured. (See How Spectrum Organizes Data on page 13 for information on the different configurations of Spectrum Plus.) The remaining menus provide the following functions: Analysis * Check the image analysis queue. See Chapter 10, Analyzing Images on page 59. Administrative Use the My Settings command to change your password. See If You Want to Change Your Password on page 6 (Spectrum Plus only). Help Open help for the Spectrum page you are on. Font Size Adjust the display font to a larger or smaller size. See the next section. Log Off Log off the Spectrum site. Changing the Spectrum Page Font Size You can customize the appearance of the Spectrum page by increasing or decreasing the font size: 1. Click Font Size on the menu bar: a) Click Increase (+) to increase the font size. b) Click Decrease ( ) to decrease the font size. c) Click Reset to reset the font size to the default. 10 Spectrum/Spectrum Plus Operator s Guide

15 Chapter 3 A Tour of Spectrum s Main Page General Spectrum Tips Here are some tips concerning the general operation of Spectrum: Slide images created by the ScanScope scanner are automatically associated to a digital slide created in the Digital Slide table. The barcode string populates the slide data table barcode field, and may also fill in other data fields for the slide. (This latter feature may require custom software from Aperio.) See Using Barcodes on page 19 for more information. In Spectrum Plus, gross specimen images captured in the Milestone Grossing Station will automatically be associated with specimens in the Specimens data table. All data fields accept alphanumeric input with the exception of date fields, which require a specific format of yyyy mm dd (year month day), for example: Documents can be added to most items in data tables. See Chapter 8, Adding Documents to Data on page 51. Status and Error Messages Whenever you change data on a Spectrum page (for example, when adding information to a case, changing a data table, or adding digital slides to a case), a green message lets you know that the update was successful. For example: After making an update, Spectrum returns you to the appropriate page. When an error occurs, a short, simple error message appears in red on the page where the error occurred. If you want more information on the error (for example, to send the information to Aperio Technical Support), holding the cursor over the short error message causes a longer, more detailed message to appear. Spectrum/Spectrum Plus Operator s Guide 11

16 Chapter 3 A Tour of Spectrum s Main Page Monitor Requirements Because Aperio digital slides 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: Screen Resolution: Screen Size: Color Depth: Brightness: Contrast Ratio: CRT minimum, LCD (flat panel) recommended 1024(h) x 768(w) pixels minimum 1920 x1050 or larger recommended 15 minimum 19 or larger recommended 24 bit 300 cd/m 2 minimum 500 or larger recommended 500:1 minimum 1000:1 recommended * Aperio s image analysis algorithms are FDA cleared for specific clinical applications, and are intended for research use for other applications. 12 Spectrum/Spectrum Plus Operator s Guide

17 4 Working with Spectrum Data This chapter describes the features and functionality of Spectrum data tables. How Spectrum Organizes Data Spectrum Plus organizes and displays data in a hierarchy that is tailored to the needs of three different types of users: Clinical Installation Data is displayed and organized with cases at the top, followed by specimens and digital slides. Research Installation Data is displayed and organized with projects at the top, followed by specimens and digital slides. Educational Installation Data is displayed and organized with courses at the top followed by lessons, specimens, and digital slides. Your Spectrum administrator has chosen the configuration that best suits your organization. If you are using Spectrum, not Spectrum Plus, only one data table is provided, Digital Slides. You can add data to the tables in any order, although there is an optimal workflow to maximize efficiency of the system see Chapter 5, Adding Slides and Specimens to a Case for more information. The data entered into Spectrum is displayed in data tables. Spectrum/Spectrum Plus Operator s Guide 13

18 Chapter 4 Working with Spectrum Data Digital gross specimen images can be associated with specimen data in Spectrum. If the image was captured in the Milestone Grossing station, the specimen is automatically created and associated with the image in the Spectrum Specimen data table. Once a slide is scanned on a ScanScope, the resulting ScanScope whole slide image and associated image data are automatically added to the Digital Slide data table. If there is a barcode on the glass slide, it will populate the barcode field with the barcode string; otherwise, the information fields in the digital slide data table will be empty until you enter data. The digital slide can now be associated with a specimen and case, project or course. Should you not require the functionality of associating digital slides with specimen and cases or projects, you have the ability to work within just the digital slide table in Spectrum to organize your data. The sections below describe the functions within the different data tables. Data Groups In addition to organizing data in data tables, Spectrum also organizes data in data groups. Data groups define what data an operator can see. If an operator doesn t have access to a data group, the data in that group will not appear on the Spectrum page when that operator logs in. A data group can be a pathologist, sample type, project or department or whatever grouping makes sense to accommodate your workflow. When you create data, such as when you create a new case, you have the option of selecting which data group the new item belongs to. If your Spectrum installation does not use data groups, all data will automatically be assigned to the Default data group. If you have questions about what data groups are available, or which data groups you should use, contact your Spectrum administrator. It is the administrator who defines the data groups and decides what operators have access to which data groups. General Data Table Functionality You may add, list or search data for all data tables (Case, Specimen, Digital Slide, etc.) from the blue menu bar or from the list under each heading. Functions at the top of the data table apply to all items selected in a list. You must select one or more items to enable the commands at the top of the list. 14 Spectrum/Spectrum Plus Operator s Guide

19 Chapter 4 Working with Spectrum Data Icons to the left of an item in a list will open data. To prevent also automatically launching a viewer to view an image if one is associated with that item, see Disabling Automatic Image Viewing on page 44. Clicking on any header in a column in a data table will sort the list based upon that column. If child data is associated with parent data in Spectrum, when you open the parent you will be able to see the child data. For example, if you open a case that has a specimen and slides associated with it you will see the associated specimens and digital slides. Clicking Open Data displays the data associated with the item. o If you want to bulk edit information on multiple items, select the box to the left of each item and click Open Data at the top of the list. This will display the Information page. Any data entered at this time applies to all of the items selected. Data can be exported from any table to an Excel file by clicking Export at the top of the table. The export file will contain the data contained on that page for that data table level only. See Chapter 7, Exporting Data on page 47. Viewing Your Data in Lists and Folders There are two ways of viewing Spectrum data as lists or folders. The default view is list view. Using folder view provides another way to see your data grouped in the way that is most useful to you. List View To use list view, go to a data table in the menu bar and click the (As List) option: Spectrum/Spectrum Plus Operator s Guide 15

20 Chapter 4 Working with Spectrum Data Or click the list option in a data table on the page: The list view appears: You can temporarily change the number of items to display whenever using a page by typing a new number in the Display field, which appears at the bottom of the page. This is especially useful when you want to tag a large number of items or, alternatively, quickly view short lists. 16 Spectrum/Spectrum Plus Operator s Guide

21 Chapter 4 Working with Spectrum Data Folder view is a virtual grouping of your data. Using folder view does not create disk folders or move your data into folders. Folder View To use folder view, go to a data table in the menu bar and click the (As Folders) option: Or click the folder option in a data table on the main page: The folder view appears, with data organized by data group: Now click the File By drop down list to select how you want to group the data (in this case, we want to group by hospital): Spectrum/Spectrum Plus Operator s Guide 17

22 Chapter 4 Working with Spectrum Data Now you see the new folder view with virtual folders grouping your data: Click on a virtual folder to see what data has been grouped in it. Multi-Level Folder View You can continue refining the folder view by selecting additional criteria. For example, to create the following example: 1. We first select Hospital to see all cases by the hospitals associated with the cases. 2. Then we click on one of the hospital folders and select Physician Name. 18 Spectrum/Spectrum Plus Operator s Guide

23 Chapter 4 Working with Spectrum Data 3. Finally, we click on a physician name folder and select DOB (date of birth): Using Barcodes Spectrum Plus includes support for automating data entry and building data hierarchies using barcodes that are interpreted when the glass slide containing a label with such a barcode is scanned by the ScanScope scanner. Decoding some types of barcodes requires some custom work, so contact Aperio Professional Services for assistance. Spectrum can decode 2D DataMatrix, 1D 2 of 5, Code 39, and Code 128 barcodes and: Place the barcode value into the Spectrum barcode field Configure and parse the data from the barcode to the specified data table fields and; Build the appropriate data hierarchy for that data For example, a 2D DataMatrix barcode containing the case number, patient name, specimen type and slide stain is decoded into Spectrum as AP061111, Jane Doe, breast, ER. Spectrum automatically associates the digital image with the digital slide and creates the following data hierarchy: Case o o Case Number: AP Patient Name: Jane Doe Specimen o Specimen Body Site: breast Digital Slide o Stain: ER For information on enabling this feature, contact your Aperio representative. Spectrum/Spectrum Plus Operator s Guide 19

24 Chapter 4 Working with Spectrum Data Auto-Complete Feature When you begin to type in a Spectrum data field, if values have already been defined for that field in the Spectrum database (for example, a Stains library exists), a blue box displays with matching values from the Spectrum database. For example: Click on one of the suggestions listed to select it. Note that your Internet browser can also display an auto complete list if you have that feature turned on (see the Spectrum/Spectrum Plus Administrator s Guide for details on enabling/disabling browser auto complete), which displays in a white box. If you see the browser white box with selections and want to see the Spectrum blue auto complete box instead, press the ESC key on your keyboard. Case Data Table A Case is the highest data level in the clinical installation hierarchy. A Project is the highest level data table in the research installation hierarchy. A Course is the highest level data table in the educational installation hierarchy. The educational hierarchy also contains a Lessons level which is the child of the Course. The descriptions of the feature and functions within the highest data table hierarchy are the same across installation types. This section applies to all list pages. To view a list of cases: 1. Click List all Cases under the Cases heading or go to the Cases menu and select All Cases (As List): 20 Spectrum/Spectrum Plus Operator s Guide

25 Chapter 4 Working with Spectrum Data The list displays the data table fields that were defined by the administrator. You also see the number of pages and number of items that are currently in the list. The number of items displayed on a page can be changed by the administrator in the configuration file or can temporarily be changed by the operator by using the Display field at the bottom of the page. You can temporarily change the number of items to display by typing a new number in the Display field, which appears at the bottom of the page. 2. Click any column header to sort the data in the list based upon the information in that column. You see a small arrow in the header of the data field that indicates that the list has been sorted on the column value. a) The first time you click on the column header, the data is sorted in ascending order (the arrow in the header points up): Spectrum/Spectrum Plus Operator s Guide 21

26 Chapter 4 Working with Spectrum Data b) Click a second time to sort the data in descending order (the arrow in the header points down): 2. Select the upper left check box at the top of the list to select all items in the list. You may select individual items as well. Case List Commands At the top of the Case list are several commands which become active when one or more cases are selected. Selecting the check box in the upper left corner of the list selects all items in the Case list. The commands available are: Open Data Open the Information page which contains information about the case, including information on specimens and digital slides it is associated with. For information on using the information page, see Using the Case Information Page below. Delete Use this command to delete the selected cases. New You can create one or more cases. See Adding New Cases on page 25. Export See Chapter 7, Exporting Data on page 47 for information. Using the Case Information Page 1. Click Open Data while multiple cases are selected to open the Case Information page. Any changes made at this time apply to all of the cases selected. 22 Spectrum/Spectrum Plus Operator s Guide

27 Chapter 4 Working with Spectrum Data If you have selected a single case, clicking Open Data or clicking on the icon will cause any data entered at this time to apply to that single case. 2. Click Save to accept and save the changes. You must have Full Control permission to all data groups that belong to child data (such as Specimens, Digital Slides or Images) that you will be associating to parent data such as Cases or Projects. Deleting Cases Click Delete to delete the selected cases from the case list. This also deletes the related specimens and slides. If you do not want to delete digital slides and specimens associated with a case when you delete the case, you must first disassociate the item from the case before deleting the case. See Removing Slides and Specimens from a Case below. Removing Slides and Specimens from a Case Because deleting a case deletes any slides and specimens associated with that case, if you want to retain those items you must first remove them from the case before deleting the case. Removing a slide or specimen from a case does not delete it, but simply disassociates it from the case. Spectrum/Spectrum Plus Operator s Guide 23

28 Chapter 4 Working with Spectrum Data To remove a slide or specimen: 1. Go to the Case list display (see List View, on page 15). 2. On the Case list display, select the case you will be deleting later. 3. Click Open Data at the top of the list to open the Information page for that case. 4. In the Case Specimens section of the Information page, select the specimens you want to remove from the case: 5. Select the Remove command at the top of the list. To disassociate digital slides for this case, repeat this procedure by going to the Case Digital Slides section of the Information page, selecting the digital slides you want to save, and clicking Remove at the top of the list. Now you can delete the case without deleting the specimens or digital slides associated with it. 24 Spectrum/Spectrum Plus Operator s Guide

29 Chapter 4 Working with Spectrum Data Adding New Cases 1. Go to the Case list display (see View List on page 15). 2. On the Case list display, click New to open the Add New Cases page. You may enter the number of cases to add. This allows you to bulk create multiple cases that may share some information. Then each case can be opened to add the information that is different. 3. Click Add to accept and save the changes or Cancel to exit. Spectrum/Spectrum Plus Operator s Guide 25

30 Chapter 4 Working with Spectrum Data Specimen Data Table To view a list of specimens: 1. Click List all Specimens under the Specimens heading or go to the Specimens menu and select All Specimens (As List): The specimen list appears: Specimen List Commands At the top of the Specimens list are several commands which become active when one or more specimens are selected. Selecting the check box in the upper left corner of the list selects all items in the Specimens list. 26 Spectrum/Spectrum Plus Operator s Guide

31 Chapter 4 Working with Spectrum Data The commands available are: View Images View all selected specimen images in ImageScope. See Chapter 6, Viewing Images on page 41 for details. Open Data Open the Information page which contains information about the specimen, including information on digital slides associated with it and the case it is associated with. For information on using the information page, see Using the Case Information Page on page 22, as the information pages for cases and specimens are similar. Delete Use this command to delete the selected specimens. New You can create a new specimen. See Creating a New Specimen on page 34. Add to Existing Case You can add the specimen to an existing case. See Adding a Specimen to a Case on page 33 for more information. Add to New Case You can create a new case to add the specimen to. See Adding a New Case on page 32 for more information. Export See Chapter 7, Exporting Data on page 47 for information. Digital Slide Data Table The Digital Slide data table is different from the other data tables in a couple of ways: The images automatically populate this list as slides are scanned. The ScanScope image data automatically populates the digital slide data fields. o You may have added additional data fields to the digital slide table that require user data entry. Spectrum/Spectrum Plus Operator s Guide 27

32 Chapter 4 Working with Spectrum Data To view a list of slides: 1. Click List all Digital Slides under the Digital Slides heading or go to the Digital Slides menu and select All Digital Slides (As List). The Digital Slides list appears: Digital Slides List Commands At the top of the Digital Slides list are several commands which become active when one or more digital slides are selected. Selecting the check box in the upper left corner of the list selects all items in the Digital Slides list. 28 Spectrum/Spectrum Plus Operator s Guide

33 Chapter 4 Working with Spectrum Data The commands available are: View Images View all selected digital slide images in ImageScope. See Chapter 6, Viewing Images on page 41 for details. Open Data Open the Information page which contains information about the digital slide, including information on the case it is associated with. For information on using the information page, see Using the Case Information Page on page 22, as the case and digital slides information pages are similar. Analyze * You can analyze the selected digital slides using Aperio image analysis algorithms. For details, see Chapter 10, Analyzing Images on page 59 Delete Use this command to delete the selected digital slides. New Create a new digital slide. See Adding Slides to a Specimen on page 36. Add to Existing Specimen Add the digital slide to an existing specimen. See Adding Slides to the Specimen (in a Case) on page 36 for more information. Add to New Specimen Create a new specimen to add the digital slide to. See Creating a New Specimen on page 34 for more information. Add to Existing Case Add the digital slide to an existing case. Add to New Case You can create a new case to add the digital slide to. See Chapter 5, Adding Slides and Specimens to a Case on page 31 for more information. Export See Chapter 7, Exporting Data on page 47 for information. Spectrum/Spectrum Plus Operator s Guide 29

34 Chapter 4 Working with Spectrum Data * Aperio s image analysis algorithms are FDA cleared for specific clinical applications, and are intended for research use for other applications. 30 Spectrum/Spectrum Plus Operator s Guide

35 5 Adding Slides to Specimens and Cases The examples in this chapter show using cases. Many of these procedures also apply to projects, courses, lessons, digital slides, or specimens. This chapter describes the steps to associate slides to a specimen and case. These steps may be performed independently from each other depending on your workflow. One workflow scenario is to create cases and specimens and then associate existing slides to the specimen that is in the case. When adding child data to parent data in Spectrum, you must have Full Control permission to both the child s and the parent s data groups. For example, if you add a new digital slide, you must have Full Control permission to the image that will be associated with that slide. If you only have Read Only access to the Default data group and you try to add that image (from the Default data group) to a new slide that you created, you see the message: User not authorized to edit current parent data. If you see this message, contact the Spectrum administrator and ask to have your user permissions adjusted. Typical Workflow How you use Spectrum depends on your organization and the way you work. Here are some notes on typical workflows: Clinical Installation In a clinical situation, the operator typically creates a case for each patient. Each case usually has one specimen and multiple digital slides. In this scenario, the operator will create cases first and then add specimens and digital slides to them. Research Installation Researchers often organize data by projects, with each project having multiple specimens. Multiple stained digital slides are usually associated with each specimen. Education Installation Educators often pull interesting digital slides from archive for teaching. Their data is organized by courses and lessons, with each specimen containing multiple digital slides. In this scenario, the educator creates the course first, then the lessons, and finally adds specimens and digital slides to the lessons. Spectrum/Spectrum Plus Operator s Guide 31

36 Chapter 5 Adding Slides to Cases and Specimens Adding a New Case 1. From the main page, under Cases, click Add New Cases or click Add Cases from the Cases menu. 2. In the Add New Cases page, enter the number of cases to be added in the Case(s) box. 3. Enter the appropriate information in the Case Information page. If more than one case is added, the data entered in the fields below will apply to each case created. 4. Select the appropriate Data Group to be applied to the case. 32 Spectrum/Spectrum Plus Operator s Guide

37 Chapter 5 Adding Slides to Cases and Specimens 5. Click Add to add the case(s) or Cancel to exit. Adding a Specimen to a Case 1. Under the Cases menu, click All Cases (As List). You can also search for the case by selecting Search all Cases and entering a unique identifier to locate the case. 2. In the Cases list, click on the icon or select the case and click Open Data. 3. In the Specimens section of the Information page, click Add New Specimen or Add Existing Specimen. When you select Add Existing Specimen, only unassigned specimens are listed in the specimen list. Adding a Specimen That Already Exists in Spectrum 1. Click Add Existing Specimen. 2. Select the box to the left of the appropriate specimen in the Unassigned Specimen list. 3. At the bottom of the specimen list click Add to save. Spectrum/Spectrum Plus Operator s Guide 33

38 Chapter 5 Adding Slides to Cases and Specimens Creating a New Specimen 1. Click Add New Specimen. 2. In the Add New Specimens page, enter the number of specimens to be added in the Add Specimen(s) box. Enter the appropriate specimen information. If more than one specimen is added, the data entered in the fields will apply to each specimen created. 3. Click Add to save the information and exit. Adding a Gross Image to the Specimen 1. In the Case Specimens portion of the Case Information page, click on the icon or select the box to the left of the specimen and click Open Data. 34 Spectrum/Spectrum Plus Operator s Guide

39 Chapter 5 Adding Slides to Cases and Specimens 2. In the Specimen Gross Images section of the Specimen Information page, click Add Image. 3. Select Reference an Image or Upload an Image to add an image to your specimen. (Your administrator may have configured Spectrum to not display the Reference an image selection.) Only small images can be uploaded. Gross images tend to be small and can be uploaded. If the image is too large, the upload will time out. Note that you cannot upload a Composite WebSlide file. a) Select the image file, click Open and Add to reference this image. Selecting Reference an Image, allows you to browse to an image that is accessible to the server. b) Select the image file, click Open and Add to upload the image. Selecting Upload an Image allows you to browse to an image that can be uploaded to the data table. 4. Click Add to save and exit. Spectrum/Spectrum Plus Operator s Guide 35

40 Chapter 5 Adding Slides to Cases and Specimens Adding Slides to the Specimen (in a Case) The specimen does not have to be in a case to add a slide to it. You may directly add slides to a specimen and omit the case level if you wish. 1. Open the case of interest by searching or listing the cases, selecting the case, and clicking Open Data. 2. Click the icon or select the box to the left of the specimen and click Open Data. Spectrum automatically creates a slide and associates the.svs image to it in the Digital Slide table. This opens the Specimen Information page. 3. In the Specimen Digital Slides section of the Information page, click Add New Slides or Add Existing Slides. Adding Existing Digital Slides to the Specimen 1. In the Specimen Digital Slides page, click Add Existing Slide. When you select Add Existing Slides, only unassigned slides are listed in the slide list. 36 Spectrum/Spectrum Plus Operator s Guide

41 Chapter 5 Adding Slides to Cases and Specimens 2. In the Unassigned Digital Slide list, select the boxes to the left of the slides to be added. 3. At the bottom of the unassigned slide list, click Add to save the changes or Cancel to exit. Adding a New Slide to the Specimen 1. In the Specimen Digital Slides portion of the Information page, click Add New Slide. 2. In the Add New Digital Slides page, enter the number of slides to be added. 3. Enter the appropriate slide information. Spectrum/Spectrum Plus Operator s Guide 37

42 Chapter 5 Adding Slides to Cases and Specimens If multiple slides are added, the information entered will apply to all slides. 4. Click Add or Cancel to exit. Adding an Image to a Digital Slide 1. To add an image to a slide, in the Specimen Digital Slides list view, click on the icon or select the box to the left of the slide of interest and click Open Data. 2. In the Digital Slide Images section of the Information page, click Add Image. (For information on the auto view check box, see Chapter 6, Viewing Images. ) 3. Select Reference an Image or Upload an Image. (Your administrator may have configured Spectrum to not display the Reference an image selection.) Selecting Reference an Image allows you to browse to an image that is accessible to the server. Select the image file, click Open and click Add to reference this image. Most virtual slide images are too large to upload. If the file is too large to upload Spectrum will time out before the image is loaded and you should use Reference an Image. When you reference an image, Spectrum points to and remembers the image location. Note that you cannot upload a Composite WebSlide file. 38 Spectrum/Spectrum Plus Operator s Guide

43 Chapter 5 Adding Slides to Cases and Specimens Selecting Upload an Image allows you to browse to an image that can be uploaded to the data table. Select the image file, click Open and Add to upload the image. Creating Slides from Images in a Server Folder or SubFolder 1. Go to the Digital Slides data table and click New. 2. In the Add New Digital Slides page, select Add Slides with images in server folder and subfolders. 3. Type or paste the exact data path into the box. 4. Click Add to create slides for all of the images in that folder or Cancel to exit. Spectrum/Spectrum Plus Operator s Guide 39

44 Chapter 5 Adding Slides to Cases and Specimens 40 Spectrum/Spectrum Plus Operator s Guide

45 6 Viewing Images This chapter discusses how to view images in Spectrum. At various locations in Spectrum where you can see data in list view, the View Images command is provided to open associated images in the ImageScope viewer. If you do not have ImageScope installed on your workstation, the image will open in the web based WebViewer application. The View Images Command You can find the View Images command in several areas of Spectrum: Specimens list view Digital Slides list view Case Specimens section of the Case Information page. Specimen Digital Slides section of the Specimen Information page. To view an image: In list view, select an image by selecting the check box next to it and click View Images to launch ImageScope to view the image. Or, click the image thumbnail to launch ImageScope. Tips on Viewing Images If you select multiple images and then click View Images in the list menu, ImageScope will launch and all of the images selected will appear in the Filmstrip view in the ImageScope window. Spectrum/Spectrum Plus Operator s Guide 41

46 Chapter 6 Viewing Images Clicking View Images opens the image in ImageScope unless ImageScope is not installed on that local computer; in that case the image will open in WebViewer. In list view, clicking on the icon (for specimens) or icon (for digital slides) to the left of the thumbnail will open the information page for that item and also launch ImageScope for that single image (no matter how many are selected in the list). (If you do not wish to automatically view the image, see Disabling Automatic Image Viewing on page 44.) See the ImageScope User s Guide for detailed instructions and ImageScope features and functions. After opening multiple images, you may then switch between the images or set the ImageScope Window choice to Cascade, Tile Vertical or Tile Horizontal to display all of the selected images at the same time. In ImageScope, going to the View menu and selecting Filmstrip will display all of the selected slides in a filmstrip to the left of the ImageScope image. 42 Spectrum/Spectrum Plus Operator s Guide

47 Chapter 6 Viewing Images Automatic Image Viewing When you click on an image thumbnail or select an image and click View Images in Spectrum, ImageScope (or WebViewer if ImageScope is not installed) automatically opens that image. When you click on the information icon (for example, for a digital slide) or select the item and click Open Data, you see the information page for that item and the image associated with that item. This feature assures that the proper Spectrum data entry screen is open for the correct corresponding image. In the case of digital slides, it is up to the operator to confirm that the slide labels match the digital slide data for further quality assurance. If you want to disable automatically opening the image when using the Open Data command or clicking on the information icon, see Disabling Automatic Image Viewing on page 44. Spectrum/Spectrum Plus Operator s Guide 43

48 Chapter 6 Viewing Images Disabling Automatic Image Viewing To disable a data item s image from opening in a viewer when you open the information page for the item: 1. Go to the Administrative menu on the menu bar at the top of the Spectrum page and click My Settings. 2. On the User Details page, clear the Enable Auto View Images checkbox: Clearing this check box prevents a viewer from opening and displaying the image when you open an information page for an item. 44 Spectrum/Spectrum Plus Operator s Guide

49 Chapter 6 Viewing Images ImageScope Toolbar Quick Reference Please refer to the ImageScope User s Guide for a full explanation of ImageScope features. However, here is a quick reference tour of the more frequently used items on the ImageScope toolbar: Icon Action Go to the Open Image window where you can browse for a local digital slide to open for viewing. Close the digital slide that is currently being viewed in ImageScope. Create a snapshot image of the digital slide currently being viewed. Manually synchronize navigation for all digital slides currently being viewed. (Used when multiple digital slides are open in the ImageScope window.) (Yellow) Smart synchronization differs from manual synchronization; not only is navigation synchronized between the slides, but corresponding regions in the digital slide images are also synchronized. Useful when viewing multiple digital slides that were cut from the same tissue block. Show or hide the magnifier window. Show or hide the thumbnail window. Open the Annotations window where you can create multiple annotation layers and organize and add descriptions to annotations. Pan the digital slide. Zoom the selected area of the digital slide. Extract a region of a digital slide. Draw a free-form annotation. Draw a free-form annotation to be excluded from analysis *. (This creates a negative annotation.) Measure an object on a digital slide. Draw a rectangular region (or a square if you hold down the Shift key while you draw). Draw an elliptical annotation (or a circle if you hold down the Shift key while you draw). Draw an arrow pointing to an area of interest. See help information for ImageScope. Spectrum/Spectrum Plus Operator s Guide 45

50 Chapter 6 Viewing Images * Aperio s image analysis algorithms are FDA cleared for specific clinical applications, and are intended for research use for other applications. 46 Spectrum/Spectrum Plus Operator s Guide

51 7 Exporting Data This chapter discusses how to export data into a format that can be read by Excel or other spreadsheet program. Spectrum provides the ability to export data into an Excel compatible CSV (Comma Separated Value) file. When using the List All link for Spectrum data, the Export command is available on the list menu. If Microsoft Excel is installed on your workstation, you can open the exported data directly in Excel. If you don t have Excel on your workstation, you won t be able to open the file directly, but you can save it to open later using a text editor like Notepad or move it to another workstation that does have Excel installed. To export one or more cases: 1. Click on List All Cases on the main Spectrum page to go to list view. 2. Select one or more cases. 3. Click Export on the list menu to create an Excel compatible commaseparated value (CSV) file of all data for the selected items in the list. The first time you export a CSV file, your Internet browser may ask you to select the program with which to open the CSV file. If you have Excel on your workstation, select Excel or you can save the file directly to disk and open it later. To open the exported file in Excel: 1. Start Excel. 2. Go to the Excel File menu and select Open. 3. Navigate to the exported file (look for a file named SpectrumData.csv) and open it. Spectrum/Spectrum Plus Operator s Guide 47

52 Chapter 7 Exporting Data Here is a partial sample of exported case information in Excel: Exporting Digital Slide Data To export data for one or more digital slides: 1. Click List All Digital Slides on the main Spectrum page to go to list view. 2. Select one or more digital slides. 3. Click Export Data on the list menu. You see the Export Options page: This page allows you to select what analysis data, if any, resulting from analyses * of the digital slides will be exported: Do not include analysis data Include only the most recent analysis data Include all analysis data 48 Spectrum/Spectrum Plus Operator s Guide

53 Chapter 7 Exporting Data 4. Click Export to create an Excel compatible comma separated value (CSV) file of all data for the selected digital slides in the list. The first time you export a CSV file, your Internet browser may ask you to select the program with which to open the CSV file. If you have Excel on your workstation, select Excel or you can save the file directly to disk and open it later. Spectrum/Spectrum Plus Operator s Guide 49

54 Chapter 7 Exporting Data * Aperio s image analysis algorithms are FDA cleared for specific clinical applications, and are intended for research use for other applications. 50 Spectrum/Spectrum Plus Operator s Guide

55 8 Adding Documents to Data The examples in this chapter show adding documents to a case. This procedure also applies to adding documents to projects, courses, lessons, digital slides, or specimens. This chapter describes how to associate a document with a case (project, course, lesson), specimen or slide. 1. To add a document to a case (project, course or lesson), specimen, or digital slide, open the item of interest. List cases (projects, courses or lessons) or specimens, select the item of interest and click Open Data at the top of the list. 2. In the Information page, go to the Documents section and click Add Document. 3. On the Add Document page, click Browse to navigate to the document. You may enter a document description if desired. 4. Click Upload to add or Cancel to exit. Spectrum/Spectrum Plus Operator s Guide 51

56 Chapter 8 Adding Documents to Data 52 Spectrum/Spectrum Plus Operator s Guide

57 9 Searching Spectrum Data This chapter describes the features and functionality of searching within Spectrum data tables. Using the Spectrum search function, you can search the database on the majority of data fields defined within the data tables. Queries can assist you in refining your search in order to find or compare cases, specimens or slides of interest. 1. From the Main menu, click Search for a Case (Project, Course or Lesson), Specimen, or Digital Slide. And the search page appears: Spectrum/Spectrum Plus Operator s Guide 53

58 Chapter 9 Searching Spectrum Data Selecting Search Parameters On each search page is a list of types of fields you can search. Only fields that are displayed in the data table will be available for a search. Memo fields cannot be searched. For example, on the Case search page: 1. Click the + sign next to the type of field you want to search and a blue box appears listing the fields you can search for: 54 Spectrum/Spectrum Plus Operator s Guide

59 Chapter 9 Searching Spectrum Data 2. Select a field to search on by clicking it in the blue box. The field appears (for example, Physician Name), and you can select the type of search you want to perform by clicking the down arrow in the box next to the field name: 3. You can enter multiple search criteria. For example: Click Search to start the search. Click Clear to empty the search fields. Click Reset to set the search fields back to their previous values. Search Operators Search Operator All Equal to Not equal to Description Selects all data. Selects data for which the database field equals the exact data entered in the search field. Selects data for which the database field does not equal the data entered in the search field. This could be useful for a status search, when status does not equal complete. Spectrum/Spectrum Plus Operator s Guide 55

60 Chapter 9 Searching Spectrum Data Search Operator Less than Greater than Contains Between Description Selects data that is less than the data entered in the search field. Data is searched in alphabetic or numeric order, starting at the beginning of the text or numeric string. For example, in the patient name search you ask for less than Doe: The search returns any patient name that begins with D, C, B, A and any names that begin with Do, Dn, Dm etc., Dod, Doc etc. For example, in a case number search, you ask for cases less than 30: The search returns any cases numbers that begin with 2 or 1, including 29, 11, 100, 20000, 2324, 1120 etc. Selects data that is greater than the data entered in the search field. Data is searched in alphabetic or numeric order, starting at the beginning of the text or numeric string. For example, in the patient name search you ask for greater than Mary: The search returns any patient name that begins with M, N, O, P, etc., Mb, Mc, etc., Maq, Map etc., Marx, Marw etc. See below. See below. The Contains Search Parameter The contains parameter allows you to search based on one or more characters that you enter. For example, below we typed the letter E and the Spectrum database returned a list of physician names that contain that letter from which to choose. 56 Spectrum/Spectrum Plus Operator s Guide

61 Chapter 9 Searching Spectrum Data The Between Search Parameter The between parameter allows you to search for all fields that match the two search entries and all data that lies between them alphabetically. For example, entering Dr. A and Dr. G as the entries to search between: Returns results of: Dr. A Dr. B Dr. C Dr. D Dr. E Dr. F Dr. G Spectrum/Spectrum Plus Operator s Guide 57

62 Chapter 9 Searching Spectrum Data 58 Spectrum/Spectrum Plus Operator s Guide

63 10 Analyzing Images This chapter discusses using algorithms to analyze digital slides. Aperio s image analysis algorithms are FDA cleared for specific clinical applications and are intended for research use for other applications. This chapter describes the terminology, features and functions available to analyze images in Spectrum. Aperio Algorithms Analyzing digital slides helps you to examine slide staining to find patterns that will tell you more about the slide. Using an algorithm to look for these patterns provides precise, quantitative data that is accurate and repeatable. The process of analyzing a digital slide is done by applying algorithms directly to the digital slide or selected regions of the digital slide. Several algorithms developed for specific applications are available, including: Positive Pixel Count This algorithm looks for: o o o Positive areas and shades them orange Negative areas and shades them blue Neutral areas areas that are neither positive nor negative and shades them white. The intensity of colors reflects the intensity of the staining. IHC Nuclear Used, for example, for ER, PR slides IHC Membrane Used, for example, for HER2 slides Micrometastasis The micrometastasis algorithm is a rare event detection algorithm, specifically developed to detect micrometastasis of tumor cells found in circulating blood. SnapShot Generator This algorithm creates a series of snapshot images that can be analyzed by a separate application. Color Deconvolution This algorithm separates the image into three channels, corresponding to the actual colors of the stains used. This allows the pathologist to accurately measure the area for each stain separately, even when the stains are superimposed at the same location. The Positive Pixel Count algorithm is licensed without charge with other Aperio software. Other algorithms are available from Aperio for a license fee. Algorithms have also been developed by third parties and tools are available from Aperio for creating your own algorithms contact Aperio for details. Spectrum/Spectrum Plus Operator s Guide 59

64 Chapter 10 Analyzing Images These algorithms all have control parameters for example, intensity and hue settings that allow the algorithm to be tailored to your specific needs. Analyzing Digital Slides in Spectrum Spectrum provides a convenient tool for batch analysis of slides. Before you can batch analyze selected slide images in Spectrum, the Spectrum administrator must first create a macro for each image analysis algorithm you want to use for analysis. You can then select one or more slides from the slide list to batch analyze with a specified macro. You can display the status of all slides that have been submitted for analysis (see Viewing the Analysis Job Queue, below). As slide analyses are complete, they drop off the queue. Analysis can be taking place while you continue to work within Spectrum, organizing data and annotating images. Batch Analyzing Slides with a Macro 1. Display the desired list of digital slides. You may list all slides by going to the Digital Slides menu and selecting All Digital Slides (As List). Or, you may want to search within the slides for a specific stain or status. (See Chapter 9, Searching Spectrum Data for more information.) Adding Image Analysis Macros is done by the Administrator. See the Spectrum/Spectrum Plus Administrator s Guide. 2. Select the box to the left of each slide to be batch analyzed. 60 Spectrum/Spectrum Plus Operator s Guide

65 Chapter 10 Analyzing Images 3. Click Analyze. The Analysis page appears: 4. Select the Analysis Macro of choice. If you don t see the algorithm you want to use, contact your Spectrum administrator for assistance. 5. If you want to analyze only a portion of the image, click the Select Input Annotation Layer drop down list to select the annotation layer on which the annotations that define the area to be analyzed are located: 6. Select the Create markup image(s) box if desired. 7. Click Analyze. The slides chosen for analysis will be added to the Analysis Job Queue. Spectrum/Spectrum Plus Operator s Guide 61

66 Chapter 10 Analyzing Images Viewing Digital Slide Analysis History On any Spectrum page that contains a list of digital slides (for example, the main digital slide list page or a Specimen Information page), the Analysis Progress column lists status information on the analysis of that slide. Click on the status (for example, Completed ) to go to a page that gives information on all analyses of that digital slide: Viewing the Analysis Job Queue 1. To check the status of current analyses, go to the Analysis menu and select, Jobs. The Analysis Job Queue page appears, which displays the status of the image analysis. The status reads Submitted or In Progress. For longer jobs, you may see percentage complete displayed. As slides complete analysis, they disappear from the job queue. 62 Spectrum/Spectrum Plus Operator s Guide

67 Chapter 10 Analyzing Images Canceling Analysis Jobs If you want to cancel one or more analysis jobs: a) To cancel a single job, click Cancel on the line for that job: b) To cancel multiple jobs, select the check box next to each job and then click Cancel at the top of the list: c) To cancel all jobs, click the check box at the top of the list to select all jobs and then click Cancel at the top of the list: Spectrum/Spectrum Plus Operator s Guide 63

68 Chapter 10 Analyzing Images 64 Spectrum/Spectrum Plus Operator s Guide

69 A Creating a Workspace (Dashboard) This appendix describes the features and functions of the Aperio Dashboard After the Spectrum client software is installed on your computer, you see two icons at the bottom right of your desktop in the system tray: These icons are for the Aperio Service Manager and the Aperio Desktop Manager. The Dashboard tool allows you to set up the windows on your desktop and save the settings for each user configuration. For example, you may want to open a browser for Spectrum, your Outlook calendar, Word and ImageScope in a particular desktop arrangement and save it as Joe s Desktop.. Creating a Workspace 1. Open all of the applications that you want to be displayed in your dashboard view. Size the windows accordingly. 2. Click on the Dashboard icon to open the Dashboard tool. 3. Click Create Workspace. Spectrum/Spectrum Plus Operator s Guide 65

70 Appendix A Creating a Workspace (Dashboard) 4. Select the desired applications to be saved in your workspace. 5. Click Create to save or Cancel to exit. 6. Enter the name of the workspace and click Create. 7. Click OK. 66 Spectrum/Spectrum Plus Operator s Guide

71 Appendix A Creating a Workspace (Dashboard) 8. Click on the Dashboard icon to open the Dashboard tool. 9. Select Preferences to select your workspace preferences. Opening an Existing Workspace 1. Click on to open the Dashboard tool. 2. Select Open Workspace. 3. Select the workspace of choice. The default workspaces are Spectrum and Spectrum 4 Panel Display. Choose Spectrum if you have a single monitor Choose Spectrum 4 Panel Display if you have a multiple monitor setup. The Spectrum workspace automatically opens a windows browser on the left and ImageScope on the right. Other Dashboard Features Other features in the Dashboard menu are: Close Workspace Spectrum/Spectrum Plus Operator s Guide 67

72 Appendix A Creating a Workspace (Dashboard) o Closes all workspace windows Edit Workspace o Select this menu item to add or remove programs in an existing worklist. Before editing a workspace, make sure all of the new windows that you want to add to the workspace are open. When the Edit Workspace menu item is selected, a window is displayed that lists the program names for all the windows currently in the worklist, followed by the program names for all that are not in the worklist. Select the check box next to each of the programs that you want to include in the workspace. Uncheck the check box for programs that you want to remove from the workspace. Click OK to save the edited workspace. Delete Workspace o Select this menu item to delete one or more of your workspaces. When selected, a window is displayed that lists the names of all your workspaces. Select the check box next to each workspace that you want to delete and then press OK. If you delete the currently open workspace, the workspace windows are not automatically closed. Help About Dashboard o Displays the version Close Dashboard o o Select this menu item to close the DashBoard program. If a workspace is open, it is not automatically closed when DashBoard exits. Selecting Close Dashboard will remove the icon from your desktop, unless you have set the default preference Start Dashboard When You login. If this is not your preference, you can display the Dashboard icon again by selecting Start> Programs> ScanScope> Dashboard. 68 Spectrum/Spectrum Plus Operator s Guide

73 B Managing Aperio Services The Aperio Service Manager allows you to stop or restart various Aperio services. You may be asked to access this tool by Aperio Technical Services if you have a problem with opening or accessing images or data. After the Spectrum client software is installed on your computer, you see two icons at the bottom right of your desktop in the system tray: These icons are for the Aperio Service Manager and the Aperio Desktop Manager.. Accessing the Aperio Service Manager 1. Hold your cursor over the icon to see the status of the Aperio services: Spectrum/Spectrum Plus Operator s Guide 69

74 Appendix B Managing Aperio Services 2. Click the icon to open the Service Manager tool: A green light on this menu indicates that the service is currently running, while a red light indicates the service has stopped. 3. To start a stopped service, click the stopped service on this menu. To stop a running service, click the service on this menu. 4. To restart a service, select Restart Services on this menu and then select the service you want to restart. If you select Stop All, Start All, or Restart All, we recommend that you restart your workstation. As a service starts or stops, you see a status message. For example: 70 Spectrum/Spectrum Plus Operator s Guide