Digital Slidebox v4.4. Administrator Handbook 01/05/2008

Transcription

1 Digital Slidebox v4.4 Administrator Handbook 01/05/2008 FOR YOUR REFERENCE: Digital Slidebox URL: Username: Password: 1

2 Table of Contents Section 1: Setting up content within Digital Slidebox 1.1 Logging in to Digital Slidebox 1.2 My Admin Home 1.3 Creating Folders 1.4 Adding Folder Content 1.5 Adding Digital Slides to a Folder 1.6 Editing Slide Details 1.7 Addition of Attribute Categories to Slide Details 1.8 Adding Multimedia 1.9 Adding Hyperlinks 1.10 Setting Multimedia Visibility 1.11 Adding Content Post-Scoring 1.12 Copying folder content Section 2: The Digital Slide Viewer 2.1 Examining Slides 2.2 Measurement Tool 2.3 Snapshots 2.4 Slide Joystick 2.5 Information Window 2.6 Colour Control 2.7 Multi-Focal Plane Slides 2.8 Saving Snapshots 2.9 Viewer Launch Configuration Section 3: Annotations 3.1 Annotating Slides 3.2 Annotation Details 3.3 Annotation List 3.4 Annotation Layers Section 4: Questionnaires 4.1 Questionnaire Manager 4.2 Questionnaire Display Options 4.3 Add or Modify Questionnaires 4.4 Add or Modify a Question 4.5 Compulsory Answering 4.6 Linking Questions to Fields of View / Multimedia 4.7 Sort & Review Questions 4.8 Dependant Questions 4.9 Dependency Rules Work Flow Example 4.10 Modifying Dependency Rule 4.11 Deleting a Question with Dependencies 4.12 Removing, Deleting and Copying Questionnaires 4.13 Replacing and Editing Scored Questionnaires Section 5: User Management 5.1 Adding Users to a Folder 5.2 Creating user groups 5.3 Manually adding users to a User Group 5.4 Adding Existing User Groups 5.5 Shared User Groups 5.6 Sending a Group Mail 5.7 Setting a Gold Standard User 5.8 Creating an Activation Key 5.9 New User Registration 5.10 Existing User Registration Section 6: User Activity & Monitoring 6.1 Viewing User Activity 6.2 Downloading User Data Submissions Section 7: Useful Information 7.1 Search Menu 7.2 Slide Search 7.3 Files & Folders Search 7.4 Adobe flash Player Plugin 7.5 Image Resolution / Pixelation 7.6 Contacting SlidePath

3 Section 1 Setting up content within Digital Slidebox 1.1 Logging in to Digital SlideBox 1.2 My Admin Home 1.3 Creating Folders 1.4 Adding Folder Content 1.5 Adding Digital Slides 1.6 Editing Slide Details 1.7 Addition of attribute categories to slide details 1.8 Add Multimedia to a folder 1.9 Adding Hyperlinks 1.10 Setting Multimedia Post Scoring 1.11 Adding Multimedia Post Scoring 1.12 Copying Folder Content

4 Welcome to the Digital Slidebox, a multimedia content management system for web-based microscopy. This guide will take you through the administrator functionality, including all aspects of project authoring and maintenance. 1.1 Logging In to Digital Slidebox To login to the Digital Slidebox, go to enter your username and password in the fields provided and click the LOGIN button. Important: Before accessing the Digital Slidebox, ensure your technical resources meet the required specifications. For more information, visit 4

5 1.2 My Admin Home Once you have logged in, your default view is the Administration Home Page where it is possible to access Help functions, Language settings and edit your Profile. From this page, you can directly link to all aspects of project management. The workflow within Digital Slidebox allows users to create projects in a stepwise fashion, from creating folders through to monitoring user access. Workflow Overview 1. Create Folder Create Subfolder(s) 2. Add Slides Annotate Create Questionnaire 3. Add Multimedia 4. Add Hyperlinks 5. Add Users Define User Groups Set Gold Standard Users Set Access Privileges Add Activation Keys 5

6 1.3 Creating Folders Clicking on the CREATE FOLDER icon allows you to add new folders. You can create any number of folders depending on how you want to group slides. When creating a folder, add a folder name and description. These can be edited at a later stage. You can nest folders to structure your content as desired. You can keep track of the folder you are currently working in by using the orange NAVIGATION BAR at the top of the screen. Click on a folder name within the navigation bar to return to folders above the one you are currently working in 1.4 Adding folder content New folders can be populated with Subfolders, Digital Slides and multimedia content. Subfolders are created in an identical way to primary folders. You can click and drag folders / slides / multimedia to present them in your preferred list order 6

7 Adds a new folder / subfolder Click the Edit icon to modify a folder name / description Click to copy selected folder contents (excluding user groups and scores) You can use ALL / NONE to select or deselect the entire folder contents respectively. To copy individual items, use the check boxes to mark the items you want to copy. Click to paste the copied content into the current folder BLUE: Click the Delete from a folder Icon to remove content GREY: Click to Delete a folder which contains content such as slides, users groups and statistics. Note, you will be asked to confirm deletion of folders containing any content. Be aware that you cannot undo a delete action. 7

8 When files are re-arranged by drag & drop, click to restore grouping & alpha-numeric ordering Click to add a questionnaire to the slide(s) in the current folder. When a questionnaire exists, Add MCQ becomes EDIT MCQ. If you click this before the questionnaire has been answered, you can edit the questionnaire. If you click this after the questionnaire has been answered, it will reset the questionnaire and delete all answers. You will be prompted with a warning should you try to reset a questionnaire. Be aware you cannot undo a reset action. Note: For more info on questionnaires please view Section. 4. Once you have created a folder, click on it to view the FOLDER CONTENTS. This page lists all the content currently associated with this folder. There are four options for configuring content within a folder: The ADD SLIDES tab allows you to upload digital slide content into the current folder. The ADD MULTIMEDIA tab allows you to upload multimedia files (e.g. JPG, PDF, PPT, video) and hyperlinks to on-line resources. The USERS tab allows you to set up user groups and access privileges for your folder. The STATISTICS tab allows you track the Module Activity in an associated groups scoring user login and annotations via the Morph function. 8

9 1.5 Adding Digital Slides to a folder Clicking on the ADD SLIDES tab will take you to a list of servers from which you can add slides. Click on one of the available links to access folders on the slide server. Server folders may contain sub-folders that can be accessed by clicking on their links. You can add slides one at a time or in batches as well as import annotations or metadata by selecting those you wish to add using the check boxes, and clicking the ADD SELECTED SLIDES button. Once you have added slides, you will be asked to specify a stain and magnification for the slides. The data you enter here will apply to all the slides you have selected to add to the current folder. This will be automatically populated if you are retrieving images from a SlidePath Digital Slide Server (DSS) and can be edited if needed. 9

10 Click ADD THESE SLIDES TO FOLDER to upload your slides. Clicking on the FOLDER CONTENTS tab will allow you to see what content is included in the current folder. Note: If you find you have added a batch of slides with different stains, don't worry! You can edit the details of any slide by clicking the DETAILS icon beside a slide when viewing the FOLDER CONTENTS tab. 1.6 Editing Slide Details Click on the FOLDER CONTENTS tab to view the slides you have added. From the FOLDER CONTENTS tab, you can perform the following tasks: Click the DETAILS icon to modify details associated with a slide, e.g. Name, Description, Stain Click on the DELETE icon to remove a slide from the folder Click the VISIBILITY icon to change access privileges for a slide in the Slide Configuration section. 10

11 GREEN: Users can access this slide at any time ORANGE: Users can access this slide only after completing the questionnaire for the folder (only available when a questionnaire has been associated with the folder) RED: Users cannot access this slide at any time There are three tabs you can access from the EDIT SLIDE DETAILS button. VIEW SLIDE DETAILS shows you a thumbnail of the slide, and a list of any current attributes associated with the slide. EDIT SLIDE DETAILS allows you to modify the name and description of a slide, and create new metadata attributes. Whenever you make a change to slide information, be sure to click the SAVE VALUES button to record your changes. 11

12 The PREVIOUS / NEXT arrows allow you to quickly cycle through slides in the current folder as you make amendments to the details. Note, you need to click SAVE VALUES for each slide individually. Prev / Next Slide Slide Details Attribute Addition Note: The IMAGE QUALITY effects the compression of the image and is designed to provide marginal improvements for low bandwidth users when reduced. Increasing this value to maximum may have a negative impact on the speed at which the image loads. If unsure, leave at the default setting. 1.7 Addition of Attribute Categories to Slide Details It is possible to add Attributes to a slide on the EDIT SLIDE DETAILS page. An attribute could be a patient ID, a TMA core number or tissue type. To add a category, simply add a NAME and click ADD. 12

13 When you have added a category type, you can create attributes in the boxes provided. When complete, Click ADD to associate this information to the individual slide you are working on. SLIDE CONFIGURATION field allows you to specify whether or not metadata and annotations will be visible for this slide. GREEN: Users can access the metadata / annotations at any time ORANGE: Users can access metadata / annotations only after completing the questionnaire for the folder (only available when a questionnaire has been associated with the folder) RED: Users cannot access the metadata / annotations at any time Note: Why use attributes? Attributes are descriptive terms that are stored in the database, which the Search system uses to quickly retrieve a slide / slides. They are not essential, but are useful for large slide libraries. 13

14 1.8 Adding Multimedia to a folder From the ADD Multimedia tab, you can add a variety of multimedia types to a folder, you can also add hyperlinks to useful web resources from this page. To upload a multimedia file, give the file a name, then locate the file you want from your computer by clicking the BROWSE button. When you have done so, enter a description for the file. When you are ready, click UPLOAD FILE. The system will automatically determine the file type. When you have Uploaded the file it will become added to the current folder. Note: Digital Slidebox will determine the correct file type, but it is important to make sure your users computers have the right program to open the file type(s) you upload. Be aware that the maximum file size you can upload is 20 MB. 14

15 1.9 Adding Hyperlinks To add a hyperlink, first give the link a name. Copy the address of the link from your browser, or else type the link into the URL box. Enter a short description for the link, and then click UPLOAD HYPERLINK to upload it to the folder Setting Multimedia Visibility You can set access rights for multimedia files and hyperlinks in a similar fashion to digital slides. Toggling the visibility icon allows or denies access depending on scoring status. Multimedia details can be edited after they are uploaded. Click on the DELETE icon to remove multimedia from the folder Click the VISIBILITY icon to change access privileges for a file or hyperlink. GREEN: Users can access this slide at any time ORANGE: Users can access this slide only after completing the questionnaire for the folder (only available when a questionnaire has been associated with the folder) RED: Users cannot access this slide at any time 15

16 Files that are not available to users will appear greyed-out, indicating that they cannot be accessed at this time. The file description will be replaced with a warning that the folder questionnaire must be answered before this multimedia file can be accessed Adding Content Post-Scoring It is possible to add slides / multimedia / hyperlinks to a folder after users have already completed the questionnaire for the folder. In doing this, you will be prompted with a warning that any slides / multimedia / hyperlinks added will by default be set to the VISIBLE status. 16

17 1.12 Copying folder content The tools used for copying and pasting content are as follows: Click to copy selected folder contents (excluding user groups and scores) You can use ALL / NONE to select or deselect the entire folder contents respectively. To copy individual items, use the check boxes to mark the items to want to copy. Click to paste the copied content into the current folder Content which can be copied: Digital Slides Sub-folders Multimedia Questionnaire Annotations Hyperlinks Please note, in order to protect user identities; User Groups, Scoring Data and Statistics are NOT copied along with other folder content. If there are sub-folders in the directory you are copying, the same constraints apply as above. 17

18 Section 2 The Digital Slide Viewer Examining Slides Advanced Options Narrative Slide Joystick Information Window Colour Control Multi-Focal Plane Slides Saving Snapshots Viewer Launch Configuration

19 2.1 Examining Slides You can access the slide viewer by clicking on the slide thumbnail from any of the folder / slide configuration screens. The slide viewer allows you to examine, annotate and add scoring forms to digital slides within the current folder. A number of tools are available to aid your examination of slides: Changing Magnification Lateral Scrolling Adjusting Image Quality Through-focussing of multi-focal plane slides Note: The slide viewer is the first of it's kind to be vendor neutral. This means that Digital Slidebox can support images scanned from any of the main scanner hardware vendors. You can scroll through the entire slide by clicking and dragging on the image in the main viewer window. Alternatively, the following controls are available to assist in your examination of the digital slide: The NAVIGATION CONTROLS allow a user to scroll laterally in the digital slide. The four arrow icons scroll the slide in the X and Y directions. The central button returns the user to a lowpower overview image 19

20 The SLIDE OVERVIEW can also be used to navigate the slide. Users click on a particular region of interest within the overview, and they will be directed to that region in the main viewer. The green box at the centre of the red cross-hair indicates the current field of view The SLIDE OVERVIEW has the capacity to record a viewers analysis of a slide by way of HEAT MAPPING with corresponding colours for the various magnifications. Various colours represent the different magnification and a corresponding grid system directs you to where the USER has viewed the slide. This unique feature allows you to follow the virtual diagnosis pathway of the USER. The MAGNIFICATION CONTROLS allow users to zoom in and out of the digital slide. The (+) and (-) icons at either end of the toolbar increase and decrease magnification respectively. The four arrows allow the user to rapidly switch between 4x (left-most arrow), 10x, 20x and 40x (right-most arrow) magnifications, similar to switching objectives on a microscope. At higher magnifications, you will see an additional arrow for 60x at the extreme right. Note, you can also right-click on the viewer window to change magnifications. Click on the BACK ARROW to return to the FOLDER CONTENTS page Click the SELECT SLIDE button to switch between slides in the current folder. 2.2 Advanced Options Note: The slide viewer uses a windows-style dialogue box for each of the different tools. Click the dash to minimise, the red X to close and click / drag to move. Click the VIEW OPTIONS button to access advanced viewer tools. 20

21 The options menu lists additional tools available within the viewer. Note, a blue border and tick when the option is currently displayed within the viewer. You can toggle display status by clicking on the circle icon. Displays a list of annotations on the slide Toggles display of the slide overview window Toggles the slide joystick control Toggles the display of annotations on the slide As an administrator you can click the VIEW TOOLS to access the slide attributes that can be created and/or edited. This tab is not visible in the User view. Allows you to cluster annotations into groups. Allows you to create and edit a questionnaire for the folder. Allows you to build up a textbook-style narrative for the Case. 2.3 Slide Narrative The slide narrative tool allows you to build up a review of the slide, associating external links, multimedia and links to other slides from keywords within the text. 21

22 As you write the narrative, you can highlight text and apply formatting changes such as title and bulleted. You can also link to specific phrases or keywords within your narrative by highlighting the text (displayed in italics in the bottom left hand corner), and selecting a link from the dropdown: LINK TO A URL by typing the website into the box and clicking OK. When a user clicks on the highlighted text, their browser will open a new window displaying the website LINK TO A FILE by browsing your computer for the file required, or by selecting from a list of multimedia already uploaded into the folder. Files added from your computer are automatically uploaded as multimedia within the folder contents also, with their visibility status set to notvisible. LINK TO ANOTHER SLIDE by selecting from a list of all the slides in the current folder, and clicking OK 22

23 LINK TO A LAYER by selecting from a list of annotation layers created for this slide Link To An Annotation by selecting from a list annotation layers created on the slide. Click OK followed by SAVE to store your narrative, or DELETE to remove it. You can open the narrative from the view tools menu at any time to make changes. Note: Be sure to click SAVE on the narrative screen each time before you close it, to ensure your changes are not lost. 2.4 Slide Joystick The slide Joystick is a simple control designed to allow users to screen a digital slide rather than examine field by field. To use the joystick, click and hold your mouse over the blue button. As you move your mouse, the joystick will indicate which direction you are moving across the digital slide. 23

24 2.5 Information Window The information window displays any additional details about the current slide, including slide Metadata and Thumbnails. The slide Metadata gives a comprehensive overview of the slide details that can be edited if required in the EDIT SLIDE DETAILS tab on the main Folder Contents page. The THUMBNAILS tab allows you to view a macro image of the slide not shown in the scan area Colour Control User's can adjust brightness, contrast and colour settings to optimise the digital slide for their monitor. These tools can be accessed from the COLOUR CONTROL button in the toolbar. Adjust Red / Green / Blue Saturation Adjust Brightness Adjust Contrast Use the sliders to adjust parameters to suit your viewing requirements. You can reset all parameters at any stage by clicking the RESET button. Note: The balances you set are stored in Digital Slidebox, even after you close the colour control toolbox. Once you leave the slide, they will be reset to default automatically. 24

25 2.7 Multi-Focal Plane Slides The digital slide viewer is now capable of displaying multi-focal plane (MFP) slides. MFP slides are created at point of scanning, whereby a number of scans at different focal depths are embedded within a single image. If the slide being viewed has been scanned using MFP, the FOCUSSING button will appear in the toolbar. Click to activate the SLIDE FOCUSSING controls or right click on the VIEWER window and select it from the menu The Focus Controls allow you to through-focus the digital slide. You can adjust focus by moving the slider to along the focus bar. As you move the slider, you will observe the focus changing on the slide in the background. By clicking on the MODE button, you can switch from MANUAL to AUTO focus. Auto focus initiates a throughfocus scrolling, whereby the slide will scroll back and forth through all the focal planes within the image After you have adjusted the focussing, you can continue to examine the entire slide at the specified focus plane. At any point, you can open the MFP controls again and readjust your focussing before you continue examining the slide. Note, you can also access the slide focussing tool by right-clicking on the main viewer window. Note: MFP slides contain multiple images, and thus are multiples of the standard digital slide file size! Pay particular heed to our recommended computer specifications for viewing these type of slides. More information is available at 25

26 2.8 Saving Snapshots Use the SNAPSHOT button to capture a still image of the current field of view, and export it as a JPEG. When you take a snapshot, it opens in a new window. Use the snapshot button or Right-click on the image and choose SAVE AS or SAVE PICTURE AS to store the image to your computer. Note that the snapshot records annotations and measurements that have been marked on the slide, along with associated text descriptions. At the bottom of the snapshot window, there are two links given: STATIC LINK is a URL that allows you to retrieve a copy of this still image again in the future. DYNAMIC LINK is a URL that, when opened in your web browser, will bring you back to the current slide, at the exact region and magnification at which the snapshot was captured. This is a useful way to distribute a single digital slide among a large group of users via an existing web-portal (e.g. WebCT, Moodle, etc.) Note: If you the dynamic link to a group of users, they can access this slide only, and will not be able to access any of your other slides. They do not need a username or password to access this slide but this means they will not be able to complete any questionnaires. Click CLOSE WINDOW to return to the VIEWER to continue viewing your slides. 26

27 2.9 Viewer Launch Configuration You can customise the behaviour of the slide viewer for each individual folder you create, by defining which toolsets will automatically appear to the user when they access a slide within that folder. On your list of folders, click the DETAILS icon beside the folder in which you would like to define viewer behaviour. Click on the VIEWER CONFIGURATION tab. Note: Narratives can be switched to Orange by Clicking on their visibility Icon. This means they will only become visible after the scoring of the associated questionnaire. You can set which tools will be present upon viewer start-up by clicking the STATUS icon. GREEN: Tool appears automatically when viewer starts RED: Tool does not appear automatically when viewer starts ORANGE: Tool is only accessible after questionnaire has been completed (e.g. Narrative All tools can still be user-controlled from the viewer interface. Note: The changes you make apply to the current folder only. Viewer behavior in subfolders will be default unless you change them manually. 27

28 Section 3 Annotations Annotating Annotation Annotation Annotation Slides Details Information Layers

29 3.1 Annotating Slides Slides can be annotated to highlight features of interest or provide diagnostic cues to individuals reviewing the slides at a later date. To annotate a slide, select from the ANNOTATION TOOLS within the slide toolbar. Free Hand Measurement Add Arrow Add Ellipse Add Box Click on the desired tool to begin annotating. Notice that the cursor changes from a hand to a cross-hair; this indicates that you are in drawing mode. When drawing an ARROW, position the mouse pointer at the origin of the arrow, and click-and-drag towards the feature of interest. When drawing a BOX or Ellipse, position the mouse at the topleft corner of the region of interest, and click-and-drag the box over the desired region. The FREEHAND tab allows you to use a pencil to write or draw at ease to highlight/outline specific shapes. When you mark an annotation, you will be asked to enter some details: You can choose a colour for the annotation (default is GREEN) You will be asked to give the annotation a title (mandatory) You can enter a description (optional) You can associate a URL to an external site (optional) You can associate files (optional) To add a URL, simply type it into the box. 29

30 To add a file, click icon and browse for files stored on your PC, or within the current folder. Files added from your computer are also uploaded to the FOLDER CONENTS as multimedia, with their visibility status set to (RED) not-visible. After you fill in text, select the colour that your annotation will appear in, and click SAVE. The information you enter for an annotation will be visible when you mouse-over it on the main viewer window. When you select the Measurement type annotation, you can draw a marker on the image with an associated measurement. This measurement is calibrated based on the slide magnification and the original capture conditions. Once you draw the marker, the length of the measurement is filled in automatically. The only information you can edit is the colour. 30

31 Note: The measurement tool scales automatically from Micrometers, to millimeters, to centimeters as you draw the marker. By clicking on a saved annotation, you can edit the information, or delete the annotation. If you right-click on an annotation, you can do the following: Reposition: use your mouse to move an annotation within the viewer Redraw: Draw a new annotation with the existing one still in view as a reference. Once you complete the replacement, the original annotation is deleted. Note, this function is not available for Measurement type annotations By right-clicking on the main viewer window, you can access the annotation drawing tools (i.e. Arrow, Box, Ellipse, Measure and Freehand). You can also add an associated question to the annotation (See section 4 for more information on questionnaires). When you have completed your examination / annotations, use the SELECT SLIDE button to open a drop down menu, and select from other slides within the current folder. 3.2 Annotation Details From the FOLDER CONTENTS screen, click the EDIT DETAILS icon to access the VIEW SLIDE CONFIGURATION tab. Under Annotations you will see the number of annotations you have made for the slide. Click REVIEW to return to the slide viewer and go back through your annotations. 31

32 The ANNOTATION VISIBILITY button allows you to hide all the annotations on a digital slide. Click to toggle between visible and invisible statuses. GREEN: Users can view annotations / answer MCQ ORANGE: Users can view annotations only after completing the scoring form for the folder (only available when a scoring form has been associated with the folder) RED: Users cannot view annotations at any time 3.3 Annotation Information If a digital slide has been annotated, the annotation information appears automatically when you open the slide. The list shows all annotations made on all slides in the current folder. The annotations are in blue text Click on these to navigate to the position of the annotation. Annotations beneath a bold heading are associated to a layer. The bold text is the name of the layer click on this text to show ONLY that layer. Click the slide name underlined at the top of the list to show all annotations. You can manage your annotation layers by clicking the LAYER MANAGER button via the VIEW TOOLS tab in the viewer. You can also review the slide narrative by clicking on the NARRATIVE button. 32

33 3.4 Annotation Layers Annotation layers allow you to cluster together similar annotations. To create a layer / layers, click LAYER MANAGER via the VIEW TOOLS tab in the viewer. Click CREATE NEW LAYER and give the layer a name. This name will appear in the annotations list. In the Layers on Slide list, select the layer you wish to edit (selected layer is indicated by a blue tick mark). Using the Annotations in Layer and Ungrouped Annotations lists, you can add / remove slides to / from the current layer. Click on the circle icon beside an annotation to select it (indicated by a blue tick mark), and click to ADD an annotation to the current layer Click on the circle icon beside an annotation to select it (indicated by a blue tick mark), and click to REMOVE an annotation from the current layer 33

34 You can add all unused annotations to the current layer by clicking the ADD ALL arrow You can remove all annotations from the current layer by clicking the REMOVE ALL arrow The layers are automatically saved, and are visible immediately upon creation. Note, if you remove all the annotations from a layer, the layer will remain visible in the Slide Layers List, however will not be visible in the Annotations List. Note: You can order Layers and Annotations within a specific layer by clicking and dragging them within the Layer Manager. 34

35 Section 4 Questionnaires Questionnaire Manager Questionnaire Display Options Add or Modify a Questionnaires Add or Modify a Question Compulsory Answering Linking Questions to fields of View or Multimedia Sort & Review Questions Dependant Questions Dependency Rule Work Flow Example Modifying Dependency Rule Deleting a Question with Dependencies Removing Deleting and Copying Questionnaires Replacing and Editing Scored Questionnaires

36 Important: The Questionnaire system has been completely overhauled compared to it's predecessor. Be sure to read carefully through this section to understand how the system works. You can access the questionnaire builder in two ways: The ADD MCQ button from the folder contents page allows you to create a questionnaire. When a questionnaire already exists, this button will change to EDIT MCQ. The Questionnaire Editor tab from the View Tools menu in the Slide Viewer allows you to set up a questionnaire Note, in both cases, the viewer will launch the first slide in your folder before the questionnaire manager appears. This is to facilitate the new linking system utilised by the questionnaire system. Before you begin... Folders on the system are similar to Cases. Each folder is an individual Case and all the slides / multimedia in the folder are part of the Case. When you create a questionnaire in a folder, it applies to all slides within the folder. If your users answer the questionnaire from any of the slides, it will count as the folder being scored. You can use the new linking system to point each question at a specific slide in the current folder, however if each slide needs to have its own questionnaire, it should be put in a separate folder. 36

37 4.1 Questionnaire Manager The Questionnaire Manager allows you to do the following: Create a Questionnaire Edit a Questionnaire Preview (Test) a Questionnaire When creating a questionnaire you can chose to build a new one or use an existing one from another folder. Use the drop down menu to select the existing questionnaire you want to use. Whether you create a new questionnaire or use an existing one, you can specify a name and description for your questionnaire, to help you keep note of what your different questionnaires are for (e.g. 1st year histology, 2nd year mock exam etc...) 37

38 4.2 Questionnaire Display Options You can specify how the questionnaire is displayed to users: Each question appears one at a time on screen for your users to view Questions are presented as a list within a single scrolling window You can also specify how users should answer the questionnaire: Students must answer questions in sequence Students can go back and modify their answers 38

39 4.3 Creating / Modifying a Questionnaire When creating or modifying a questionnaire you have 4 key tools: Return to change the configuration of the questionnaire Add a new question to the questionnaire Complete the questionnaire as a user would see it and test the layout of questions you have created. You can Preview your questionnaire at any stage during the build process. Saves your questionnaire questionnaire manager. and closes the 4.4 Add or Modify a Question When you add a new question, you will be asked to enter the following information: Question text (e.g. What is shown in this slide?) Answer Type Is the question compulsory? Question Link 39

40 There are five types of answer you can have for your question: 1. Multiple Choice: Users are required to select from a number of options. You can set the question such that they can select only single selection (e.g. Yes or No) or multiple selections (e.g. Select the features present from this list). Type each option into the text box and click ADD. It will appear in the list below. You can delete any of the options by clicking DELETE beside it, or click and drag options into a specific order. Click on the icon beside any option to add a URL. This can be a URL to a website, or even to a Snapshot (see section 2 for more information on snapshot URLs) 40

41 2. Text Input: Allows the user to enter their own commentary. 3. Number: Requires the user to enter a numeric value. You can set the question such that the number is constrained (e.g. What percentage of the slide is necrotic you would constrain the answer between 0 and 100) or open (e.g. Count the number of mitotic cells in this slide). Note, if you constrain the value, the user will not be allowed to enter a number outside these constraints. 4. Measure: Requires the user to use the measurement tool to measure on the slide 5. Instructional Text: This answer is a statement that appears and requires no answer from the user. This can be used creatively in a number of ways, for example, advising a student if they have selected the correct / incorrect option from a multiple choice question, or asking the user to mark an annotation on the slide. Note: Students now have the ability to make their own annotations. Use this to your advantage when building your questionnaire. For more information on how to review student annotations, see Section Compulsory Answering For any question type you can set whether it is compulsory or not by simply clicking the YES or No. 41

42 4.6 Linking Questions To Specific Fields of View or Multimedia Use the drop down menu if you want to create a link from this question. You can link to 4 different resources: A field of view on one of the slides in the current folder An annotation on one of the slides in the current folder A multimedia file uploaded into the current folder A URL (either to a website or a Snapshot URL) Link To A Field Of View When you select this type of link, you will be asked to navigate to the filed of view you require, and click OK. Use the viewer to select the slide you want (from the Select Slide menu) and go to the region and magnification you want. Click OK to create the link. When you have created a link to a field of view, you can check the field you have chosen on the edit question page, by clicking on the icon. 42

43 Click NEXT once you are finished. Link To An Annotation When you select this type of link, you will be asked to select from a list of annotations you have created on any of the slides in the current folder. As you click on slides in the dropdown menu, the viewer will shift to show you each annotation, assisting you in making your decision. Click NEXT once you are finished. Link To A File The Select File box allows you to upload a new file (upload button) or add a file from your folder contents to the current question (dropdown menu). Click on the icon to select the file you wish to link to this question. 43

44 Click the UPLOAD button to browse your computer for a file. When you have selected the file you want to link, click OPEN. You will then be asked to give the file a name (if you want to change this from the name of the file on your computer). You can also add a description (optional) to explain the file. Click UPLOAD to attach the file, and click NEXT once you are finished. 44

45 Link To A URL To link to a URL, copy & paste the address from your web browser / snapshot or simply type the web address into the box provided. Click NEXT once you are finished. 4.7 Sort and Review Questions Each time you create a new question, it is added to the list on the SORT & REVIEW screen. You will see the Question Text you entered, and the position of each question within your questionnaire. Click to modify this question; changing the text, answer type and links. Click to add a dependent question to this one. Click to delete this question. 45

46 Sort and Review : Drag a Drop a Function The questions in the Questionnaire Editor are ordered numerically. When you want to re-order the questions within a questionnaire simply place the cursor on the Question you wish to move, Click on the Question and DRAG it to the new ordering position. You can move the Question up or down and when a question has been moved the Question number is re-ordered within the Editor. Note: If a Question has dependencies associated to it, it is not possible to reorder it unless you remove the dependency constraints. No options will be given to place it above or below except where multiple choices are involved, even if you attempt to move a dependent choice the order will still not change dew to the dependency constraint. 46

47 4.8 Dependent Questions Click the edit dependency rule to create a new dependent question. You can either create a new question or use an existing question that will be dependant on the answer of your source question. It is possible to select from the questions you have previously created in a drop down menu format if you want to create a dependency using an Existing Question. Dependent questions appear on the SORT & REVIEW page, indented beneath the source question shown in RED. 47

48 You can create create dependency rules from three types of source question. Question Type Dependency Rule Multiple Choice Question appears when a specific option(s) is / are selected from the list. Number Question appears when a specific value or a value within a specified range is entered. Text Input Question is displayed when an exact word for word match to a specified phrase is entered. 48

49 Dependent questions are answered the same way as ordinary questions. You can also create links on dependent questions the same way as you would for ordinary questions. If you delete a question which has subordinate dependent question(s), you have two options: Delete the dependent questions Keep the dependent questions but remove the dependency rule If you choose to keep the questions, they will appear in line with the other questions on your questionnaire and will no longer be indented. 4.9 Dependency Rule - Workflow Example The the example below, users are asked to select from LCIS, DCIS and Paget's. The work flow is demonstrated in a basic format of linking diagnosis to a comment by way of diagnostic choices set by you. Selecting LCIS or DCIS opens a subsection requesting the User to grade the carcinoma. Selecting Paget's opens no dependent questions. In each case the user arrives at the final diagnosis question. Please diagnose this case: LCIS DCIS Paget s What class of LCIS is this? Lobular LCIS Pleomorphic LCIS What grade of DCIS is this? Low Intermediate High Support your diagnosis with a comment 49

50 1. Create your question and multiple choice answer type. ADD your 3 choices. As before you can link your choices to hyper links and/or a specific field of view. Click NEXT to proceed to the SORT & REVIEW page. 2. Click the Dependency Icon and choose to create a new question. Select the options which will make the dependent question appear- in this case, if the user selects LCIS, they will see the dependent question. 50

51 3. You will see a summary of the dependency rule in RED at the top of the questionnaire window. Create your dependent question here in this case, should the user select a diagnosis of LCIS, they will be asked whether it is classed as Lobular or Pleomorphic. 4. Follow the same procedure for creating your DCIS dependent question 5. When you have completed this, TEST & PREVIEW to check your questionnaire. 51

52 In the above scenario, the final question asking for a diagnostic comment will appear regardless of whether the user selects DCIS, LCIS or Pagets. Any questions that are not governed by a dependency rule will appear to the user in sequence as they proceed through the questionnaire. You can set dependencies for all options from the original question multiple choices leading to a final input. Within the Questionnaire Manager there are also additional functional Icons that allow you to modify your scoring form dependencies Modifying a Dependency Rule You can edit any dependency rule you have created from the SORT & REVIEW page The Delete Dependency button allows you to remove the dependency rule from a question, but keeps the question in the questionnaire. The Adding or Editing Dependency Rule button allows you to modify the dependency rule settings for a question Click to modify this question; changing the text, answer type and links Click to delete this question 52

53 4.11 Deleting a Question with Dependency If you require to delete a question that contains a dependency rule the following warning will appear allowing you to view the questions associated to it, outlining the over all effect of deletion. You are given two choices on how to proceed with deletion: 1. Remove the dependency rule associated to this question. or 2. Delete all questions dependent on this one Removing, Deleting & Copying Questionnaires On the FOLDER CONTENTS page, you will see that there is an MCQ associated with a slide or folder. 53

54 Click the VISIBILITY icon to change availability of statistics after a user has answered the questionnaire GREEN: Users can access anonymised group answers, goldstandard answers and consensus data for each slide in the case RED: Users can only access their own answers for each slide in the case Click the DELETE icon to remove a questionnaire from the current folder BLUE: Remove the current questionnaire GREY: Answers have been submitted to this questionnaire. By deleting this questionnaire, you will delete any submitted answers also. Be aware, a delete action cannot be undone. You should download a CSV of any submitted answers before you proceed. See Section 6for more information. When you delete a questionnaire from a folder, it is not removed from the system permanently. You can still select it from the drop-down menu if you choose ADD EXISTING QUESTIONNAIRE from another folder. You can COPY your questionnaire in two ways: 1. On the folder contents screen, use the check-box to select it, click COPY, go to your new folder and click PASTE 2. Go to your new folder. From the Questionnaire Manager, click ADD EXISTING QUESTIONNAIRE and select it from the drop-down menu To help you find questionnaires you can use the Previously Defined Search page. This will allow you search your own questionnaires in MY EXISITING QUESTIONAIRES or shared questionnaires you may have with colleagues. By populating the text boxes with key words in the search for specific questionnaires tab you can refine your search outputs and choose from a list of results that are most relevant to. 54

55 In the search results page scroll through the list of questionnaires and Click the one you want making it flash once in Green. You will be requested to give a TITLE and DESCRIPTION for your chosen scoring form. Click NEXT to Sort and Review in the Questionnaire Manager Replacing and Editing Scored Questionnaires It is possible to replace the questionnaire in a folder after users have scored. On the FOLDER CONTENTS screen, the ADD MCQ becomes EDIT MCQ when there is a questionnaire attached. Note, when users have already submitted answers, the EDIT MCQ button can be used to reset the questionnaire and delete any responses that have been recorded to date. Be aware, the reset action cannot be undone. 55

56 Similarly in the Viewer if you Choose to EDIT a scored case a warning will show up as follows: Note: Before replacing a questionnaire, it is advisable to download a Comma Separated Value (CSV) file of submitted answers for the questionnaire (See Section 6.2 for more Information). 56

57 Section 5 User Management Adding Users to a Folder Creating user groups Manually adding users Adding Existing User Groups Shared User Groups Sending a Group Mail Setting a Gold Standard User Creating an Activation Key Registering as a New User Registering as an Existing User

58 5.1 Adding Users to a folder Users are added to a folder through USER GROUPS. 5.2 Creating User Groups Click CREATE NEW GROUP to set up a new user group. The first step in this process is to give your user group a name. On the USER screen, you will see which groups are added to the current folder. Under MEMBER COUNT, you can see how many users you currently have in this group. 5.3 Manually Adding Users to a User Group Click on the name of the group that you want to add users to. 58

59 CREATE NEW MEMBER allows you to add new users to this group. You will need to enter a name and valid address for your user, along with creating a username and password. Click SUBMIT to confirm the details for this user. This new user will now be a member of your group Note, if you have pre-existing users on the system (from other user groups) you can add these to the current group by ticking the check boxes beside the users you wish to add, then clicking ADD MEMBERS. Note: Once you have created a user group, you can return to that group and manually add / remove users at any point. By clicking on the name of a user, you can review and edit their username and reissue a forgotten password. 59

60 5.4 Adding existing user groups By clicking ADD GROUP on the users screen, you can select user groups you have already created to add to the current folder. Use the check boxes to select the group(s) you wish to add, then click ADD GROUP. Alternatively, you can select from SHARED USER GROUPS. 5.5 Shared User Groups As an administrator on Digital Slidebox, you are permitted to create user groups. Other administrators can also do this. If multiple administrators are part of the same Administrator group on the system, they can share user groups and access shared user groups. Simply check the boxes in the shared user groups that you want to add to your folder 60

61 From the USERS screen, click ADD GROUPS. Here you will see a list of all groups you have created on the system. You can specify whether each group is shared or is private, using the SHARE icon. Group is Shared Group is Private Important: Groups that you are sharing are not your own, therefore you cannot make any changes to the group activation key or users within that group. You can click through to access users names and addresses, but not their access details for the system. It is possible to rename a group by Clicking the EDIT tab to the right of a Group Name, this can be done for both your own and Shared Groups. 5.6 Group Mail Click on the SEND icon to the entire user group. It is important to ensure all your members have a valid address recorded on the system for this to function correctly. 5.7 Setting a Gold Standard User By clicking on the name of a User Group, you can see all the users currently assigned to that group. You can select any one of these users as the gold standard for this folder. From a statistics point of view, their 61

62 answers would be deemed as the correct answers. To set a gold standard user, click on the GOLD STANDARD icon beside their name in the folder. GREEN: User is gold standard for this folder. Their answers will be treated as the statistical right answers for the scoring form in this folder. Other users answers will be compared to this set for accuracy. RED: User is not gold standard. Their answers are treated normally. 5.8 Creating an Activation Key You can allow users to SELF REGISTER for your folder. To do this, click the ACTIVATION key button beside your user group. 62

63 The random code given allows users to register for your folder from the Digital Slidebox homepage. When users self register, they will automatically be added into the user group, allowing you to monitor registration to your folder. By clicking MANAGE KEY, you can edit the key to custom text. We recommend using a combination of numbers and capital letters as lower-case letters can be easily misread. 5.9 Registering as a New User Activation keys allow large groups of users to register for modules within Digital Slidebox, without the need for the administrator to manually set up individual user accounts and assign them to the appropriate group. The workflow for first-time registration to the system is as follows: 1. Click on NEW USER within the registration area on the Digital Slidebox homepage 2. Enter your name and a valid address 3. When asked for an ACTIVATION KEY, enter the assigned key from the module owner 63

64 4. Click NEXT and create a username and password 5. Click SUBMIT to register 5.10 Registering as an Existing User If you have an existing account on the system, you can use the same access details for new modules once you have the activation key: 1. Click on EXISTING USER within the registration area 2. Enter your username and password 3. When asked for an ACTIVATION KEY, enter the assigned key from the module owner 4. Click SUBMIT to register Important: You only need to use the activation key once once you have created a username and password, you can login with them at any stage in the future. 64

65 Section 6 User Activity & Monitoring 6.1 Viewing User Activity Downloading User Data Submissions 71 65

66 6.1 Viewing User Activity Using the STATISTICS page, it is possible to review the activity of individual users within your group, for the folder to which the group is assigned. No activity details / CSV is available as no users have logged in or scored this case Click to view user activity for this folder Case CSV: Downloads a CSV file for the current case Scoring Scenario (see section 6.2 below for more information) By Clicking on the View Activity tab you can view the number of times an individual user has logged in and the last login date. On this page you may also access USER STATS, the Morph to User function or send a User an by Right Clicking on their NAME. 66

67 User Statistics You can view an individuals answers to the case questionnaire associated to the folder by clicking on the USER STATS icon beside their name. The Primary Questions are shown in the question column along with the answer the individual gave. The STATISTICS column displays the percentage consensus between user group. The GOLD STANDARD column allows you to directly compare the user's responses with the Gold Standard (if defined). The GRAPH Icon give allows you view graphical analysis of answering within the user group, showing where an individuals answer lies in relation to the whole group. 67

68 User MORPH Click the MORPH icon to go directly to an individual user's slide viewer to look at any annotations they have made, and review their diagnostic heatmap of the slides. Heat Mapping The SLIDE OVERVIEW has the capacity to record a viewers analysis of a slide by way of HEAT MAPPING with corresponding colours for the various magnifications. Various colours represent the different magnification and a corresponding grid system directs you to where the USER has viewed the slide. This unique feature allows you to follow the virtual diagnosis pathway of the USER. The magnification the slide was viewed at corresponds to a colour Red: Maximum Magnification (e.g. 40x) Yellow: High Magnification (e.g. 20x) Green: Intermediate Magnification (e.g. 20x) Blue: Low Magnification (e.g. 4x) Note: to enlarge the Slide Overview place the cursor on on the edge of the box and use the drag arrows to increase its size. 68

69 As an Administrator when viewing a Users Heat Map you can Right Click the Slide Overview Box to reveal two options: 1. Hide Heat MAP: Removes Heat Mapping from the Slide Overview window. 2. Clear heat map data and reset: This wipes the current heat Map associated to a slide and resets it for the Users next Visit. 69

70 6.2 Downloading User Data Submissions You can download a global CSV of all user's submissions for this folder by clicking on the DOWNLOAD CSV icon. The CSV file is not a statistical program itself but can be opened with statistical packages such as Microsoft Excel, Open Office Calc and SPSS. The data within the CSV can be further analysed to calculate means, modes or the construction of pie charts or graphs. One of the underlying functions of the CSV is in being a permanent record that you can save and use as a back up. Also if a submission date is dew you can down load the CSV and see the Users that have submitted within the time while allowing late submissions by keeping a scoring form open and taking the CSV at a later date. Important: Be sure that the SEPARATED BY field has COMMA selected in order for the CSV (COMMA SEPARATED variable) file to be compiled correctly. 70

71 Section 7 Useful Information 7.1 Search Menu 7.2 Slide Search 7.3 Files and Folders Search 7.24Adobe Flash Player Plugin 7.5 Image Resolution / Pixelation 7.6 Contacting SlidePath

72 7.1 Search Menu The Search Menu helps you find slides, files and folders available to you in Digital Slide Box. To help you retrieve the most comprehensive search try limiting the number of words and ensure correct spelling of your requirements to yield the most effective search. 7.2 Slide Search For Slide Searching there are numerous ways of retrieving files. It is possible to search by the Name, Description, Slide Attribute or Annotation Attribute. The operator field allows you choose further search parameters to best fit the files you get back. The Operator field contains a drop down menu to help you define your search. The symbols represent the following: = Direct Match!= Does Not Match > Greater Than (numbers & letters) >= Greater Than or Equal to (numbers / letters) < less than (numbers / letters) <= Less Than or Equal to (numbers / letters) *wild = matching term after the asterisk wild* = matching term before the asterisk *wild* = matching term between asterisk 72

73 The Wild setting works as follows: If you search for a slide named Pathology_A12B the following search results will be returned using the wild function. *wild A12B : knowing the pathology term wild* Pathology : knowing the A12B term *wild* 12 : knowing the 12 term The Slide Attribute option permits searches by way of meta data associated to a slide (i.e. Name, Stain, Image Quality etc.). The Annotation Attribute option allows searches for data associated to an area of interest on a slide. 7.3 Files and Folder Search To search for files and folders choose a parameter and input your search terms in the box provided and Click Search. 73

74 7.4 Adobe Flash Player Question: I have received a warning about Adobe Flash Player and am unable to access digital slides. How do I proceed? Answer: Adobe Flash Player is a plug-in for Internet browsers, enabling users to view certain types of multimedia on the web. Many different websites use content that requires the flash player, thus it is a common application. If you login to Digital Slidebox and do not have Adobe Flash Player version 8 (or higher) installed, you will see this message: To install Flash, click on the FLASH PLAYER button within the notification, and follow the on-screen installation instructions. Once you have installed Flash, close your Internet browser. Open a new Internet browser window, and return to Digital Slidebox. You should now be able to access on-line content. Important: Flash player installation can sometimes be hindered by access privilege restrictions on your computer. If you still cannot access on line material, you will need to contact your IT department or computer administrator, and ask them to install Flash for you. 74

75 7.5 Image Resolution / Pixelation Intermittent users report difficulty in obtaining a clear image, citing pixelation as the main problem. Pixelation occurs while the loading; this process can sometimes be hindered by poor bandwidth. It is possible however, that you cannot see the image technical fault. typically image is Internet due to a In order to check if the image has completed loading, look at the navigation controls on the slide viewer. The circular control panel is bordered by a grey ring, which builds as the slide loads. If the grey ring appears broken, the image has not loaded correctly on your PC, and you should return to the folder contents screen using the BACK ARROW in the toolbar, and try to access the slide again. Image has not yet loaded into the slide viewer Image has partially loaded into the slide viewer Image has fully loaded into the slide viewer 75