PathXL Training EQA/Whole Slide Scoring · 2 days ago · Service Hours The PathXL (hosted) website...

PathXL Training – EQA/Whole Slide Scoring

• User Training

• Overview of PathXL EQA/Whole Slide Scoring

• PathXL Support

• Quick Start

• Viewing Content

• PathXL Viewer

• Taking a Study

• Manager Training

• Creating a Study in PathXL EQA/Whole Slide Scoring

• Assigning Permissions

• Questions

Agenda

Overview

Overview

Available entirely online

• Web Browsers Supported

• Firefox (latest)

• Chrome (latest)

• Internet Explorer 10

• Internet Explorer 11

• Safari (latest) on Windows and Mac

No browser plugins are required. The only requirement is that the web browser must have

• JavaScript enabled

• Popup Blockers Disabled

• Cookies Enabled

Overview

Vendor Neutral• SVS (Aperio – JPEG/JP2 Compressions, Sakura, Ventana)• NDPI (Hamamatsu)• MRXS (3D Histech)• SCN (Leica)• SCN (Ariol)• CZI (Zeiss)• VSI (Olympus)*• Objective Imaging (Mikroscan)• TIFF (Standard Tiled TIFF).• TIFF (Huron, Ventana, Mikroscan, Trestle)• TIFF (Philips)**• BIFF (Ventana)• SVSlide (Sakura)• In addition we also support image formats such as JPEG and PNG.

* Requires the Olympus Net Image Server (NIS)** Requires the Philips Image Server & Viewer

PathXL Components

PathXL Database PathXL Image server

PathXL Image Viewer PathXL Administration Platform PathXL Analysis Framework

PathXL digital slide server farm

Support

Report a Problem

Access the PathXL Support

• Click on ‘report a problem’

• Click on ‘Submit a ticket” OR email [email protected]

• You will be assigned a ticket ID and receive an auto response to acknowledge your ticket has been received

• A support engineer will respond to your query within 4 hours

• All tickets tracked and you are notified automatically of any status change in the ticket

Service Hours

The PathXL (hosted) website at www.pathxl.co.uk will be available 24 hours a day, 365 days a year, with core business hours of Monday – Friday between hours 9.00 am and 5.30 pm (GMT/BST)

Priority CodesPriority Description

1 Service non-functional with high impact on Customer operations

2 Service functional but with impact on Customer operations. System possibly unavailable to large amount of users or is experiencing performance issues.

3 Minor problems with very low impact on Customer operations.

4 Cosmetic and documentation errors

5 Change Request

Maintenance Agreement

Subject to agreement on the Priority Code of the fault, PathXLwill use all reasonable endeavours to respond to and fix (including by means of a workaround, temporary fix or emergency bypass procedures) faults within the target timescales set out below:

Priority Response Times Target Resolution Times

1 Within 1 normal working hour Next working day

2 Within 2 normal working hours 3 working days

3 Within 4 normal working hours Next release

4 Within 5 working day Subsequent Release

5 Within 10 working day Agreed with Client

Quick Start

Logging in

• Go to http://www.pathxl.co.uk

• Enter your account name, username & password.

• Click ‘Login’

http://www.pathxl.co.uk/

Training Area

Access the product videos & PathXL User manuals online at:-• www.pathxl.co.uk

• Account: pathxltraining

• Username:

• Password:

NB your welcome pack will include your login details for the training area

http://www.pathxl.co.uk/

Creating Content

Control Panel

Access the Control Panel• Click on ‘Control Panel’

• You will now see the Dashboard

• Click on “Manage Content” to start adding slides and creating content.

Create your homepage

• Click on ‘Manage Content’ from the Dashboard

• Click HOME from the icons at

• the top

• Click the media icon

• Click Upload to browse your desktop

• and choose your company logo image file

• This will transfer the image from your local machine to the PathXL Server

• Click OK to close the media window

Create your homepage

• Type text directly into the Editor Window

• Use the tools to format the text

• Click the “Insert Image” icon to add your logo image onto the homepage

• The Insert Image window will appear

• Check the logo you wish to upload

• Set the height and the width

• Click insert – your logo will now appear inside the homepage

• Click Apply to save and close

PathXL EQA

Creating a Study

Create a study in PathXL EQA

• Go to Control Panel

• Select the content tab

• Choose your topic

• Create a new module or sub-module

• Click Add Study to create a new EQA study

EQA Settings

• Title• Enter the study name

• Description• Further information about the test

• Maximum Points per Question• (OPTIONAL) Define a max. point per • question

• Test Period• Start Date/Time and End Date/Time for which study is available

• Make all Questions Mandatory• Make all questions in the study mandatory

• Disable Previous Button• You are unable to move back to a previous study question

• Redirect URL• Link to a website/URL when the study is submitted e.g. surveymonkey

EQA Settings

• Open Test• Ability to retake the study again and again

• Authenticate Anonymous ID• At study start-up prompts the user to double

enter an anonymous ID• Results Name Format

• When marking the study how the username is displayed to the scorer - PathXL username or Anonymous ID

• Scoring Name Format• When scoring the study how the username is

displayed to the scorer - PathXL username or Anonymous ID

Adding a Case

• Click Cases from the top menu

• Click “Add Case” to launch the SlideBox

• Select either a single case and click “Add”

• If adding one case at a time you can enter a case name

• Or to add multiple cases Select ALL and “Add Multiple Cases”

Adding Case information

• Your cases will now be displayed in the Cases Page

• To rename your case edit the text in the box at the top of the case

• You can also edit the slide/stain name• You can add Case History• To add additional stains to the case click

“Add Resources” and select your additional stains from the image box.

• NB if adding multiple slides/stains to a case we recommend adding the H&E first and then use the Add Resources to add the additional stains to ensure the H&E is first in the list of images displayed

• Use the arrow keys to move through the additional stains. The number in brackets represents how many slides are in the case

Add an annotation to a slide

• Click Annotations to annotate the slide

• This will launch the PathXL Viewer

• Click the Annotations Icon to open the panel

• The annotations panel allows you to choose and draw a square, circle, freehand or arrow annotation

• The current annotations will be listed down the left hand panel in annotation boxes

• Click anywhere on the annotation box to expand the text and drive to the region of interest and at the drawn magnification

• Click the back button in your browser to return to your study

Add a multiple choice question

• Click Add Question

• Type your Question Text

• Choose your Question Type – multiple choice

• Select if the question is mandatory

• Click Add Answer – Add all possible answers

• Question Assignment

• Choose “Add to all cases (Existing & Future)” to apply this question to all cases in the EQA Study

• Choose “Add to selected Cases” to apply this question either to only this case OR to cases selected using the radio buttons

• Click “Add another question” to continue adding questions to the case

• OR “Return to Cases” if you are finished adding questions

Add a free-text question



• Choose your Question Type – free-text







Add a “Mark an Area” question



• Choose your Question Type – Mark an Area







Add a multi-choice question




• Check the option “Allow multiple answers” to create a multi-choice question



• Question Assignment• Choose “Add to all cases (Existing & Future)” to apply this question to all

cases in the EQA Study




Add an “is other” question

• Click Add Question• Type your Question Text• Choose your Question Type – multiple choice• Check the option “Include “is other” answer” to create a

free-text option as part of this MCQ• Select if the question is mandatory • Click Add Answer – Add all possible answers• Question Assignment





Add a contingent question






• Select the contingent checkbox against a specific answer and apply a sub-question to the question (MCQ, Free text or Mark an Area)

• Each separate MCQ answer may have a contingent question

• NB – contingent questions are available only on MCQ questions

Preview Study

• Click Preview

• Work through your cases

TIP: Please note you will not be able to submit answers to a test when in preview mode

You will not be able to Mark An Area when in preview mode

Score the EQA Study

• Click the OLT tab from the main menu in Control Panel

• Click Score beside your study

• This will allow you to score each case in turn and assign a score for the user for that case

• Click the dropdown or “Next Case” button to move and score the next case

• Click “View Case” to view the original case in the viewer

• Use the scroll bars to navigate up and down through all users or left and right through all questions

• Click Save & Close to save the progress of your scoring

Viewing Results

• Click the OLT tab from the main menu in Control Panel

• Click View Results beside your study

This will allow you to view the final results in the webpage OR download all results (combined) or individuals results to an Excel (CSV) file

Move a Study

• In Control Panel -> Content

• To move a study to a different module choose the folder you wish to move the study to.

• Click the study and drag and drop it into the chosen folder.

Copy a Study

• In Control Panel -> Content

• Click copy and choose the folder you wish to create a copy of the study into

• Click to edit the copied study

TIP: If repeating a study for different circulation we recommend you make a copy of the study for each sitting so you do not lose past results

Navigating the EQA Study

Click the EQA button to hide/show the question panel

View your Case History

Click the i button to hide the case history

Click the + to annotate a “Mark an Area” question then choose your annotation shape square, circle, freehand pen or arrow from the popup

Skip to a specific case from the dropdown menu

Use the previous and next arrows to move to the previous/next case

Click “Close Slide” to exit the study and allow you to return at a later date to your study and continue answering questions.

Click “Submit Study” to submit your final answers. You will not be allowed to return and change your answers once answers are submitted.

Indicates the current case and total number of cases in the study

Use the thumbnail to navigate to a specific region of the slide

The scalebar will update as you zoom shift magnification

The resources panel will show in brackets the total number of stains in the case

Use the arrow buttons to navigate back and forth through the stains. The current stain will be highlighted in red. The stain name will appear under the thumbnail

The name of the stain or slide will appear here (if enabled in permissions)

Indicates the Case Name

PathXL Viewer

Navigating the PathXL Viewer

• The toolbar on the left hand side of the PathXL Viewer allows you to toggle on/off all the key functions inside the PathXL Viewer.

• To pan around an image, hold the left mouse key and drag the mouse in the direction

• You can also pan using the 4 arrow keys on the keyboard up, down, left, right and also by pressing up/right, up/left, down/right, down/left simultaneously

• You may also pan using the thumbnail image in the top right corner either by a single click on a specific region or also by holding the left mouse key and dragging the mouse in the desired direction

• Double click with the mouse to zoom through the default magnification levels

• Use the mouse scroll wheel to zoom incrementally

Viewer Controls

Fullscreen

• Click the fullscreen button to launch the viewer in full screen mode in the browser

• To return to normal mode, click the full screen button again or F11 on your keyboard

Magnification

• Click to open the magnification drawer and select the magnification required

• The maximum magnification (e.g. the mag the slide was scanned at) will automatically be listed in the drawer

Viewer Controls - Annotations

• The annotations icon will show a number icon on the top right corner to indicate the number of annotations on the current slide.

• When the annotation button is clicked, the left hand panel will open the annotations window. When active the button will turn red as shown

• The annotations panel allows you to choose and draw a square, circle, freehand, arrow or curly bracket annotation

• The current annotations will be listed down the left hand panel in annotation boxes

• Click anywhere on the annotation box to expand the text and drive to the region of interest and at the drawn magnification

Viewer Controls - Annotations

Drawing an Annotation

• Navigate to the region of the slide you wish to annotate and at the desired magnification

• Choose your shape – square, circle, freehand pen, arrow or curly bracket

• Click on the region and the annotations window will open to add your name, description, URL hyperlink and change the colour

• Click on the shape to adjust the dimensions or rotate the annotation

• Toggle the sharing button on if you wish to share the annotation with other users.

• Click Edit to adjust the name, description or dimensions

• Click info to see what user created the annotation and when

• Click save to save the changes to your annotation

Viewer Controls - Measurements

• The measure icon will show a number on the top right corner to indicate the number of measurements saved for the current slide.

• When the measure button is clicked, the left hand panel will open the measurements window. When active the button will turn red as shown

• The measurements panel allows you to choose and measure using either a linear (ruler tool) or area measurement

• The current saved measurements will be listed down the left hand panel

• Click anywhere on the measurement box to expand the text and drive to the region of interest and view the saved measurement

Drawing a Measurement

• Navigate to the region of the slide you wish to measure and at the desired magnification

• Choose either the linear or area measurement tool

• Click on the slide and drag the mouse to draw the measurement• The linear measurement will show the length in mm or microns of the

line• The area measurement is a freehand polygon which will show the

area of the region drawn• If you wish to redraw the measurement at any time, release the

mouse and click on a new region to redraw• To save the measurement click the save button otherwise click cancel

to remove the measurement• Click Edit to adjust the name, description or dimensions of the

measurement• Click info to see what user created the measurement and when• Click save to save the changes to your measurement

Viewer Controls

Label• Click the label icon to view the slide label.• The label will show in the right hand side under the thumbnail• Click again to close the label.NB if the slide scanner has not scanned the slide label, this button will not appear in the viewer

Information• Click to open the information panel. • This will show the following information pertaining to the slide:-

• Slide Name• File Type (e.g. SVS, NDPI etc)• Magnification• Z-stacks• MPP• Width• Height

Viewer Controls

Scalebar• The scalebar icon will remain on by default when you open a

slide• Click the scalebar icon to disable the scalebar• The scalebar sits in the bottom right of the viewer and will adjust

in size as you zoom in and out• The scalebar will display sizes greater that or equal to 1mm in

mm and less than 1mm in micronsNB the scalebar will not be displayed for standard JPEG images

Thumbnail• The thumbnail icon will remain on by default when you open a

slide• Pan the slide using the thumbnail image in the top right corner

either by a single click on a specific region or also by holding the left mouse key and dragging the mouse in the desired direction

Adjustments

• Click the Adjustments icon to open the adjustments drawer

• Drag the slider to adjust the gamma

NB Hamamatsu slides will be automatically set with a gamma offset of 1.8

• Drag the slider or type a value directly into the text box to adjust the brightness and contrast

• Single click the colour balance RGB icons to toggle on off the RGB channels on a fluorescent image

• Toggle on/off the sharpen button to sharpen an image

• Click apply to save your changes

• Click reset all to return the slide to the default values

Viewer Controls

Rotate

• Click the rotate icon to launch the rotation wheel

• This will open in the bottom right-hand corner above the scalebar

• Click on the wheel to drag the ball around and adjust the rotation

• The degree of rotation will be displayed in the centre of the wheel

• Click the centre to return the position to 0 degrees

Z-stacks

• If a slide has been scanned with z-stacks (Layers) the z-stack icon will appear and switched on by default

• You will see a slider bar in the top left of the viewer

• Click the arrows to focus up and down through the layers incrementally

• Use the slider to drag through the focus layers

Screenshots

Screenshot

• Click the screenshot icon to open the screenshot drawer

• Choose from either Whole or Draw• Whole – Captures the whole area visible on screen

• Draw – pen tool to draw around the area of interest

• Choose the resolution – Original, Medium or High

• Choose the output type – JPEG or PNG

• Share – copy and paste the link to the screenshot via email/chat

• Print – send directly to printer

• Cancel to close the window

• Save – export the screenshot as a JPEG/PNG to your desktop

Split Screen

Click the Slides Icon to view multiple slides in a case

• This will launch the slides panel

Click the Split Screen icon in the bottom right of the thumbnail to identify which slides you wish to view in Split Screen mode.

• The active window will be outlined in green

Click the Sync Views icon in the viewer to activate the syncing of both magnification and panning of the images in Split Screen mode

Viewer Controls

Close Slide

• Click the close slide button to exit the viewer from the browser tab and return to the main PathXL application

Slide Name

• If enabled in the permissions the slide name will appear above the thumbnail image

Scroll the toolbar

• If working on a laptop or screen with a small resolution not all icons may be visible on screen in the toolbar. Hover over and use your mouse wheel to scroll up and down

Permissions

Create a user

• Navigate from the Control Panel to the Users tab

• Click New to add a new user, the * denotes mandatory fields from the below• User Name* - Unique username

• Password* - Password with strength indicator

• User Type* - Choose from user or manager

• Disable User – To deny access to a particular user in the system without deleting

• Security Question – Prompt if a user forgets their password

• Security Answer – As above

• Email* - users email address

• Password Lock – Deny a user the ability to reset their password

• Starts On – User start date – prevents a user from logging in prior to this date

• Ends On –User end date – prevents a user from logging in following this date

• First Name – Users first name

• Last Name – Users last name

• Click apply to save

Create a Group

• Go to Control Panel -> Groups -> New• Name – name of the group

• Starts on – date/time from when content in the group is visible

• Expires – date/time when content allocated to the group expires

• Add Images – For instructors - access to control panel -> content to add images to a module/case

• Edit All content – For instructors –ability to EDIT ALL all content in PathXL

• View All content – Ability to view ALL content in PathXL Tutor

• IP Restriction – Ability to limit viewing for content for the group by an IP range

Group Permissions - Instructors

The access permissions section is applicable only to users (instructors) who will be responsible for editing and creating content. This section should NOT be completed for a standard student group.

NB by default the manager will automatically have all permissions available in the system.

• Servers – Ability to configure/edit Image Servers

• Content – Ability to create content from the control panel

• OLT – Ability to create tests and download results in PathXL OLT

• Allow users to add new groups – Ability for the instructor to create groups

Groups – Viewer Settings

• Measurements – Ability to enable/disable the drawing of measurements in the viewer

• View Shared Annotations – gives the user the opportunity to view annotations shared with them

• Save annotations/measurements – Ability to save annotations and measurements

• Share annotations – Ability to share saved annotations or measurements

• Enable Split Screen – Ability to view up to 4 slides side by side

• The Viewer Settings determines what functions the group can use/see in the PathXL Viewer.• Take Screenshot – Whether a user has oermission in

the viewer to draw or capture a screenshot• View Slide Name – Whether the user sees the slide

name in the viewer e.g. may want to keep the name anonymous

• View Slide Attributes – Disables the information panel which displays the name, file type etc.

• View Slide label – Ability to disable the label button

Add users to a group

• Go to Control Panel -> Groups

• Beside the group choose the “Users” ICON

• Select the user (s) from Available users

• Click Add to Group

• They will now appear in “Users in Group”

• Click Apply to Save

Assign content to a group

• Choose the module(s) or case(s) you wish to give read/no read/write access to for the group by toggling the icon under “permissions”

• NB when you permission a parent/root folder all sub-folders within the module will automatically inherit the permissions from the parent therefore you must set each sub-folder with individual permissions if required

• Click on the content icon to the right of the group

Manager Access

• A manager has full access for the entire account and will have read/write access for all topics.

• The manager will have all viewer settings enabled

• The manager can see all tests and final results

PathXL Training EQA/Whole Slide Scoring · 2 days ago · Service Hours The PathXL (hosted) website...

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Transcript of PathXL Training EQA/Whole Slide Scoring · 2 days ago · Service Hours The PathXL (hosted) website...