Summary

Triggering Analysis with Newer Protocols

To streamline the workflow for ML engineers and other stakeholders, Gaia provides an intuitive mechanism to trigger analysis with the latest protocols.

Navigate to the Trigger Analysis option

• Navigate to the left pane
• Click on 'Phases' menu item

• Click on the Kanban card under Phases to navigate to the "Well Heatmap View" page.

• On the "Well Heatmap View" page, click on a well position to navigate to the Image Viewer page.

Image Viewer page top bar

The Image Viewer page consists of:

• Top Bar Options:
  • On the top left back button to go to the Well heatmap view page
  • Besides that, there is an option to change the well position by selecting it
  • Besides that, there is an option to adjust the Z-axis zoom level using the indicators
  • Besides that, there are a bunch of options that help in creating:
    • Polygon
    • Findings
    • Patch objects
    • Measurement
    • Trigger Analysis
    • Complete

How to trigger any analysis using the Trigger Analysis option

User Flow for Trigger Analysis in the Image Viewer

1. Trigger Analysis Button

• The Trigger Analysis button is located on the top-right corner of the image viewer' stop bar.
• Click the Trigger Analysis button.

2. Trigger Analysis Dialog Box

Upon clicking the button, a dialog box opens with the following options:

• Analysis Type: Dropdown with:

  • Cluster Detection
  • Cluster Tracking
  • Confluence
  • Density
  • Energy Map
  • Feature Generator
  • Pluripotency
  • Scan Assessment
  • Scan Object
  • Developer Mode: Toggle button (True/False)

• Preconditions Before Selecting Analysis -#### Cluster Detection - Before triggering cluster detection analysis, confluence analysis must be available. - If confluence analysis is not already completed, run it first and then proceed to cluster detection.

  -#### Cluster Tracking - It cannot be run directly on the last time point; it requires prior analysis of previous time points before reaching the last. - Cluster Detection must be completed at the desired time point before running cluster tracking..

  -#### Scan Object - Scan Object analysis requires a Reference Analysis Request to be present. - If no Reference Analysis Request exists, it must be created before triggering Scan Object analysis.

Triggering Analysis

• Confluence

  • Select Confluence from the Analysis Type dropdown.
  • Once Confluence is selected, a Protocol dropdown will appear.
  • Choose a protocol from the dropdown to perform the analysis.
  • Use the Developer Mode toggle to set it to either true or false, as needed. Click Trigger.
  • Click on the Trigger button to complete the operation

• Clicking the trigger will display a brief, non-intrusive message (toast) at the bottom of the screen to confirm the action.

• Once the analysis is complete, a notification message will be posted to the #gaia-notifications Slack channel

• The slack notification will include a link to view the analysis in the gaia image viewer.

• Cluster Detection

  • Start the Analysis: To begin cluster detection analysis, click the "Trigger Analysis"button.
  • Choose Analysis Type: Select "Cluster Detection" from the dropdown list.
  • Configure Parameters: A dialog box will open, prompting you to configure the analysis.
  • Specify Protocol: In the "Protocol" field, enter the protocol you wish to use for the cluster detection analysis.
  • Select Reference Analysis: Choose "Confluence" as the "Reference Analysis Request." This is a required step for cluster detection.
  • Run Analysis: Click on the trigger button to complete the operation

• Clicking the trigger will display a brief, non-intrusive message (toast) at the bottom of the screen to confirm the action.

• Once the analysis is complete, a notification message will be posted to the #gaia-notifications Slack channel

• The slack notification will include a link to view the analysis in the gaia image viewer.

• Cluster Tracker

  • Initiate Analysis: Click the "Trigger Analysis" button to begin the cluster tracker analysis.
  • Choose Analysis Type: Select "Cluster Tracker" from the dropdown list.
  • Configure Parameters: A dialog box will open, prompting you to configure the analysis.
  • Specify Protocol: In the "Protocol" field, enter the protocol you want to use for the cluster tracker analysis.
  • Select Reference Analysis: Choose "Cluster Detection" as the "Reference Analysis Request." This is required for cluster tracker analysis.
  • Finalize: Click the "Trigger" button to complete the operation.

• Clicking the trigger will display a brief, non-intrusive message (toast) at the bottom of the screen to confirm the action.

• Once the analysis is complete, a notification message will be posted to the #gaia-notifications Slack channel
• The slack notification will include a link to view the analysis in the gaia image viewer.

• Energy Map

  • Initiate Analysis: Click the "Trigger" button to begin the energy map analysis.
  • Choose Analysis Type: Select "Energy Map" from the dropdown list.
  • Configure Parameters: A dialog box will open, prompting you to configure the analysis.
  • Specify Protocol: In the "Protocol" field, enter the protocol you want to use for the energy map analysis.
  • Select Reference Analysis: Choose "Energy Map" as the "Reference Analysis Request." This is required for energy map analysis.
  • Finalize: Click the "Trigger" button to complete the operation.

• Clicking the trigger will display a brief, non-intrusive message (toast) at the bottom of the screen to confirm the action.

• Once the analysis is complete, a notification message will be posted to the #gaia-notifications Slack channel
• The slack notification will include a link to view the analysis in the gaia image viewer.

• Density

  • Initiate Analysis: Click the "Trigger" button to begin the density analysis.
  • Choose Analysis Type: Select "Density" from the dropdown list.
  • Configure Parameters: A dialog box will open, prompting you to configure the analysis.
  • Specify Protocol: In the "Protocol" field, enter the protocol you want to use for the density analysis.
  • Finalize: Click the "Trigger" button to complete the operation.

• Clicking the trigger will display a brief, non-intrusive message (toast) at the bottom of the screen to confirm the action.

• Once the analysis is complete, a notification message will be posted to the #gaia-notifications Slack channel
• The slack notification will include a link to view the analysis in the gaia image viewer.

• Pluripotency

  • Initiate Analysis: Click the "Trigger" button to begin the pluripotency analysis.
  • Choose Analysis Type: Select "Pluripotency" from the dropdown list.
  • Configure Parameters: A dialog box will open, prompting you to configure the analysis.
  • Specify Protocol: In the "Protocol" field, enter the protocol you want to use for the pluripotency analysis.
  • Select Reference Analysis: Choose "confluence" as the "Reference Analysis Request." This is required for pluripotency analysis.
  • Finalize: Click the "Trigger" button to complete the operation.

• Clicking the trigger will display a brief, non-intrusive message (toast) at the bottom of the screen to confirm the action.

• Once the analysis is complete, a notification message will be posted to the #gaia-notifications Slack channel
• The slack notification will include a link to view the analysis in the gaia image viewer.

• Scan Object

  • Initiate Analysis: Click the "Trigger" button to begin the Scan Object analysis.
  • Choose Analysis Type: Select "Scan Object" from the dropdown list.
  • Configure Parameters: A dialog box will open, prompting you to configure the analysis.
  • Specify Protocol: In the "Protocol" field, enter the protocol you want to use for the scan object analysis.
  • Select Reference Analysis: Choose "Cluster Detection" as the "Reference Analysis Request." This is required for Scan Object analysis.
  • Finalize: Click the "Trigger" button to complete the operation.

• Clicking the trigger will display a brief, non-intrusive message (toast) at the bottom of the screen to confirm the action.

• Once the analysis is complete, a notification message will be posted to the #gaia-notifications Slack channel
• The slack notification will include a link to view the analysis in the gaia image viewer.

• Scan Assessment

  • Initiate Analysis: Click the "Trigger" button to begin the Scan assessment analysis.
  • Choose Analysis Type: Select "Scan assessment" from the dropdown list.
  • Configure Parameters: A dialog box will open, prompting you to configure the analysis.
  • Specify Protocol: In the "Protocol" field, enter the protocol you want to use for the Scan assessment analysis.
  • Finalize: Click the "Trigger" button to complete the operation.

• Clicking the trigger will display a brief, non-intrusive message (toast) at the bottom of the screen to confirm the action.

• Once the analysis is complete, a notification message will be posted to the #gaia-notifications Slack channel
• The slack notification will include a link to view the analysis in the gaia image viewer.

• Feature Generator

  • Initiate Analysis: Click the "Trigger" button to begin the Feature Generator analysis.
  • Choose Analysis Type: Select "Feature Generator" from the dropdown list.
  • Configure Parameters: A dialog box will open, prompting you to configure the analysis.
  • Specify Protocol: In the "Protocol" field, enter the protocol you want to use for the Feature Generator analysis.
  • Select Reference Analysis: Choose "Cluster Detection" as the "Reference Analysis Request." This is required for Feature Generator analysis.
  • Finalize: Click the "Trigger" button to complete the operation.

• Clicking the trigger will display a brief, non-intrusive message (toast) at the bottom of the screen to confirm the action.

• Once the analysis is complete, a notification message will be posted to the #gaia-notifications Slack channel
• The slack notification will include a link to view the analysis in the gaia image viewer.

Link to the Video

For detailed video instructions, refer to the following link: User Guide Video