2024-03-25: Status check-in: Mouse-QC 24Q1 priorities

[macarenasa]

Agenda:
-Review milestone and progress towards completing the open issues.

[macarenasa]

Summary of issues and current status:

• Issue Wheel Encoder Plot: Excluding Wheel Artifacts #287 - Clark working on generating a report of how the wheel encoder measurements has changed over time to visualize changes.
• BUGS: Issues Report Status not updating correctly when status changes via manual override #387 Regenerating QC with reload=True adds new thresholds that have previously been overridden #388 and qc module status change if metrics and/or plots missing #369 will be addressed this week - 3/25 by @seanmcculloch
• Controlled language tags: omFISHRbp4Meso Crosstalk Tag #365 and Field of View Matching: New Controlled Language Tag #312 - will merge with wheel encoder
  • omFISH crosstalk tag - introduce new tag to account for configurations with "extreme cross talk"
  • FOV matching - "surface does not match in Z"
• Issue Dev-QC: Move controlled language tag from FOV Integrity to Full Field Module #327 - controlled language tag into a full field module - no full field image QC. Need to wait until this can be addressed.
  - Hand off to the mFISH team - helps guide them to the sectioning.
  - Change this issue to be "add a full field of view" ---- existing issue already requesting this Full FOV two-photon image QC #154 -- QC process of LIMS file generation.
  - Additional description to this issue: Include in ROI validation step of experiment report.
  - Difficult to see the overlay - might be helpful to see a red box around the ROI in stitching. The overlay is difficult to see.
  - Feasible only if the coordinates are available.
  - Sam shared an example image in our Mouse-QC Q1 priorities - status check in meeting chat.
  - Manual labeling of higher order visual areas based on overlayed ISI map.
  - Experimental Module: Rotate stitched image containing ROI imaging area with rotated ISI map overlayed.
  - Old analysis server is still running on old Mouse-seeks computer - @seanmcculloch migrating the Jupyter notebook server.
  - @seanmcculloch set up environment to run minscope-qc-metrics and brain-observatory-qc
• Issue Pull valid QC logs from Dev DB #389 - @seanmcculloch will being process of pulling Valid QC logs asap with Sam and Shiella this week.
• Issue Module Deployment Inconsistent Between Projects #399 - different projects are running different modules (some modules do not exist, schemas are not matched up). Fixed in Dev instance but need to update in the Production space.
  - @samiamseid look at the updates in the Dev instance.
• Issue Brain Health and Window Clarity: Duplicated Images #394 - also updated by Clark - @samiamseid please provide feedback on updates. Rotating images happens in LIMS (keep in mind for when moving pipelines to code ocean).

Action items:

• @seanmcculloch this week (3/25 - 3/29) Work on issues qc module status change if metrics and/or plots missing #369 Report Status not updating correctly when status changes via manual override #387 Regenerating QC with reload=True adds new thresholds that have previously been overridden #388
• @DowntonCrabby @seanmcculloch: Create a new experimental module to QC ROI to ISI map overlay (issue Full FOV two-photon image QC #154)
• @samiamseid provide feedback on updates from Module Deployment Inconsistent Between Projects #399 and Brain Health and Window Clarity: Duplicated Images #394 - currently in Dev Space, when will this be ready to move into production?