CDE Y3 feature requests

[LibbyUX]

Future versions of the CDE from the VCCF meeting 6.24.2024

• Meeting: Vasculature Common Coordinate Framework Visualizations Across Organs and Imaging Technologies
• Slide Deck

Clarence Yapp

Archie E

Gloria Pryhuber

• It would be helpful to select areas to include/exclude.
  

Is 1000 microns (1mm) too much?

1000 microns (1mm) currently being used for these visualizations

• Perhaps a feature is needed to adjust the distance: We are currently using the top of the reference.
• Gloria: 100 microns generally used, but 1000 microns may be reasonable for 2D visualizations
• Ellen shares: Molecular Biology of the Cell. 4th edition

Almost every cell, in almost every tissue of a vertebrate, is located within 50–100 μm of a capillary. What mechanism ensures that the system of blood vessels ramifies into every nook and cranny?

[LibbyUX]

@katyb adds additional feature requests today.

[LibbyUX]

Hey @bherr2, I asked @J-Yash to prioritize features. We ideated together this afternoon on a priority list for the product team.

Visualization app page features:

1. Downloads: Headers on edge download Updates for CSV downloads: Header letter casing unification & add column headers for edge downloads #647
2. New module: Violin Plot Add violin plot module to visualization application #627
3. Visualization module: Select mode with delete for minimum functionality. Deleting nodes from the visualization module = deleted from the rest of the plots, cell types list, downloads. Nice to have: Add show/hide select functionality if possible. Hidden = No longer visible in the visualization module, but still included in the plots, cell lists, and downloads. Add new functionality to vis app's visualization module #643
4. Visualization module/cell types module menu: Show/hide all edges in visualization module. This does not impact CSV table downloads. This does alter the png/svg images of the visualization.
5. New feature: Full screen modal for visualizations. Add full screen mode to vis app #640
6. Visualization module: Inspect nodes functionality. Click a node to open modal of information about the specific node/cell. Add new functionality to vis app's visualization module #643

[LibbyUX]

CDE MVP2 design/approval/handoff progress update

@axdanbol, @bherr2 - Status update on my CDE MVP2 design/approval/handoff progress. If I can borrow some of Katy's time for approvals, I am hoping to handoff several of these features by the end of this week. I will submit relevant components during handoff for the design system as well. Please ping me if you need anything!

Design iterations in progress

Create vis

• Create Vis App MVP2 #579
• Add functionality for anchor cell step:
  • Rename from Select an Anchor to Configure Parameters
  • Add configurable Distance Threshold mat-input: By default at 1000
  • Add configurable Pixel Size mat-input (move up from metadata area and make it computational): By default at 1
• Potential checkbox/radio switch/toggle switch for consolidating similar cells by CL ID.

Vis app

• New module: Violin Plot Add violin plot module to visualization application #627
• Visualization module: Select mode with delete for minimum functionality. Deleting nodes from the visualization module = deleted from the rest of the plots, cell types list, downloads.
  • Nice to have: Add show/hide select functionality if possible. Hidden = No longer visible in the visualization module, but still included in the plots, cell lists, and downloads. Add new functionality to vis app's visualization module #643
• Visualization module/cell types module menu: Show/hide all edges in visualization module. This does not impact CSV table downloads. This does alter the png/svg images of the visualization exclusive to the visualization module.
• New feature: Full screen modal for visualizations. Add full screen mode to vis app #640
• Visualization module: Inspect nodes functionality. Click a node to open modal of information about the specific node/cell. Add new functionality to vis app's visualization module #643

Ready for dev

Vis app

• Downloads: Headers on edge download Updates for CSV downloads: Header letter casing unification & add column headers for edge downloads #647
• Scale bar with fixed position in CDE visualization module #424

[LibbyUX]

Violin plot feature request for future versions

• @J-Yash provides a link to Yingnan's interactive viz: https://hubmapconsortium.github.io/vccf-visualization-release/html/violin_cell_all_region.html

Slack conversation from 9.5.2024

[LibbyUX]

[LibbyUX]

[LibbyUX]

@J-Yash links: https://app.enablemedicine.com/portal/atlas-library

[LibbyUX]

@katyb sends https://cellhub.nygen.io/?_gl=1*nylkex*_gcl_au*MTYzNDAzOTI2LjE3MjcyMDUzNzg with feature requests:

• EUI EUI Y3 feature requests #379
• CDE Catalog

[LibbyUX]

Meeting notes from Tarek & Andrea's visit

@J-Yash & I debrief after our meeting/CDE demo with Andrea and Tarek.

• Google Doc: Visit Agenda

Visitor feature requests

Tarek

Define/customize distance visualization options:

• by neighborhood
• by radius

Andrea

Perhaps collaborate with these groups, and/or market the CDE app on:

• https://forum.image.sc/
• https://qupath.github.io/

Features being tracked for future versions

@J-Yash + I create lists:

General features:

• ability to add marker expressions
• ability to add underlying imaging
  • histology
  • imaging data
• extending the analysis: regions of interest
  • multiple regions of interest to compare
• ability to upload multiple datasets for comparisons
• ability to see cell abundance analysis
  • note: this could change the UI substantially
  • note: see Tarek's suggestion for more information
  • maybe silo the workflow, maybe automate it based on the dataset
• CDE catalog on landing
  • add specific datasets to catalog
• add link to Nov preprint on landing page?
  • this may need to happen for 8th release

Analysis vs Embed Downloads

Two use cases are emerging from table downloads: Embedding and analyzing. The uploads need to be different to best serve each use case.

Perhaps analysis downloads could look like:

• add distance column to cell links
  • export edge distances via edge/cell links file
  • pull edges file for further analysis
    • power user feature
• consolidated files/merged downloads
  • one analysis table file for:
    • nodes/cells
    • connections/cell links
    • cell types
    • distance
  • note: people are already doing this manually for analysis

Violin Plots normalization feature

• By:
  • area
  • count
• Note: This could easily be a "More" menu option, see: