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 #647
2. New module: Violin Plot #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. #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. #640
6. Visualization module: Inspect nodes functionality. Click a node to open modal of information about the specific node/cell. #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

• 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 https://github.com/hubmapconsortium/hra-ui/issues/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. https://github.com/hubmapconsortium/hra-ui/issues/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. https://github.com/hubmapconsortium/hra-ui/issues/640
• Visualization module: Inspect nodes functionality. Click a node to open modal of information about the specific node/cell. https://github.com/hubmapconsortium/hra-ui/issues/643

Ready for dev

Vis app

• Downloads: Headers on edge download https://github.com/hubmapconsortium/hra-ui/issues/647

• 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 #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:

[LibbyUX]

@andreasbueckle forwards:

Yang Miao:

I have discussed with Dr. Hickey today and shared my results from the workshop with him. We got really excited about the overlay of multi levels of tissues. This is very helpful for our spatial analysis and biological discovery. Thanks for sharing your code with us!

We also came up with some ideas for potentially improving the interpretability of visualization, and it would be great if you could provide some insights or suggestions:

1. Customize the widgets to include checkboxes of layers, so that we can select the layers flexibly.
2. Enable flexible selection of the edges that we want to show. My current idea is that maybe we could provide a complete list of all the edges that we need and use checkboxes to select.
3. (Minor) It would be clearer if we could change the size of nodes. We noticed that in some dense areas, the cells can be overlapped, which makes them hard to see.