AllenInstitute / AllenInstitute/vis

Respect the omero channels `active` flag and don't render it when false

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#137 0 comments 0 reactions 0 assignees View on GitHub

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bug
Dominant language
TypeScript
Stars
10
Forks
1
Avg merge
10h 24m
Merged PRs (30d)
7

Description

Describe the bug
There is an active flag in the omero channels metadata that indicates whether it should be shown by default. We currently assume all channels will be shown, and that assumption no longer holds true for all datasets that we are interested in showing.

To Reproduce
Steps to reproduce the behavior:

  1. Render https://d3hik2dwvr9wk1.cloudfront.net/A549/organelle_box_crop_v1.zarr/ACTB/MeOH/003002 (depends on bugs #134 and #135 being fixed to see)
  2. See that it doesn't match the rendering of the OME-Zarr viewer found here: https://organelle-box-portal-git-main-czbiohub.vercel.app/gene/2025_03_31_A549_ACTB?condition=MeOH
  3. Turn on the Phase3D channel in the app linked above
  4. See that it now looks like our Example app's default display

Expected behavior
Expected to not render channels that the metadata disables by default

Screenshots
Looks like this:
Image

Should look like this:
Image

Additional context
We'll want to add ways to toggle those channels on and off in a future update as well, but we should at least start with respecting the defaults

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the rendering URL in the issue and compare it with the linked OME-Zarr viewer and Example app, focusing on how OMERO channel metadata reaches the display. Done means channels marked inactive by the metadata are omitted from the default rendering, while the current behavior remains otherwise unchanged.

Written by the indexing model from the issue text.

Assessment

Tech stack
typescript
Domain
data-visualization, frontend
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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