Metadata: User stories for named channels
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Description
I have the following user story:
Batch analysis of many multi-channel images, where the channel that contains the nuclei should be segmented.
The data is messy in a sense that the nucleus channel sometimes is the first one, and sometimes the second one.
To deal with this it seems useful to me to have something like int channelIndex = omeZarrDataset.getChannelIndex( String channelID ), where channelID in my case would be "nuclei". To be able to do this, I think some optional metadata inside the OME-Zarr that would allow one to store and retrieve a mapping from a channel name to its index along the channel axis could be useful.
What do people think?
Does anyone else have a need for named channels?
ping @bogovicj @joshmoore
EDIT by @lubianat in 2026:
Please share your user stories for named channels here!
If comments re more general design/scope for channel metadata, #580 is preferred
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Research direction
Start with the user stories and the 13-comment discussion, then compare the general channel-metadata design discussion in #580. Done is not defined in this issue; it would require an agreed scope and a documented specification for storing and retrieving channel names and indices.
Written by the indexing model from the issue text.
Assessment
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Active
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100