ome / ome/ngff

Metadata: User stories for named channels

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#173 13 comments 6 reactions 0 assignees View on GitHub

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enhancement
Dominant language
Python
Stars
171
Forks
75
Avg merge
2d 3h
Merged PRs (30d)
20

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

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