relax omero metadata
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Description
Motivation
With this issue, I would like to discuss whether ngff could relax the omero metadata requirements by making "visualization specific" parameters ("window" and "color" ) optional.
As discussed in https://github.com/ome/ngff/issues/155 , there seems to be agreement that the channel name information (e.g. in a microscopy image, the name of the fluorescent markers/antibodies such as "DAPI", "Actin" etc.) should be saved in omero metadata. This information would be stored under "label" according to current spec. This type of information is critical to be stored especially in highly-multiplexed imaging techniques such as CyCIF, Codex, Imaging Mass Cytometry etc.
Users might want to save the channel name information without specifying "color" or "window" information. Currently, it is not possible, as there are two required arguments by the omero specs which are, imho, purely for "visualization" purposes. Users would therefore have to specify "arbitrary" information on aesthetics that is not necessarily useful/actionable.
Potential solution
Make the current required parameters ("color" and "window") as optional. This would enable the use case of only saving channel name information without having to specify the remaining visualization parameters.
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with 0.4/schemas/image.schema at the linked color and window definitions, then read the latest omero metadata section and the discussion in issue 155. Determine whether label-only channel metadata is supported when color and window are absent. Done means the specification clearly permits that use case without requiring visualization values.
Written by the indexing model from the issue text.
Assessment
- Domain
- documentation
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 30/100