scverse / scverse/spatialdata-io
Selecting specific stains when reading merscope files into a sdata object.
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 103
- Forks
- 65
- Avg merge
- 1h 8m
- Merged PRs (30d)
- 3
Description
The merscope image files that I use are currently quite big, and it is often useful for me to only select specific stains. Currently it is hard coded in the merscope function to read in all stains. However, it is an option in the _rioxarray_load_merscope function. It would be nice to set this ourselves as one of the kwargs or as a keyword argument in the merscope function itself.
Contributor guide
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 the merscope function and follow how it calls _rioxarray_load_merscope, which already accepts stain selection. Check the reader's existing tests or usage paths before choosing the argument form. Done means callers can select specific stains instead of always loading all stains.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100