Unique cell_ID issue with cosmx reader

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
25/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
python
Domain
data

Research direction

Start with the CosMx reader and reproduce the cell_ID uniqueness error using the same data under spatialdata-io 0.1.7, comparing it with 0.1.4. Determine whether per-FOV identifiers are expected to load, and document or verify the required handling for data whose cell_ID values repeat across FOVs.

Written by the indexing model from the issue text.

Description

Hi, after having updated my spatialdata-io from version 0.1.4 to 0.1.7, I am having an issue with the cosmx reader to create a spatialdata object. Using the same data that I did not have an issue with using the older version, I am now getting an error that the cell_IDs are not unique.

This column does seem to only uniquely label cells per field of view (FOV), so indeed that column does not uniquely label each cell in the whole dataset.

Could I please get some help on using this latest version with this data, would you recommend I change these IDs to be unique across the whole dataset in each input file to satisfy this? Is this compatible with newer versions of CosMx output?

Thank you!

Dominant language
Python
Stars
103
Forks
65
Avg merge
1h 8m
Merged PRs (30d)
3

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