search

angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
70 stars 25 forks source link

Incorrect cell cluster mapping in mantis #1082

Closed camisowers closed 8 months ago

camisowers commented 9 months ago

Please refer to our FAQ and look at our known issues before opening a bug report.

Describe the bug Currently, the cell_cluster_mask.csv that is generated and loaded into mantis does not contain the correct integer IDs for each cell cluster.

Expected behavior When we updated the way we generate cell_masks to allow for colored masks, the integer IDs for the clusters changed. If before they were [1,4,10] they are now [1,2,3]. The currently saved cell_meta_cluster_mapping.csv does not reflect this change.

To Reproduce Run cell clustering and create new metaclusters.

janinemelsen commented 8 months ago

I was wondering whether this is now fixed in the newest release? I downloaded the latest version but am still experiencing the issue of incorrect cluster mapping in Mantis.

camisowers commented 8 months ago

Hi @janinemelsen, the fix has just been merged into main! I was not included in the latest release, but if you're running ark from a local environment you can just pull the repository and update ark_env.