Single mantis directory

angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis

https://ark-analysis.readthedocs.io/en/latest/

MIT License

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Single mantis directory #1061

Closed camisowers closed 11 months ago

camisowers commented 11 months ago

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What is the purpose of this PR?

Closes #669 and closes #1059. Creates a single top level mantis directory for notebooks 2, 3, and 4, to avoid duplicate files.

How did you implement your changes

Set the mantis folder to be created as one subdirectory within the base_dir, rather than within each specific notebook folder.
Change the output masks from notebook 4 to be named with _post_clustering_cell_mask instead of just _cell_mask to avoid overwriting notebook 3 cell cluster output files.
Change the output masks from the generic_cell_clustering notebook to be named _generic_cell_mask.

Remaining issues

[x] Run mantis generation in all clustering notebooks

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ngreenwald commented 11 months ago

I think we should have a prefix so that all the masks are next to one another in alphabetical order when opening files in Mantis. Makes it easier to find the one you're looking for

cliu72 commented 11 months ago

I think we should have a prefix so that all the masks are next to one another in alphabetical order when opening files in Mantis. Makes it easier to find the one you're looking for

They all start with "population_" then with the suffix after - which will make them all easy to find I think? Since you're opening one FOV in mantis at a time anyways, you can just look for all the files that start with "population"

camisowers commented 11 months ago

I think we should have a prefix so that all the masks are next to one another in alphabetical order when opening files in Mantis. Makes it easier to find the one you're looking for

Currently they all have a built in prefix of "population". So masks by default are population_pixel_mask.tiff, population_cell_mask.tiff, etc. We can change that to be something higher alphabetically if that would be more convenient.

ngreenwald commented 11 months ago

Okay perfect