starting a CLI to QC FOVs#175
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mattersoflight wants to merge 1 commit intoreadme-claude-configfrom
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Thanks @mattersoflight! I'll turn this into a draft PR while we're working on it |
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We realized that the data at
/hpc/projects/virtual_staining/training/ipsc/4_1_fluor.zarrmay have been corrupted by a collaborator. This prompted me to write a pedestrian parallelized CLI to read min, max, median of each channel and QC if they are empty.The qc table is written at
qc_fovs.csvin the zarr store. I tested local sequential execution and slurm parallelization. SLURM parallelization needs some more testing - it looks like some jobs were failing.