angelolab/ark-analysis

Duplicate FOV name issues with cell table generation

camisowers opened this issue · 0 comments

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Describe the bug
If the user has a naming convention of fov1 and fov1_duplicate, this causes an issue in generate_cell_table() due to some ezseg updates. Specifically, the function get_existing_mask_types() is run per FOV to detect any masks that may exist for that image, so when processing fov1 it returns the "mask types": ['whole_cell', 'nuclear', 'duplicate_whole_cell', 'duplicate_nuclear'].

After chatting with @bryjcannon, we think it would be best for the user to just specify which mask names to look for (defaulted to ['whole_cell'] for the cell segmentation notebook and an argument in the ezseg notebook) rather than automating something so simple.

Expected behavior
Be able to generate a cell table no matter any odd FOV naming conventions.

To Reproduce
Try to run the segmentation notebook with the specified FOV names.