Adjust mask suffix input to generate_cell_table #1164
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@camisowers the example dataset is fixed up. |
alex-l-kong
approved these changes
Oct 8, 2024
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What is the purpose of this PR?
Allow for users to generate a cell table for segmentation masks that have slightly different formatting for file names. For example, simply 'fov1.tiff' or 'fov1-cell_mask.tiff' instead of always requiring _suffix (i.e. 'fov1_whole_cell.tiff').
How did you implement your changes
Add in an extra argument
add_underscorewhich is defaulted to True. Also allow None as a mask_type input. These adjustments will not be used internally in ark-analysis, but are intended to allow for more flexibility of segmentation masks generated with methods other than Mesmer and fed into SpaceCat.Remaining issues
Need to make a new release so the changes can be used in SpaceCat.