Please refer to our FAQ and look at our known issues before opening a bug report.
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.
Please refer to our FAQ and look at our known issues before opening a bug report.
Describe the bug If the user has a naming convention of
fov1andfov1_duplicate, this causes an issue ingenerate_cell_table()due to some ezseg updates. Specifically, the functionget_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.