Please refer to our FAQ and look at our known issues before opening a bug report.
Describe the bug
In the Pixie notebooks, img_sub_folder is not in the function call for create_mantis_dir, so the single-channel TIFs are not copied over into the mantis directory (when there is an image subfolder).
Expected behavior
In both the pixel and cell clustering notebooks, add img_sub_folder to the function call for create_mantis_dir (it's already an input parameter so no need to change the function code).
The cell clustering notebook currently doesn't have the img_sub_folder variable - easiest solution is probably to save img_sub_folder to the json at the end of the pixel clustering notebook. Related to this, it looks like the user specifies tiff_dir again at the beginning of the cell clustering notebook although they already do so in the pixel clustering notebook - we can probably save tiff_dir to the json as well so users don't have to specify it twice.
Please refer to our FAQ and look at our known issues before opening a bug report.
Describe the bug In the Pixie notebooks,
img_sub_folderis not in the function call forcreate_mantis_dir, so the single-channel TIFs are not copied over into the mantis directory (when there is an image subfolder).Expected behavior In both the pixel and cell clustering notebooks, add
img_sub_folderto the function call forcreate_mantis_dir(it's already an input parameter so no need to change the function code).The cell clustering notebook currently doesn't have the
img_sub_foldervariable - easiest solution is probably to saveimg_sub_folderto the json at the end of the pixel clustering notebook. Related to this, it looks like the user specifiestiff_diragain at the beginning of the cell clustering notebook although they already do so in the pixel clustering notebook - we can probably savetiff_dirto the json as well so users don't have to specify it twice.