mask_cellpose

This script is provided for the user to be able to segment nuclei or other objects (e.g. mask images) using cellpose.

For more information, follow this tutorial: Running cellpose to create 3D masks for pyHiM

Invoke

To process

$ mask_cellpose.py --input my_image.tif

Inputs

Name shape	Quantity	Mandatory	Description
<image_name>.tif	1	Yes	3D image in tif format.
parameters.json	1	Yes	Parameter file.
register_global/data/shifts.json	1	Yes	Output JSON file of register_global with the shift values.

Outputs

Name shape	Quantity	Description
mask_3d/data/*_3Dmasks.npy	1	NUMPY 3D array. The output labeled image.
mask_2d/data/*_Masks.npy	1	NUMPY 2D array. The output labeled image, projected by maximum.