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. |