neuralib.segmentation.cellpose

Cellpose

API Mode

Example of run an image segmentation in 2D mode and visualize using napari

python -m neuralib.segmentation.cellpose.run_api -F <IMAGE_FILE> --napari

  • It produces an output <IMAGE_FILE>_seg.npy in the same directory, If the output exists, the napari will directly use the output. If need run again and rewrite the output, use --force-eval option

Example of run an image segmentation in 2D mode and visualize using Cellpose GUI

python -m neuralib.segmentation.cellpose.run_api -F <IMAGE_FILE> --cpose

Example of run batch image segmentation in 2D mode from a directory (.tif files)

python -m neuralib.segmentation.cellpose.run_2d -D <DIRECTORY> --suffix .tif

  • It produces multiple *_seg.npy in the same directory.

See help using -h option

python -m neuralib.segmentation.cellpose.run_api -h

Subprocess Mode

Example of run an image segmentation in subprocess call

python -m neuralib.segmentation.cellpose.run_subproc -F <IMAGE_FILE>

  • It produces an output <IMAGE_FILE>_seg.npy in the same directory, If the output exists, the napari will directly use the output. If need run again and rewrite the output, use --force-eval option

Example of run batch image segmentation in subprocess call

python -m neuralib.segmentation.cellpose.run_subproc -D <DIRECTORY>

  • It produces multiple *.npy in the same directory.

See help using -h option

python -m neuralib.segmentation.cellpose.run_subproc -h

Modules: