neuralib.segmentation

Provide CLI for cellular segmentation and visualization

Design mainly for quick visualization of results and batch processing (i.e., whole-brain image), and save as imageJ/Fiji .roi.

Supported packages

1. Cellpose

• See usage neuralib.segmentation.cellpose

2. Stardist

• See usage in neuralib.segmentation.stardist

If only small amount of images, the native GUI are recommended.

Modules:

• neuralib.segmentation.base
• neuralib.segmentation.cellpose
• neuralib.segmentation.stardist

Notebook Demo

• Example usage of neuralib.segmentation