Medical Imaging Toolbox Interface for Cellpose Library

Use Cellpose library in MATLAB

Segment cells from microscopy images using the Medical Imaging Toolbox™ Interface for Cellpose Library. The support package provides functionality for downloading pretrained models from the Cellpose Library [1,2], segmenting 2D and 3D images using Cellpose models, and training new models using your own image data. To learn more, see the Getting Started with Cellpose documentation page.

Using the support package, you can:

• Configure a Cellpose model by using a cellpose object.
• Segment 2D images by using the segmentcells2D function.
• Segment 3D images by using the segmentcells3D function.
• Train a custom Cellpose model by using the trainCellpose function.
• Download and save all pretrained models from the Cellpose library by using the downloadCellposeModels function.

The support package documentation also features examples to help get started with workflows such as selecting and tuning a pretrained Cellpose model, and segmenting large whole slide images (WSI) using Cellpose.

To learn more about the Cellpose Library, visit the Cellpose web site and the Cellpose GitHub® repository.

References

[1] Stringer, Carsen, Tim Wang, Michalis Michaelos, and Marius Pachitariu. “Cellpose: A Generalist Algorithm for Cellular Segmentation.” Nature Methods 18, no. 1 (January 2021): 100–106. https://doi.org/10.1038/s41592-020-01018-x.

[2] Pachitariu, Marius, and Carsen Stringer. “Cellpose 2.0: How to Train Your Own Model.” Nature Methods 19, no. 12 (December 2022): 1634–41. https://doi.org/10.1038/s41592-022-01663-4.