Cellpose for Microscopy Segmentation

Segment microscopy images using Medical Imaging Toolbox Interface for Cellpose Library

You can import large microscopy image files to segment using the OpenSlide and Bio-Formats libraries by using the Medical Imaging Toolbox™ Interface for Whole Slide Imaging File Reader support package. Segment cells from microscopy images using the Medical Imaging Toolbox Interface for Cellpose Library support package, which provides functionality for downloading pretrained models from the Cellpose Library, segmenting 2-D and 3-D images using Cellpose models, and training new models using your own microscopy data. The support package also requires Deep Learning Toolbox™ and Computer Vision Toolbox™. You can install support packages from the Add-On Explorer. For more information about installing add-ons, see Get and Manage Add-Ons.

Functions

expand all

openslideinfoRead whole slide image file metadata using OpenSlide library (Since R2026a)
openslidereadRead whole slide image data using OpenSlide library (Since R2026a)
bioformatsinfoRead whole slide image file metadata using Bio-Formats library (Since R2026a)
bioformatsreadRead whole slide image data using Bio-Formats library (Since R2026a)
cellposeConfigure Cellpose model for cell segmentation (Since R2023b)
segmentCells2DSegment 2-D image using Cellpose (Since R2023b)
segmentCells3DSegment 3-D image volume using Cellpose (Since R2023b)
trainCellposeTrain custom Cellpose model (Since R2023b)
downloadCellposeModelsDownload pretrained models from Cellpose Library (Since R2023b)

Topics

Featured Examples

Choose Pretrained Cellpose Model for Cell Segmentation

Choose Pretrained Cellpose Model for Cell Segmentation

Segment cells from microscopy images using a pretrained Cellpose model.

Refine Cellpose Segmentation by Tuning Model Parameters

Refine Cellpose Segmentation by Tuning Model Parameters

Explore and tune Cellpose parameters to improve segmentation results.

Detect Nuclei in Large Whole Slide Images Using Cellpose

Detect Nuclei in Large Whole Slide Images Using Cellpose

Detect cell nuclei in whole slide images (WSIs) of tissue stained using hematoxylin and eosin (H&E) by using Cellpose.

Classify Tumors in Digital Pathology Images Using Cell Nucleus Morphology

Classify Tumors in Digital Pathology Images Using Cell Nucleus Morphology

Classify whole slide image (WSI) patches as normal or cancerous using pathomics.

Train Custom Cellpose Model

Train Custom Cellpose Model

Train a custom Cellpose model, using new training data, to detect noncircular shapes.