API Reference

This class encapsulates preprocessing, segmentation, mask filtering, shape/label creation, transcript assignment, and writing results back to a SpatialData Zarr file.

GPU Utilities

Methods for checking GPU availability and clearing GPU memory.

Image Preprocessing

Methods for loading and preparing images for segmentation.

Segmentation

Methods to run Cellpose segmentation.

Masks & Shapes

Methods for refining masks, converting them to polygons, and building shapes.

Labels

Methods for upscaling masks and creating Labels2DModel.

Points & Tables

Methods for assigning transcript points to cells and creating AnnData tables.

Save Zarr File

Methods for saving processed SpatialData back to a Zarr file.