Segmentation API¶
The segmentation module provides functions for segmenting cells and nuclei in whole-slide images.
Core Segmentation Functions¶
::: smint.segmentation.process_large_image options: show_root_heading: true show_source: true show_signature_annotations: true
::: smint.segmentation.run_distributed_segmentation options: show_root_heading: true show_source: true show_signature_annotations: true
Cell Utilities¶
::: smint.segmentation.get_cell_outlines options: show_root_heading: true show_source: true show_signature_annotations: true
::: smint.segmentation.segment_chunk options: show_root_heading: true show_source: true show_signature_annotations: true
Post-processing¶
::: smint.segmentation.extract_contours options: show_root_heading: true show_source: true show_signature_annotations: true
::: smint.segmentation.save_masks options: show_root_heading: true show_source: true show_signature_annotations: true
Optional Dependencies¶
The segmentation module has several optional dependencies:
| Dependency | Required For | Fallback Behavior |
|---|---|---|
| Cellpose | Cell segmentation models | Stub implementation with helpful error messages |
| OpenCV (cv2) | Image I/O and contour extraction | Limited visualization, no mask saving/loading |
| Dask | Distributed processing | Single-process implementation only |
| Distributed | Multi-node computation | Single-node implementation only |
| CUDA | GPU acceleration | CPU-only implementation |
When a dependency is missing, SMINT will log a warning but continue to operate with limited functionality.