spatialrefinery.segmentation.instanseg.segment_wsi

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spatialrefinery.segmentation.instanseg.segment_wsi#

spatialrefinery.segmentation.instanseg.segment_wsi(wsi_path, outdir, *, pixel_size=None, gpu_id=0, model_type='brightfield_nuclei', tile_size=512, overlap=80, detection_size=20, use_otsu_threshold=True, clahe_clip=None, seed_threshold=None, skip_existing=True)#

Segment nuclei in one whole-slide image and return the GeoJSON path.

Parameters:

  • wsi_path (str | Path) – The slide to segment. Read through tiffslide, so SVS/NDPI/OME-TIFF and other TIFF-backed formats work.

  • outdir (str | Path) – Parent directory. Results go to <outdir>/<wsi_path.name>/cells.geojson; the directory is named with the full filename (extension included) so that a.svs and a.ndpi cannot collide. The zarr stage names its store for the stem instead (a.ome.tif -> a.zarr); see to_spatialdata.default_zarr_path.

  • pixel_size (float | None (default: None)) – Microns per pixel. Read from the slide metadata when omitted. InstanSeg rejects a value outside [0.1, 1] micron, so pass this explicitly for slides with missing or nonsensical resolution tags.

  • gpu_id (int | None (default: 0)) – CUDA device index, or None to force CPU. Under the SLURM worker each process sees a single GPU via CUDA_VISIBLE_DEVICES, so this stays 0.

  • use_otsu_threshold (bool (default: True)) – Skip tiles outside the tissue mask, so background is not segmented.

  • clahe_clip (float | None (default: None)) – Run CLAHE over each tile at this clip limit before inference. Off by default. Worth setting (2.0 is a reasonable start) on weakly haematoxylin-stained slides, where InstanSeg’s per-tile percentile normalisation leaves pale nuclei below the seed threshold: on a pale kidney H&E it recovered 22% more nuclei, and 27% together with seed_threshold=0.4.

  • seed_threshold (float | None (default: None)) – Override the model’s seed threshold (default 0.7). Lower detects fainter nuclei at some risk of over-segmentation.

  • skip_existing (bool (default: True)) – Return immediately if cells.geojson is already present, which makes an interrupted batch resumable.

Return type:

Path

Returns:

Path The written cells.geojson.

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