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detect-tissue

Usage Guide

atlaspatch detect-tissue runs tissue segmentation only. It does not write patch coordinates, patch feature datasets, slide embeddings, or patient embeddings.

One slide

Use this when you only want to inspect the segmentation result for a single WSI.

atlaspatch detect-tissue /path/to/slide.svs \
  --output ./output \
  --device cuda

Directory of slides

Point WSI_PATH at a directory to segment many slides in one run. Add --recursive if slides are nested in subdirectories.

atlaspatch detect-tissue /path/to/slides \
  --output ./output \
  --device cuda \
  --recursive

Arguments

Argument Type Required Default Description
WSI_PATH path yes - Path to one slide file or a directory of slides. When a directory is provided, AtlasPatch scans for supported WSI extensions and uses --recursive to control whether subdirectories are included.
--output, -o path yes - Output root for the visualization outputs generated by segmentation.
--device text no cuda Device used for tissue segmentation. AtlasPatch accepts values such as cuda, cuda:0, and cpu.
--seg-batch-size int no 1 Batch size for thumbnail-level tissue segmentation. Increase this only if the segmentation device has enough memory to handle larger thumbnail batches.
--recursive flag no off Recurse into subdirectories when WSI_PATH is a directory. Ignored when WSI_PATH is a single slide file.
--mpp-csv path no - CSV file with columns wsi,mpp that overrides the slide microns-per-pixel metadata for selected slides. Slides are matched by stem.
--verbose, -v flag no off Enable debug logging.

Outputs

atlaspatch detect-tissue writes visualization outputs under:

  • <output>/visualization/

Use this command when you want to inspect tissue masks before running patch extraction or when you only need mask overlays and no H5 outputs.