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segment-and-get-coords

Usage Guide

atlaspatch segment-and-get-coords runs tissue segmentation and patch coordinate extraction, then writes the per-slide H5 without patch feature matrices.

Use this command when you want AtlasPatch's coordinates and metadata now, but you want to defer feature extraction to a later process, encode-slide, or encode-patient run.

One slide

atlaspatch segment-and-get-coords /path/to/slide.svs \
  --output ./output \
  --patch-size 256 \
  --target-mag 20 \
  --device cuda

Directory of slides

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

atlaspatch segment-and-get-coords /path/to/slides \
  --output ./output \
  --patch-size 256 \
  --target-mag 20 \
  --recursive

Coordinates plus overlays

Add visualization flags when you want to inspect the extracted grid and segmentation outputs alongside the H5 coordinates.

atlaspatch segment-and-get-coords /path/to/slide.svs \
  --output ./output \
  --patch-size 256 \
  --target-mag 20 \
  --visualize-grids \
  --visualize-mask \
  --visualize-contours

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 H5 files and any optional overlays or patch images generated during patch extraction.
--patch-size int yes - Patch size, in pixels, at the requested target magnification. This controls the extracted grid written into the H5 file.
--step-size int no same as --patch-size Stride, in pixels, between adjacent patches at the target magnification. Use a smaller value than --patch-size if you want overlapping coordinates.
--target-mag int yes - Target magnification used when reading patches from the slide pyramid. AtlasPatch records this in the H5 metadata.
--device text no cuda Device used for tissue segmentation. AtlasPatch accepts values such as cuda, cuda:0, and cpu.
--tissue-thresh float no 0.0 Minimum tissue area fraction required for a patch to be kept after segmentation.
--white-thresh int no 15 Saturation threshold used by the optional white-filtering stage in --no-fast-mode.
--black-thresh int no 50 RGB threshold used by the optional black-filtering stage in --no-fast-mode.
--seg-batch-size int no 1 Batch size for thumbnail-level tissue segmentation.
--write-batch int no 8192 Number of coordinate rows buffered before writing to H5. Larger values reduce write frequency but increase transient memory use.
--patch-workers int no CPU count Number of worker threads used during patch extraction and optional patch PNG export.
--max-open-slides int no 200 Upper bound on how many slides AtlasPatch keeps open across segmentation and extraction.
--fast-mode / --no-fast-mode flag no --fast-mode --fast-mode skips per-patch black and white filtering after segmentation. Use --no-fast-mode if you want that extra filtering pass.
--save-images flag no off Save extracted patches as PNGs under images/<stem>/. This is optional and is not required for later H5-based feature extraction.
--visualize-grids flag no off Save patch-grid overlays under visualization/.
--visualize-mask flag no off Save tissue-mask overlays under visualization/.
--visualize-contours flag no off Save contour overlays under visualization/.
--skip-existing / --force flag no --skip-existing Reuse existing H5 outputs by default. Use --force to rebuild them even when the output files already exist.
--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 segment-and-get-coords writes one H5 file per slide:

  • <output>/patches/<stem>.h5

That H5 contains slide metadata and:

  • coords

It does not contain features/<patch_encoder> datasets unless you later run process, encode-slide, or encode-patient.

Optional outputs:

  • patch PNGs under <output>/images/<stem>/
  • overlays under <output>/visualization/