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mskmind/qupath-stardist

By mskmind

•Updated over 2 years ago

Stardist using QuPath with a sample script to run cell detection

Image
0

1.4K

mskmind/qupath-stardist repository overview

Usage:

docker run \
-v /absolute/path/to/your_image.svs:/inputs/your_image.svs:ro \
-v /absolute/path/to/your_work_dir:/output_dir:rw \
mskmind/qupath-stardist \
QuPath script --image /inputs/your_image.svs --args [cellSize=8,imageType=BRIGHTFIELD_H_DAB] /scripts/stardist_simple.groovy

Outputs:

cell objects are saved in your output directory:

  • cell_detections.tsv
  • cell_detections.geojson

Reference:

Tag summary

Content type

Image

Digest

Size

819.8 MB

Last updated

over 4 years ago

docker pull mskmind/qupath-stardist