dkomura/histopatch repository overview

docker run --rm -v /data:/data dkomura/histopatch histopatch /data/wsi/wsifile /data/output 

Usage: `histopatch [OPTIONS] PATH_TO_WSI PATH_TO_SAVE_DIRECTORY`

Options
-a, --annotation_type [ndpa|qupath]:
File type of annotation (ndpa or qupath (GeoJSON (Pretty JSON)))

-s, --annotation_shape [all|line|area]:
Annotation shape (all, line, area)

-c, --color TEXT:
Used colors (white, black, red, green, blue, cyan, magenta, yellow) in annotation for ndpa or (None, Tumor, Stroma, Immune_cells, Necrosis, Other, Region, Ignore, Positive, Negative) for QuPath

--line_as_area:
Line annotation in ndpa file is treated as a closed area

--src_size FLOAT:
Patch size in the original WSI

-m, --micrometer:
Specify src_size in micrometers (default: pixels)

--patch_size INTEGER:
Output patch size

--num_patch INTEGER:
Number of patches for each annotation shape

--nparent INTEGER:
Number of parent directories kept in the output