Using the Docker image

PyHIST can be directly executed using Docker.

docker run mmunozag/pyhist --help

To mount a local folder /path_with/images/ mapping to the folder /pyhist/images/ inside the container, use the -v flag specifying the absolute path of the local folder.

docker run -v /path_with/images/:/pyhist/images/ mmunozag/pyhist [args]

Optionally, if you want to ensure that all the generated output files are written with permissions belonging to the current host user (instead of root, which is Docker's default), specify the username and group with the -u flag (retrieval of both can be automated with id ), as well mapping the passwd file with a second -v flag:

docker run -v /path_with/images/:/pyhist/images/ \
    -u $(id -u):$(id -g) \ 
    -v /etc/passwd:/etc/passwd \
    mmunozag/pyhist [args]

A working example to process an image called test.svs located inside /path_with/images/:

docker run -v /path_with/images/:/pyhist/images/ \
    -u $(id -u):$(id -g) \
    -v /etc/passwd:/etc/passwd \
    mmunozag/pyhist --save-tilecrossed-image --output images/ images/test.svs

Using PyHIST

PyHIST can be directly executed as a script. To see all available options:

python pyhist.py --help

A working example to process an image called test.svs located inside /path_with/images/:

python pyhist.py \
    --content-threshold 0.05 \
    --patch-size 64 \
    --output-downsample 16 \
    --info "verbose" \
    --save-tilecrossed-image\
    /path_with/images/test.svs