histoqc-dsa-plugin

Slicer CLI Integration

Importing into DSA

To run the histoqc in batch mode, go into the proper subdirectory and rebuild the image:

cd ~
git clone https://github.com/Theta-Tech-AI/histoqc-dsa-plugin
cd ~/histoqc-dsa-plugin/slicer_cli_plugin
docker image build -t histoqc:latest . && docker image ls | grep histoqc

Then, assuming that DSA is running, go to the Slicer CLI plugin config:

Type in the tag of the image you just build above and click Import Image:

You can repeat these steps any time you make an update to the slicer_cli_plugin code.

Running HistoQC

Then, navigate to an pathology image and click Open In HistomicsUI:

Now, navigate to the HistoQC analysis and click Submit to begin running HistoQC: