https://github.com/digitalslidearchive/histoqc-dsa-plugin

https://github.com/digitalslidearchive/histoqc-dsa-plugin

Last synced: 7 months ago
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• Host: GitHub
• URL: https://github.com/digitalslidearchive/histoqc-dsa-plugin
• Owner: DigitalSlideArchive
• Created: 2022-09-02T22:32:10.000Z (almost 4 years ago)
• Default Branch: production
• Last Pushed: 2024-02-01T14:56:44.000Z (over 2 years ago)
• Last Synced: 2024-12-28T16:47:29.386Z (over 1 year ago)
• Language: Python
• Size: 65.4 KB
• Stars: 1
• Watchers: 1
• Forks: 2
• Open Issues: 3
• Metadata Files:
  • Readme: README.md

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README

          
# 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:

```bash

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:

![image](https://user-images.githubusercontent.com/34462353/199604503-8d2bbd8f-58cc-4d0e-a9ed-7540e91f5719.png)

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

![image](https://user-images.githubusercontent.com/34462353/199604605-20cfde51-6735-46a6-a0ad-fcc5a013b7d2.png)

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**:

![image](https://user-images.githubusercontent.com/34462353/199604996-fdf13639-0a46-4997-a551-ca729e79931e.png)

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

![image](https://user-images.githubusercontent.com/34462353/199605419-8711c99d-1080-4abc-b036-0b014daedca8.png)