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--- |
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title: 'livermask: Automatic Liver Parenchyma and vessel segmentation in CT' |
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colorFrom: indigo |
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colorTo: indigo |
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sdk: docker |
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app_port: 7860 |
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emoji: 🚀 |
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pinned: false |
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license: mit |
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app_file: demo/app.py |
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--- |
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<img width="1758" alt="Screenshot 2023-05-25 at 20 00 15" src="https://github.com/andreped/livermask/assets/29090665/039577fe-ee8b-4500-8c3f-8d7a5a2dd3d3"> |
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# livermask Hugging Face demo - through docker SDK |
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Deploying simple models in a gradio-based web interface in Hugging Face spaces is easy. |
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For any other custom pipeline, with various dependencies and challenging behaviour, it |
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might be necessary to use Docker containers instead. |
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Deployment through a custom Docker image over the existing Gradio image was |
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necessary in this case due to `tensorflow` and `gradio` having colliding |
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versions. As `livermask` depends on `tf`, the only way to get around it was |
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fixing the broken dependency, which was handled by reinstalling and changing |
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the `typing_extensions` with a version that `gradio` required for the widgets |
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we used. Luckily, this did not break anything in `tf`, even though `tf` has a |
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very strict versioning criteria for this dependency. |
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Anyways, everything works as intended now. For every new push to the main branch, |
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continuous deployment to the Hugging Face `livermask` space is performed through |
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GitHub Actions. |
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When the space is updated, the Docker image is rebuilt/updated (caching if possible). |
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Then when finished, the end users can test the app as they please. |
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Right now, the functionality of the app is extremely limited, only offering a widget |
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for uploading a NIfTI file (`.nii` or `.nii.gz`) and visualizing the produced surface |
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of the predicted liver parenchyma 3D volume when finished processing. |
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Analysis process can be monitored from the `Logs` tab next to the `Running` button |
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in the Hugging Face `livermask` space. |
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It is also possible to build the app as a docker image and deploy it. To do so follow these steps: |
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``` |
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docker build -t livermask .. |
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docker run -it -p 7860:7860 livermask |
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``` |
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Then open `http://127.0.0.1:7860` in your favourite internet browser to view the demo. |
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TODOs: |
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- [X] Add gallery widget to enable scrolling through 2D slices |
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- [X] Render segmentation for individual 2D slices as overlays |
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