https://github.com/kaczmarj/wsinfer-manuscript
Artifacts for the WSInfer manuscript
https://github.com/kaczmarj/wsinfer-manuscript
Last synced: about 2 months ago
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Artifacts for the WSInfer manuscript
- Host: GitHub
- URL: https://github.com/kaczmarj/wsinfer-manuscript
- Owner: kaczmarj
- Created: 2023-02-24T23:17:57.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2023-02-26T23:47:39.000Z (over 2 years ago)
- Last Synced: 2025-02-10T02:33:27.372Z (4 months ago)
- Language: Jupyter Notebook
- Size: 56.6 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# WSInfer Manuscript
We use the first 10 DX1 slides from TCGA-COAD. To reproduce our results,
please download these 10 SVS files and place them in the `slides` directory.
```
slides/
├── TCGA-3L-AA1B-01Z-00-DX1.svs
├── TCGA-4N-A93T-01Z-00-DX1.svs
├── TCGA-4T-AA8H-01Z-00-DX1.svs
├── TCGA-5M-AAT4-01Z-00-DX1.svs
├── TCGA-5M-AAT5-01Z-00-DX1.svs
├── TCGA-5M-AAT6-01Z-00-DX1.svs
├── TCGA-5M-AATE-01Z-00-DX1.svs
├── TCGA-A6-2671-01Z-00-DX1.svs
├── TCGA-A6-2672-01Z-00-DX1.svs
└── TCGA-A6-2674-01Z-00-DX1.svs
```
Then run the following to run both TIL detection pipelines. The time and GPU
statistics are recorded automatically.
```bash
# Download Frontier TILs container.
singularity pull docker://kaczmarj/frontiers-til:cede545
# Download wsinfer TILs container (uses same model as Frontier TILs inceptionv4).
singularity pull docker://kaczmarj/wsinfer:0.3.6-tils
# Run wsinfer pipeline.
CUDA_VISIBLE_DEVICES=2 screen -S wsinfer bash run-wsinfer.sh
# Run frontiers pipeline.
CUDA_VISIBLE_DEVICES=2 screen -S frontiers bash run-frontiers.sh
```