Medical Image Segmentation Pipeline
Note: DemoDataset folder in this repo is just to let you know how I organized my training data, therefore there is no "real" file inside.
Also, this folder structure is used as a premise in all my related scripts.
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If you're using Windows, remember to put it's bin directory in your Environment Variables.
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openslide-python 1.1.1
pip install openslide-python==1.1.1
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PyTorch 1.1.0
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Other requirements will automatically be installed when you install
misp.
Install misp:
pip install misp- How to create a subset of the original dataset for faster iterations?
Below is an example which I used to create my "smaller version" dataset.
python create_tiny_dataset.py -s CRCdataset/train -d tinyCRC/train -n 600
python create_tiny_dataset.py -s CRCdataset/valid -d tinyCRC/valid -n 100