Run workflows
Run the different workflows using
from the root of the project directory.
Workflows
create_dataset.py
Create the dataset from the slides and annotations. Creates a patch level dataset from the slides and performs Stratified k-fold at the patch level. Mainly uses the dataset
key in config.yaml.
create_dataset-MIL.py
Creates an MIL dataset from the slides.
model_train.py
Trains the model on the patch level dataset using the selected model. The trainer
key in config.yaml
is used for training configurations, while the model
key is utilised for selecting models and specifying their parameters.
model_train-MIL.py
Train on an MIL dataset.
generate_heatmaps.py
Generate heatmaps for the slides using the predictions of the trained model.
exp_summary.py
Generate a summary of the experiment over the different folds. Also packs the results (metrics, plots and heatmaps) in an exportable ZIP file.
Last updated