UNet with Optuna optimization

Optimization of UNet using Optuna with Copick data.

Arguments

--copick_config_path

Path to the Copick configuration JSON file. (default value: PARAMETER_VALUE)

--voxel_spacing

Voxel spacing used to scale pick locations. (default value: PARAMETER_VALUE)

--tomo_type

Tomogram type to use for each tomogram. (default value: PARAMETER_VALUE)

--epochs

Number of training epochs. (default value: PARAMETER_VALUE)

--num_classes

Number of classes for segmentation, excluding the background class. (default value: PARAMETER_VALUE)

--num_trials

Number of trials for Optuna optimization. (default value: PARAMETER_VALUE)

--batch_size

Batch size for the DataLoader. (default value: PARAMETER_VALUE)

--random_seed

Random seed for reproducibility. (default value: 17171)

Please follow this link for details on how to install and run this solution.