Train 3D UNet for Segmentation with Copick Dataset

Train a 3D UNet network using the Copick dataset for segmentation.

Arguments

--copick_config_path

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

--train_run_names

Names of the runs in the Copick project for training (default value: PARAMETER_VALUE)

--val_run_names

Names of the runs in the Copick project for validation (default value: PARAMETER_VALUE)

--tomo_type

Tomogram type in the Copick project (default value: PARAMETER_VALUE)

--user_id

User ID for the Copick project (default value: PARAMETER_VALUE)

--session_id

Session ID for the Copick project (default value: PARAMETER_VALUE)

--segmentation_type

Segmentation type in the Copick project (default value: PARAMETER_VALUE)

--voxel_spacing

Voxel spacing for the Copick project (default value: PARAMETER_VALUE)

--lr

Learning rate for the UNet training (default value: 0.0001)

--logdir

Output directory name in the current working directory. Default is checkpoints (default value: checkpoints)

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