Generate Segmentation Masks using UNet Checkpoint

Generate segmentation masks using a trained UNet checkpoint on the Copick dataset.

Arguments

--copick_config_path

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

--run_name

Name of the run in the Copick project for testing (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)

--voxel_spacing

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

--checkpoint_path

Path to the trained UNet checkpoint (default value: PARAMETER_VALUE)

--segmentation_name

Name of the output segmentation (default value: PARAMETER_VALUE)

--batch_size

Batch size for inference (default value: 1)

--output_probability_maps

Whether to output probability maps (default value: 0)

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