Process Copick Runs and Save Features and Labels

A solution that processes all Copick runs and saves the resulting features and labels into a Zarr zip store.

Arguments

--copick_config_path

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

--painting_segmentation_names

Comma-separated list of names for the painting segmentations. Rightmost segmentation has highest precedence. (default value: PARAMETER_VALUE)

--session_id

Session ID for the segmentation. (default value: PARAMETER_VALUE)

--user_id

User ID for segmentation creation. (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, e.g. denoised. (default value: PARAMETER_VALUE)

--feature_types

Comma-separated list of feature types to use for each tomogram, e.g. cellcanvas01,cellcanvas02. (default value: PARAMETER_VALUE)

--output_zarr_path

Path for the output Zarr zip store containing the features and labels. (default value: PARAMETER_VALUE)

--run_names

Comma-separated list of run names to process. If not provided, all runs will be processed. (default value: PARAMETER_VALUE)

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