copick / labeled-data-from-picks / 0.1.5

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.
Tags
imagingcryoetPython
Solution written by
Kyle Harrington
License of solution
MIT
Source Code

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)

Usage instructions

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