copick / paint-from-picks / 0.1.11

Paint Copick Picks into a Segmentation Layer

A solution that paints picks from a Copick project into a segmentation layer in Zarr.
Tags
imagingcryoetPythonnapari
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_name
Name for the painting segmentation. (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)
--ball_radius
Radius of the ball used to paint picks into the segmentation. (default value: PARAMETER_VALUE)
--run_name
Name of the Copick run to process. (default value: PARAMETER_VALUE)
--allowlist_user_ids
Comma-separated list of user IDs to include in the painting. Consider adding prepick if this is for a pickathon. (default value: PARAMETER_VALUE)

Usage instructions

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