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copick
/
paint-from-picks
/ 0.2.2
Paint Copick Picks into a Segmentation Layer
A solution that paints picks from a Copick project into a segmentation layer in Zarr.
Tags
imaging
cryoet
Python
napari
Solution written by
Kyle Harrington
License of solution
MIT
Source Code
View on GitHub
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_factor
Factor to scale the particle radius for the ball radius. (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. (default value: PARAMETER_VALUE)
--tomo_type
Type of tomogram to use (e.g., denoised). (default value: PARAMETER_VALUE)
Usage instructions
Please follow
this link
for details on how to install and run this solution.