copick / pick-distance-from-embedding / 0.0.5

Create Picks with Distance to Median Embedding

Creates a new set of picks for a new session ID, containing the same locations but including the distance to the median embedding in the 'score' attribute.
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)
--run_name
Name of the Copick run to process. (default value: PARAMETER_VALUE)
--session_id
Session ID to filter picks. (default value: PARAMETER_VALUE)
--new_session_id
New session ID for the newly created picks. (default value: PARAMETER_VALUE)
--feature_types
Comma-separated list of feature types to extract embeddings for. (default value: PARAMETER_VALUE)
--radius
Radius for calculating median embeddings. (default value: PARAMETER_VALUE)
--tomo_type
Tomogram type to use for each tomogram, e.g. denoised. (default value: PARAMETER_VALUE)
--voxel_spacing
Voxel spacing used to scale pick locations. (default value: PARAMETER_VALUE)
--median_embeddings_path
Path to the JSON file containing median embeddings. (default value: PARAMETER_VALUE)

Usage instructions

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