copick / pick-distance-from-embedding / 0.0.4

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.

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.