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copick / compare-picks / 0.0.37

Compare Picks from Different Users and Sessions with F-beta Score

A solution that compares the picks from a reference user and session to a candidate user and session for all particle types, providing metrics like average distance, precision, recall, and F-beta score. Computes micro-averaged F-beta score across all runs if run_name is not provided.
Tags
imagingcryoetPython
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)
--reference_user_id
User ID for the reference picks. (default value: PARAMETER_VALUE)
--reference_session_id
Session ID for the reference picks. (default value: PARAMETER_VALUE)
--candidate_user_id
User ID for the candidate picks. (default value: PARAMETER_VALUE)
--candidate_session_id
Session ID for the candidate picks. (default value: PARAMETER_VALUE)
--distance_threshold
Distance threshold multiplier for matching points (e.g., 1.5x the radius as default). (default value: PARAMETER_VALUE)
--beta
Beta value for the F-beta score. (default value: PARAMETER_VALUE)
--run_name
Name of the Copick run to process. If not specified all runs will be processed. (default value: PARAMETER_VALUE)
--output_json
Path to save the output JSON file with the results. (default value: PARAMETER_VALUE)
--weights
Comma-separated list of weights for each particle type (e.g., particle1=1,particle2=2). (default value: PARAMETER_VALUE)

Usage instructions

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