cellcanvas / mock-annotation-evaluation / 0.0.3

Model Evaluation on Copick Data

Evaluates segmentation models from the mock-annotation solution on Copick data, generating metrics like IoU and F1, and saves the predicted segmentation into the Copick project.

Arguments

--copick_config_path

Path to the Copick configuration JSON file. (default value: PARAMETER_VALUE)

--voxel_spacing

Voxel spacing used to scale pick locations. (default value: PARAMETER_VALUE)

--tomo_type

Tomogram type to use for each tomogram. (default value: PARAMETER_VALUE)

--embedding_name

Name of the embedding features to use. (default value: PARAMETER_VALUE)

--input_user_id

User ID for the input segmentation. (default value: PARAMETER_VALUE)

--input_label_name

Name of the input label segmentation. (default value: PARAMETER_VALUE)

--run_name

Name of the run to process. (default value: PARAMETER_VALUE)

--model_dir

Directory of trained model files. (default value: PARAMETER_VALUE)

--output_dir

Directory to save evaluation results. (default value: PARAMETER_VALUE)

--output_user_id

User ID for the output predicted segmentation. (default value: PARAMETER_VALUE)

--output_label_name

Name of the output predicted segmentation. (default value: PARAMETER_VALUE)

Usage instructions

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