Generate Multiscale Basic Features with Torch using Copick API (Chunked, Corrected)

Compute multiscale basic features of a tomogram from a Copick run in chunks and save them using Copick's API.

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)

--voxel_spacing

Voxel spacing to be used. (default value: PARAMETER_VALUE)

--tomo_type

Type of tomogram to process. (default value: PARAMETER_VALUE)

--feature_type

Name for the feature type to be saved. (default value: PARAMETER_VALUE)

--intensity

Include intensity features (default value: 1)

--edges

Include edge features (default value: 1)

--texture

Include texture features (default value: 1)

--sigma_min

Minimum sigma for Gaussian blurring (default value: 0.5)

--sigma_max

Maximum sigma for Gaussian blurring (default value: 16.0)

--num_sigma

Number of sigma values between sigma_min and sigma_max for texture features. (default value: 5)

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