Generate DINOv2 Features from a Copick Run

Extract multiscale features from a tomogram using DINOv2 (ViT) 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)

--batch_size

Batch size for processing. (default value: 1024)

--stride_x

Stride along the x-axis. (default value: 1)

--stride_y

Stride along the y-axis. (default value: 1)

--stride_z

Stride along the z-axis. (default value: 1)

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