copick / Segment-anything2-tomogram-slice-inference / 0.0.1

Generate segmentation masks for Copick Dataset using Segment Anything 2

Automatically generate segmentation masks for the Copick dataset. Install on a device with GPU access. Need cuda/12.1.1_530.30.02 and cudnn/8.9.7.29_cuda12 to compile.

Arguments

--copick_config_path

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

--run_name

Name of the run in the Copick project for inferencing (default value: PARAMETER_VALUE)

--tomo_type

Tomogram type in the Copick project (default value: PARAMETER_VALUE)

--voxel_spacing

Voxel spacing for the Copick project (default value: PARAMETER_VALUE)

--slice_index

Z-index of the tomogram slice (default value: PARAMETER_VALUE)

--sam2_checkpoint

Path to the pre-downloaded SAM2 checkpoints (default value: PARAMETER_VALUE)

--model_cfg

Model configuration file corresponds to the SAM2 checkpoints (default value: PARAMETER_VALUE)

--logdir

Output directory name in the current working directory. Default is outputs (default value: outputs)

Usage instructions

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