morphospaces / train_swin_unetr_pixel_embedding_copick / 0.0.3

Train SwinUNETR Pixel Embedding Network with Copick Dataset

Train the SwinUNETR pixel embedding network using the Copick dataset.
Tags
imagingcryoetPythonnapari
Citation
Solution written by
Kevin Yamauchi
Kyle Harrington
Zhuowen Zhao
License of solution
MIT
Source Code

Arguments

--pretrained_weights_path
Pretrained weights path (default value: PARAMETER_VALUE)
--copick_config_path
Path to the Copick configuration file (default value: PARAMETER_VALUE)
--train_run_names
Names of the runs in the Copick project for training (default value: PARAMETER_VALUE)
--val_run_names
Names of the runs in the Copick project for validation (default value: PARAMETER_VALUE)
--tomo_type
Tomogram type in the Copick project (default value: PARAMETER_VALUE)
--user_id
User ID for the Copick project (default value: PARAMETER_VALUE)
--session_id
Session ID for the Copick project (default value: PARAMETER_VALUE)
--segmentation_type
Segmentation type in the Copick project (default value: PARAMETER_VALUE)
--voxel_spacing
Voxel spacing for the Copick project (default value: PARAMETER_VALUE)
--lr
Learning rate for the supervised contrastive learning (default value: 0.0001)
--logdir
Output directory name in the current working directory. Default is checkpoints (default value: checkpoints)

Usage instructions

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