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morphospaces / train_swin_unetr_pixel_embedding_mrc / 0.0.1

Train SwinUnetr Pixel Embedding Network with Mrc Dtataloader

Train the SwinUnetr pixel embedding network using the provided script and dataset.
Tags
imagingcryoetPythonnapari
Citation
Solution written by
Kevin Yamauchi
Kyle Harrington
Zhuowen Zhao
License of solution
MIT
Source Code
View on GitHub

Arguments

--pretrained_weights_path
Pretrained weights path (default value: PARAMETER_VALUE)
--train_tomogram_path
tomogram mrc files directory for training dataset (default value: PARAMETER_VALUE)
--train_mask_path
mask mrc files directory for taining dataset (default value: PARAMETER_VALUE)
--val_tomogram_path
tomogram mrc files directory for validation dataset (default value: PARAMETER_VALUE)
--val_mask_path
mask mrc files directory for validation dataset (default value: PARAMETER_VALUE)
--lr
Learning reate for the supervised contrastive learning (default value: 0.0001)
--logdir
output dir name in curr working dir. Default is checkpoints (default value: checkpoints)

Usage instructions

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