GitHub - Skycocoo/MS-Lesion-Segmentation: 3D Unet for MS Lesion Segmentation

Notes

[useful] MS_segmentation.ipynb: actual training code (for testing purpose)
[useful] Post_processing.ipynb: reconstruct patches into original images, and store the results
Test_reconstruct.ipynb: previous Reconstruct file (extracted to class)
Test_weight_merge.ipynb: test the idea of weighted reconstruct
Test_weight_patch.ipynb: test original reconstruct algo
Demonstrate_result.ipynb: plot training results vs ground truth on testing data
Format_report.ipynb: format the structure of the network for latex report
Test_data.ipynb: test the shape of data
Training.py: Training with Dice Loss
Training-binary.py: Training with Binary Cross Entropy
Training-all.py: Training with all data (not selected)

data.py: fetch data into h5 format, preprocess data for training (padding, patch index, etc.), load data from h5 file
dice.py: dice score calculation function
generator.py: generate patches for training (different for training / testing dataset)
model.py: 3D U-Net model structure setup (Keras)
recon.py: reconstruct patches to original image shape (each instance: corresponds to one original image shape); 5 K-fold, 15 images, testing images: 3 (or else storing need additional counter)

Name		Name	Last commit message	Last commit date
Latest commit History 66 Commits
archive		archive
document		document
model		model
.gitignore		.gitignore
MS_segmentation.ipynb		MS_segmentation.ipynb
Multi_post_processing.ipynb		Multi_post_processing.ipynb
Multi_pre_processing_data.ipynb		Multi_pre_processing_data.ipynb
Multi_pre_processing_data_generator.ipynb		Multi_pre_processing_data_generator.ipynb
Multi_pre_processing_model.ipynb		Multi_pre_processing_model.ipynb
Notes.md		Notes.md
Playground.ipynb		Playground.ipynb
Post-process-multi-dice-learning.py		Post-process-multi-dice-learning.py
Post-process.py		Post-process.py
Post_processing.ipynb		Post_processing.ipynb
README.md		README.md
Training-dice.py		Training-dice.py
Training-multi-dice-learning.py		Training-multi-dice-learning.py
Training-multi-dice.py		Training-multi-dice.py
Training.py		Training.py
req.txt		req.txt