Awesome
Unet-Segmentation-Pytorch-Nest-of-Unets
Implementation of different kinds of Unet Models for Image Segmentation
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UNet - U-Net: Convolutional Networks for Biomedical Image Segmentation https://arxiv.org/abs/1505.04597
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RCNN-UNet - Recurrent Residual Convolutional Neural Network based on U-Net (R2U-Net) for Medical Image Segmentation https://arxiv.org/abs/1802.06955
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Attention Unet - Attention U-Net: Learning Where to Look for the Pancreas https://arxiv.org/abs/1804.03999
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RCNN-Attention Unet - Attention R2U-Net : Just integration of two recent advanced works (R2U-Net + Attention U-Net)
- Nested UNet - UNet++: A Nested U-Net Architecture for Medical Image Segmentation https://arxiv.org/abs/1807.10165
With Layer Visualization
1. Getting Started
Clone the repo:
git clone https://github.com/bigmb/Unet-Segmentation-Pytorch-Nest-of-Unets.git
2. Requirements
python>=3.6
torch>=0.4.0
torchvision
torchsummary
tensorboardx
natsort
numpy
pillow
scipy
scikit-image
sklearn
Install all dependent libraries:
pip install -r requirements.txt
3. Run the file
Add all your folders to this line 106-113
t_data = '' # Input data
l_data = '' #Input Label
test_image = '' #Image to be predicted while training
test_label = '' #Label of the prediction Image
test_folderP = '' #Test folder Image
test_folderL = '' #Test folder Label for calculating the Dice score
4. Types of Unet
Unet
RCNN Unet
Attention Unet
Attention-RCNN Unet
Nested Unet
5. Visualization
To plot the loss , Visdom would be required. The code is already written, just uncomment the required part. Gradient flow can be used too. Taken from (https://discuss.pytorch.org/t/check-gradient-flow-in-network/15063/10)
A model folder is created and all the data is stored inside that. Last layer will be saved in the model folder. If any particular layer is required , mention it in the line 361.
Layer Visulization
Filter Visulization
TensorboardX Still have to tweak some parameters to get visualization. Have messed up this trying to make pytorch 1.1.0 working with tensorboard directly (and then came to know Currently it doesn't support anything apart from linear graphs) <img src="https://github.com/bigmb/Unet-Segmentation-Pytorch-Nest-of-Unets/blob/master/images/tensorb.png" width="280">
Input Image Visulization for checking
a) Original Image
<img src="https://github.com/bigmb/Unet-Segmentation-Pytorch-Nest-of-Unets/blob/master/images/in1.png" width="480">b) CenterCrop Image
<img src="https://github.com/bigmb/Unet-Segmentation-Pytorch-Nest-of-Unets/blob/master/images/in2.png" width="480">6. Results
Dice Score for hippocampus segmentation ADNI-LONI Dataset
<img src="https://github.com/bigmb/Unet-Segmentation-Pytorch-Nest-of-Unets/blob/master/dice.png" width="380">7. Citation
If you find it usefull for your work.
@article{DBLP:journals/corr/abs-1906-07160,
author = {Malav Bateriwala and
Pierrick Bourgeat},
title = {Enforcing temporal consistency in Deep Learning segmentation of brain
{MR} images},
journal = {CoRR},
volume = {abs/1906.07160},
year = {2019},
url = {http://arxiv.org/abs/1906.07160},
archivePrefix = {arXiv},
eprint = {1906.07160},
timestamp = {Mon, 24 Jun 2019 17:28:45 +0200},
biburl = {https://dblp.org/rec/bib/journals/corr/abs-1906-07160},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
8. Blog about different Unets
In progress