python dicom unet_UNet++: 用于医学图像分割的嵌套式U-Net架构

UNet++: A Nested U-Net Architecture for Medical Image Segmentation

UNet++ is a new general purpose image segmentation architecture for more accurate image segmentation. UNet++ consists of U-Nets of varying depths whose decoders are densely connected at the same resolution via the redesigned skip pathways, which aim to address two key challenges of the U-Net: 1) unknown depth of the optimal architecture and 2) the unnecessarily restrictive design of skip connections.

Paper

This repository provides the official Keras implementation of UNet++ in the following papers:

UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation

Zongwei Zhou, Md Mahfuzur Rahman Siddiquee, Nima Tajbakhsh, and Jianming Liang

Arizona State University

IEEE Transactions on Medical Imaging (TMI)

paper | code

UNet++: A Nested U-Net Architecture for Medical Image Segmentation

Zongwei Zhou, Md Mahfuzur Rahman Siddiquee, Nima Tajbakhsh, and Jianming Liang

Arizona State University

Deep Learning in Medical Image Analysis (DLMIA) 2018. (Oral)

paper | code | slides | poster | blog

Other implementation

[PyTorch] (by 4ui_iurz1)

[PyTorch] (by Hong Jing)

[PyTorch] (by ZJUGiveLab)

[Keras] (by Siddhartha)

What is in this repository

1. Available architectures

2. Available backbones

Backbone model

Name

Weights

VGG16

vgg16

imagenet

VGG19

vgg19

imagenet

ResNet18

resnet18

imagenet

ResNet34

resnet34

imagenet

ResNet50

resnet50

imagenet

imagenet11k-places365ch

ResNet101

resnet101

imagenet

ResNet152

resnet152

imagenet

imagenet11k

ResNeXt50

resnext50

imagenet

ResNeXt101

resnext101

imagenet

DenseNet121

densenet121

imagenet

DenseNet169

densenet169

imagenet

DenseNet201

densenet201

imagenet

Inception V3

inceptionv3

imagenet

Inception ResNet V2

inceptionresnetv2

imagenet

How to use UNet++

1. Requirements

Python 3.x, Keras 2.2.2, Tensorflow 1.4.1 and other common packages listed in requirements.txt.

2. Installation

git clone https://github.com/MrGiovanni/UNetPlusPlus.git

cd UNetPlusPlus

pip install -r requirements.txt

git submodule update --init --recursive

3. Running the scripts

CUDA_VISIBLE_DEVICES=0 python DSB2018_application.py --run 1 \

--arch Xnet \

--backbone vgg16 \

--init random \

--decoder transpose \

--input_rows 96 \

--input_cols 96 \

--input_deps 3 \

--nb_class 1 \

--batch_size 2048 \

--weights None \

--verbose 1

CUDA_VISIBLE_DEVICES=0 python BRATS2013_application.py --run 1 \

--arch Xnet \

--backbone vgg16 \

--init random \

--decoder transpose \

--input_rows 256 \

--input_cols 256 \

--input_deps 3 \

--nb_class 1 \

--batch_size 2048 \

--weights None \

--verbose 1

Code examples for your own data

Train a UNet++ structure (Xnet in the code):

from segmentation_models import Unet, Nestnet, Xnet

# prepare data

x, y = ... # range in [0,1], the network expects input channels of 3

# prepare model

model = Xnet(backbone_name='resnet50', encoder_weights='imagenet', decoder_block_type='transpose') # build UNet++

# model = Unet(backbone_name='resnet50', encoder_weights='imagenet', decoder_block_type='transpose') # build U-Net

# model = NestNet(backbone_name='resnet50', encoder_weights='imagenet', decoder_block_type='transpose') # build DLA

model.compile('Adam', 'binary_crossentropy', ['binary_accuracy'])

# train model

model.fit(x, y)

To do

Add VGG backbone for UNet++

Add ResNet backbone for UNet++

Add ResNeXt backbone for UNet++

Add DenseNet backbone for UNet++

Add Inception backbone for UNet++

Add Tiramisu and Tiramisu++

Add FPN++

Add Linknet++

Add PSPNet++

Citation

If you use UNet++ for your research, please cite our papers:

@article{zhou2019unetplusplus,

title={UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation},

author={Zhou, Zongwei and Siddiquee, Md Mahfuzur Rahman and Tajbakhsh, Nima and Liang, Jianming},

journal={IEEE Transactions on Medical Imaging},

year={2019},

publisher={IEEE}

}

@incollection{zhou2018unetplusplus,

title={Unet++: A Nested U-Net Architecture for Medical Image Segmentation},

author={Zhou, Zongwei and Siddiquee, Md Mahfuzur Rahman and Tajbakhsh, Nima and Liang, Jianming},

booktitle={Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support},

pages={3--11},

year={2018},

publisher={Springer}

}

Acknowledgments

This repository has been built upon qubvel/segmentation_models. We appreciate the effort of Pavel Yakubovskiy for providing well-organized segmentation models to the community. This research has been supported partially by NIH under Award Number R01HL128785, by ASU and Mayo Clinic through a Seed Grant and an Innovation Grant. The content is solely the responsibility of the authors and does not necessarily represent the official views of NIH. This is a patent-pending technology.