greentreeys / fundus-vessel-segmentation-tmbe

One of the first steps in automatic fundus image analysis is the segmentation of the retinal vasculature, which provides valuable information related to several diseases. In this work, we present an extensive description and evaluation of our method for blood vessel segmentation in fundus images based on a discriminatively trained, fully connected conditional random field model. This task remains a challenge largely due to the desired structures being thin and elongated, a setting that performs particularly poorly using standard segmentation priors, such as a Potts model or total variation. We overcome this difficulty by using a conditional random field model with more expressive potentials, taking advantage of recent results enabling inference of fully connected models almost in real-time. Parameters of the method are learned automatically using a structured output support vector machine, a supervised technique widely used for structured prediction in a number of machine learning applications. The evaluation of our method is performed both quantitatively and qualitatively on DRIVE, STARE, CHASEDB1 and HRF, showing its ability to deal with different types of images and outperforming other techniques, trained using state of the art features.

#Retinal Vessel Segmentation Created by José Ignacio Orlando at Pladema Institute (Facultad de Ciencias Exactas, UNCPBA, Tandil, Argentina) and CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina), under the supervision of Matthew B. Blaschko (KU Leuven, Belgium).

##Introduction This code corresponds to our paper published at IEEE TBME 2016. It allows you to perform vessel segmentation in color fundus images.

##License Our code is released under the MIT Licence (refer to the LICENSE file for details).

##Citing If you find our code useful for your research, please cite:

@article{orlando2016discriminatively,
  title={A discriminatively trained fully connected Conditional Random Field model for blood vessel segmentation in fundus images},
  author={Orlando, Jos{\'e} Ignacio and Prokofyeva, Elena and Blaschko, Matthew},
  journal={Biomedical Engineering, IEEE Transactions on},
  year={2016},
  publisher={IEEE}
}

@incollection{orlando2014learning,
  title={Learning fully-connected CRFs for blood vessel segmentation in retinal images},
  author={Orlando, Jos{\'e} Ignacio and Blaschko, Matthew},
  booktitle={Medical Image Computing and Computer-Assisted Intervention--MICCAI 2014},
  pages={634--641},
  year={2014},
  publisher={Springer}
}

There are also some third party libraries included in our code. If you use it, please cite:

• Responses to 2D Gabor wavelets by Soares et al. J. V. Soares et al.: Retinal vessel segmentation using the 2-D Gabor wavelet and supervised classification. IEEE Transactions on Medical Imaging, vol. 25, no. 9, 2006

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• Line detectors by Nguyen et al. U. T. Nguyen et al.: An effective retinal blood vessel segmentation method using multi-scale line detection. Pattern Recognition, vol. 46, no. 3, pp. 703–715, 2013.

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• Efficient inference in fully connected CRF by Krahenbul and Koltun (C++ implementation) P. Krahenbuhl and V. Koltun: Efficient inference in fully connected CRFs with Gaussian edge potentials. Advances in Neural Information Processing Systems, 2012, pp. 109–117. (if you use the MEX function that wraps this code please also cite our IEEE TMBE and MICCAI papers)

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• Graph-cut for local neighborhood based CRF inference Y. Boykov and V. Kolmogorov: An experimental comparison of mincut/max-flow algorithms for energy minimization in vision. IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 26, no. 9, pp. 1124–1137, 2004.

##Contents

###Requirements

1. Set up MEX compiler according to your OS.
2. Compile the Fully Connected CRF wrapper doing:

mex ./CRF/CRF_1.0/fullyCRFwithGivenPairwises.cpp ./CRF/CRF_1.0/densecrf.cpp ./CRF/CRF_1.0/util.cpp 
mex ./CRF/CRF_1.0/pairwisePart.cpp ./CRF/CRF_1.0/densecrf.cpp ./CRF/CRF_1.0/util.cpp

###Using the code Check out the user_manual.pdf file!