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%Fraz provides a thorough literature review on retinal segmentation methods
@ARTICLE{Fraz2012,
  author = {Fraz, M.M. and Remagnino, P. and Hoppe, A. and Uyyanonvara, B. and
	Rudnicka, A.R. and Owen, C.G. and Barman, S.A.},
  title = {Blood vessel segmentation methodologies in retinal images – A survey},
  journal = {Computer methods and programs in biomedicine},
  year = {2012},
  volume = {108},
  pages = {407 -- 433},
  number = {1},
  month = {October},

}  url = {http://linkinghub.elsevier.com/retrieve/pii/S0169260712000843?showall=true}

@INPROCEEDINGS{niemeijer2004comparative,
  author = {Niemeijer, Meindert and Staal, Joes and van Ginneken, Bram and Loog,
	Marco and Abramoff, Michael D},
  title = {Comparative study of retinal vessel segmentation methods on a new
	publicly available database},
  booktitle = {Medical Imaging 2004},
  year = {2004},
  pages = {648--656},
  organization = {International Society for Optics and Photonics},
  url = {http://www.isi.uu.nl/Research/Databases/DRIVE}
}

@ARTICLE{siddalingaswamy2010automatic,
  author = {Siddalingaswamy, PC and Prabhu, K Gopalakrishna},
  title = {Automatic detection of multiple oriented blood vessels in retinal
	images},
  journal = {Journal of Biomedical Science and Engineering},
  year = {2010},
  volume = {3},
  pages = {101--107},
  number = {1}
}

@PHDTHESIS{SiddalingaswamyPhD2011,
  author = {Siddalingaswamy, P C},
  title = {Automatic detection of retinal features for screening of diabetic
	retinopathy using image processing techniques},
  school = {Manipal Institute of Technology},
  year = {2011},
  month = {September},
  url = {http://hdl.handle.net/10603/3095}
}
%survey of entropy thresholding
@INPROCEEDINGS{chang2006survey,
  author = {Chang, C-I and Du, Yingzi and Wang, J and Guo, S-M and Thouin, PD},
  title = {Survey and comparative analysis of entropy and relative entropy thresholding
	techniques},
  booktitle = {Vision, Image and Signal Processing, IEE Proceedings},
  year = {2006},
  volume = {153},
  number = {6},
  pages = {837--850},
  organization = {IET}
}
@ARTICLE{ng2006automatic,
  author = {Ng, Hui-Fuang},
  title = {Automatic thresholding for defect detection},
  journal = {Pattern recognition letters},
  year = {2006},
  volume = {27},
  pages = {1644--1649},
  number = {14},
  publisher = {Elsevier}
}

@article{otsu1975threshold,
  title={A threshold selection method from gray-level histograms},
  author={Otsu, Nobuyuki},
  journal={Automatica},
  volume={11},
  number={285-296},
  pages={23--27},
  year={1975}
}

@INPROCEEDINGS{HongQing2004,
  author = {HongQing, Zhu},
  title = {Segmentation of blood vessels in retinal images using 2D entropies
	of gray level-gradient cooccurrence matrix},
  booktitle = {Acoustics, Speech, and Signal Processing, 2004. Proceedings.(ICASSP'04).
	IEEE International Conference on},
  year = {2004},
  volume = {3},
  pages = {iii--509},
  organization = {IEEE}
}
@ARTICLE{pal1989object,
  author = {Pal, NR and Pal, Sankar K},
  title = {Object-background segmentation using new definitions of entropy},
  journal = {Computers and Digital Techniques, IEE Proceedings E},
  year = {1989},
  volume = {136},
  pages = {284--295},
  number = {4},
  publisher = {IET}
}

@ARTICLE{pal1989entropic,
  author = {Pal, Nikhil R and Pal, Sankar K},
  title = {Entropic thresholding},
  journal = {Signal processing},
  year = {1989},
  volume = {16},
  pages = {97--108},
  number = {2},
  publisher = {Elsevier}
}
@article{villalobos2010entropy,
year={2010},
issn={1343-8875},
journal={Journal of Visualization},
volume={13},
number={3},
doi={10.1007/s12650-010-0037-y},
title={A fast, efficient and automated method to extract vessels from fundus images},
url={http://dx.doi.org/10.1007/s12650-010-0037-y},
publisher={Springer-Verlag},
keywords={Retinal image analysis; Blood vessel network; Image segmentation; Fast automated analysis; Co-occurrence matrix; Entropy thresholding},
author={Villalobos-Castaldi, FabiolaM. and Felipe-Riverón, EdgardoM. and Sánchez-Fernández, LuisP.},
pages={263-270},
language={English}
}
@PHDTHESIS{chanwimaluang2006advanced,
  author = {Chanwimaluang, Thitiporn},
  title = {Advanced retinal imaging: feature extraction, 2-D registration, and
	3-D reconstruction},
  school = {Oklahoma State University},
  year = {2006}
}

@ARTICLE{chanwimaluang2006hybrid,
  author = {Chanwimaluang, Thitiporn and Fan, Guoliang and Fransen, Stephen R},
  title = {Hybrid retinal image registration},
  journal = {Information Technology in Biomedicine, IEEE Transactions on},
  year = {2006},
  volume = {10},
  pages = {129--142},
  number = {1},
  publisher = {IEEE}
}

@ARTICLE{daugman1980two,
  author = {Daugman, John G},
  title = {Two-dimensional spectral analysis of cortical receptive field profiles},
  journal = {Vision research},
  year = {1980},
  volume = {20},
  pages = {847--856},
  number = {10},
  publisher = {Elsevier}
}

@ARTICLE{daugman1985uncertainty,
  author = {Daugman, John G and others},
  title = {Uncertainty relation for resolution in space, spatial frequency,
	and orientation optimized by two-dimensional visual cortical filters},
  journal = {Optical Society of America, Journal, A: Optics and Image Science},
  year = {1985},
  volume = {2},
  pages = {1160--1169},
  number = {7}
}
%cite for similarity of gabor filter to human visual system
@ARTICLE{daugman1988,
author={Daugman, J.G.},
journal={Acoustics, Speech and Signal Processing, IEEE Transactions on},
title={Complete discrete 2-D Gabor transforms by neural networks for image analysis and compression},
year={1988},
volume={36},
number={7},
pages={1169-1179},
doi={10.1109/29.1644},
ISSN={0096-3518}
}

@ARTICLE{gabor1946theory,
  author = {Gabor, Dennis},
  title = {Theory of communication. Part 1: The analysis of information},
  journal = {Electrical Engineers-Part III: Radio and Communication Engineering,
	Journal of the Institution of},
  year = {1946},
  volume = {93},
  pages = {429--441},
  number = {26},
  publisher = {IET}
}
@inproceedings{li2006gabormultiscale,
  title={A multiscale approach to retinal vessel segmentation using Gabor filters and scale multiplication},
  author={Li, Qin and You, Jane and Zhang, Lei and Bhattacharya, Prabir},
  booktitle={Systems, Man and Cybernetics, 2006. SMC'06. IEEE International Conference on},
  volume={4},
  pages={3521--3527},
  year={2006},
  organization={IEEE}
}
%12 angles and 3 wavelengths
@article{osareh2009gabor,
  title={Automatic blood vessel segmentation in color images of retina},
  author={Osareh, A and Shadgar, B},
  journal={Iran. J. Sci. Technol. Trans. B: Engineering},
  volume={33},
  number={B2},
  pages={191--206},
  year={2009}
}
%useful for citing orientation and wavelength gabor filter bank
@INPROCEEDINGS{bhuiyan2007gabor,
author={Bhuiyan, A. and Nath, B. and Chua, J. and Kotagiri, R.},
booktitle={Image Processing, 2007. ICIP 2007. IEEE International Conference on},
title={Blood Vessel Segmentation from Color Retinal Images using Unsupervised Texture Classification},
year={2007},
volume={5},
pages={V - 521-V - 524},
doi={10.1109/ICIP.2007.4379880},
ISSN={1522-4880}
}
%adaptive contrast enhancement, uses standard deviation of gabor->applicable to normalization
@ARTICLE{wu2006gabor,
author={Wu, D. and Ming Zhang and Jyh-Charn Liu and Bauman, W.},
journal={Biomedical Engineering, IEEE Transactions on},
title={On the adaptive detection of blood vessels in retinal images},
year={2006},
volume={53},
number={2},
pages={341-343},
doi={10.1109/TBME.2005.862571},
ISSN={0018-9294},}
%citable for standard normalized gabor equation. ***A must read.
@INPROCEEDINGS{rangayyan2007gabor,
author={Rangayyan, R.M. and Oloumi, F. and Oloumi, F. and Eshghzadeh-Zanjani, P. and Ayres, F.J.},
booktitle={Electrical and Computer Engineering, 2007. CCECE 2007. Canadian Conference on},
title={Detection of Blood Vessels in the Retina Using Gabor Filters},
year={2007},
pages={717-720},
doi={10.1109/CCECE.2007.184},
ISSN={0840-7789},}
%citable for alternative standard normalized gabor equation.
@article{Kyrki2004gabor,
  title={Simple Gabor feature space for invariant object recognition},
  author={Kyrki, Ville and Kamarainen, Joni-Kristian and K{\"a}lvi{\"a}inen, Heikki},
  journal={Pattern Recognition Letters},
  volume={25},
  number={3},
  pages={311--318},
  year={2004},
  publisher={Elsevier},
issn = {0167-8655},
doi = {http://dx.doi.org/10.1016/j.patrec.2003.10.008}
}url = {http://www.sciencedirect.com/science/article/pii/S0167865503002307}

@ARTICLE{wang2005gabor,
  author = {Wang, Xuewen and Ding, Xiaoqing and Liu, Changsong},
  title = {Gabor filters-based feature extraction for character recognition},
  journal = {Pattern recognition},
  year = {2005},
  volume = {38},
  pages = {369--379},
  number = {3},
  publisher = {Elsevier}
}
%Petkov is useful for citing gabor normalization, talks about divisive normalization in page 12.
@ARTICLE{PetkovSubramanian2007motion,
  author = {N. Petkov and E. Subramanian},
  title = {Motion detection, noise reduction, texture suppression and contour
	enhancement by spatiotemporal Gabor filters with surround inhibition},
  journal = {Biological Cybernetics},
  year = {2007},
  volume = {97},
  pages = {423--439},
  number = {5--6},
  doi = {10.1007/s00422-007-0182-0},

}url = {http://www.cs.rug.nl/~imaging/spatiotemporal_Gabor_function/GaborApp.html}
%Azzopardi is useful for verbatim citing gabor normalization, uses filter bank
@ARTICLE{azzopardi2013trainable,
author={Azzopardi, G. and Petkov, N.},
journal={Pattern Analysis and Machine Intelligence, IEEE Transactions on},
title={Trainable COSFIRE Filters for Keypoint Detection and Pattern Recognition},
year={2013},
volume={35},
number={2},
pages={490--503},
doi={10.1109/TPAMI.2012.106},
ISSN={0162-8828}
}url={http://www.mathworks.com/matlabcentral/fileexchange/37395-trainable-cosfire-filters-for-keypoint-detection-and-pattern-recognition/content/COSFIRE_MatlabCode/Gabor/gaborkernel2d.m}
@inproceedings{azzopardi2011detection,
  title={Detection of retinal vascular bifurcations by trainable V4-like filters},
  author={Azzopardi, George and Petkov, Nicolai},
  booktitle={Computer Analysis of Images and Patterns},
  pages={451--459},
  year={2011},
  organization={Springer}
}
%Hursig speaks about gabor normalization
@ARTICLE{hursig2011lip,
  author = {Hursig, Robert E and Zhang, Jane Xiaozheng and Kam, Chiweng},
  title = {Lip Localization Algorithm Using Gabor Filters},
  year = {2011}
}
%localized divisive normalization, page 17.
@phdthesis{stevens2010divnorm,
  title={An analysis of grating cell features for texture discrimination},
  author={Stevens, John},
  year={2010},
  school={Colorado State University}
}
%cited by petkov for divisive normalization
@article{heeger1993divnorm,
  title={Modeling simple-cell direction selectivity with normalized, half-squared, linear operators},
  author={Heeger, David J},
  journal={Journal of Neurophysiology},
  volume={70},
  number={5},
  pages={1885--1898},
  year={1993},
  publisher={Am Physiological Soc}
}
@MISC{hall2007glcm,
  author = {Hall-Beyer, Mryka},
  title = {Glcm texture tutorial, 2007},
  year = {2007}
}

@ARTICLE{haralick1973textural,
  author = {Haralick, Robert M and Shanmugam, Karthikeyan and Dinstein, Its'
	Hak},
  title = {Textural features for image classification},
  journal = {Systems, Man and Cybernetics, IEEE Transactions on},
  year = {1973},
  pages = {610--621},
  number = {6},
  publisher = {IEEE}
}

@ARTICLE{henriksen2007tracking,
  author = {Henriksen, Jesper Juul},
  title = {3D surface tracking and approximation using Gabor filters},
  journal = {South Denmark University (March 28, 2007)},
  year = {2007}
}
@article{yin2012tracking,
  title={Retinal vessel segmentation using a probabilistic tracking method},
  author={Yin, Yi and Adel, Mouloud and Bourennane, Salah},
  journal={Pattern Recognition},
  volume={45},
  number={4},
  pages={1235--1244},
  year={2012},
  publisher={Elsevier}
}


%Hildebrand has useful retina facts for citing
@INCOLLECTION{hildebrand2011anatomy,
  author = {Hildebrand, G{\"o}ran Darius and Fielder, Alistair R},
  title = {Anatomy and Physiology of the Retina},
  booktitle = {Pediatric retina},
  publisher = {Springer},
  year = {2011},
  pages = {39--65}
}

@MISC{kolb2005,
  author = {Helga Kolb},
  title = {Simple Anatomy of the Retina Helga Kolb},
  month = {May},
  year = {2005},
  url = {http://www.ncbi.nlm.nih.gov/books/NBK11533/}
}

@book{polyak1941,
author={Polyak, SL},
title={The retina},
year={1941},  
publisher={University of Chicago Press}
}
@article{von1924,
  title={Illumination of the eye and the ophthalmoscope},
  journal={Helmholtz's treatise on physiological optics},
  author={von Helmholtz, Hermann and Southall, James PC},
  volume={1},
  pages={226--260},
  year={1924},
  doi={10.1037/13536-016},
  publisher={Optical Society of America}
}
@article{scheider1992,
  title={Detection of subretinal neovascular membranes with indocyanine green and an infrared scanning laser ophthalmoscope},
  author={Scheider, A and Kaboth, A and Neuhauser, L},
  journal={American journal of ophthalmology},
  volume={113},
  number={1},
  pages={45--51},
  year={1992}
}
@article{manivannan1993digital,
  title={Digital fundus imaging using a scanning laser ophthalmoscope},
  author={Manivannan, Ayyakkannu and Sharp, PF},
  journal={Physiological measurement},
  volume={14},
  number={1},
  pages={43},
  year={1993},
  publisher={IOP Publishing}
}
%review of retinal imaging methods from a clinical perspective 
@ARTICLE{abramoff2010retinalImaging,
author={Abramoff, M.D. and Garvin, M.K. and Sonka, M.},
journal={Biomedical Engineering, IEEE Reviews in},
title={Retinal Imaging and Image Analysis},
year={2010},
volume={3},
pages={169-208},
ISSN={1937-3333},}

@article{patton2006retinalImaging,
  title={Retinal image analysis: concepts, applications and potential},
  author={Patton, Niall and Aslam, Tariq M and MacGillivray, Thomas and Deary, Ian J and Dhillon, Baljean and Eikelboom, Robert H and Yogesan, Kanagasingam and Constable, Ian J},
  journal={Progress in retinal and eye research},
  volume={25},
  number={1},
  pages={99--127},
  year={2006},
  publisher={Elsevier}
}
%matched filters
%suggest normalization by subtracting local mean and diving by square root of local variance.
@article{chaudhuri1989matched,
  title={Detection of blood vessels in retinal images using two-dimensional matched filters},
  author={Chaudhuri, Subhasis and Chatterjee, Shankar and Katz, Norman and Nelson, Mark and Goldbaum, Michael},
  journal={IEEE Transactions on medical imaging},
  volume={8},
  number={3},
  pages={263--269},
  year={1989},
  publisher={Institute of Electrical and Electronic Engineers}
}
@article{zhang2010retinal,
  title={Retinal vessel extraction by matched filter with first-order derivative of Gaussian},
  author={Zhang, Bob and Zhang, Lin and Zhang, Lei and Karray, Fakhri},
  journal={Computers in biology and medicine},
  volume={40},
  number={4},
  pages={438--445},
  year={2010},
  publisher={Elsevier}
}
%also ref for STARE database
@article{hoover2000matched,
        AUTHOR = {Hoover, A.D. and Kouznetsova, V. and Goldbaum, M.},
        TITLE = {Locating blood vessels in retinal images by piecewise threshold probing
of a matched filter response},
        JOURNAL = {MedImg},
        VOLUME = {19},
        YEAR = {2000},
        NUMBER = {3},
        MONTH = {March},
        PAGES = {203--210},
        BIBSOURCE = {http://www.visionbib.com/bibliography/medical854v1.html#TT110926}
}
@article{odstrcilik2013matched,
        AUTHOR = {Odstrcilik, J. and Kolar, R. and Budai, A. and Hornegger, J. and Jan, J. and Gazarek, J. and Kubena, T. and Cernosek, P. and Svoboda, O. and Angelopoulou, E.},
        TITLE = {Retinal vessel segmentation by improved matched filtering: evaluation
on a new high-resolution fundus image database},
        JOURNAL = {IET-PR},
        VOLUME = {7},
        YEAR = {2013},
        NUMBER = {4},
        BIBSOURCE = {http://www.visionbib.com/bibliography/medical854v1.html#TT110991}
}
%hessian matric is an alternative to matched filters
@article{sofka2006matched,
  title={Retinal vessel centerline extraction using multiscale matched filters, confidence and edge measures},
  author={Sofka, Michal and Stewart, Charles V},
  journal={Medical Imaging, IEEE Transactions on},
  volume={25},
  number={12},
  pages={1531--1546},
  year={2006},
  publisher={IEEE}
}
@article{alrawi2007matched,
author = {Mohammed Al-Rawi and Munib Qutaishat and Mohammed Arrar},
title = {An improved matched filter for blood vessel detection of digital retinal images},
journal = {Computers in Biology and Medicine},
volume = {37},
number = {2},
pages = {262 - 267},
year = {2007},
issn = {0010-4825},
doi = {http://dx.doi.org/10.1016/j.compbiomed.2006.03.003}
}url = {http://www.sciencedirect.com/science/article/pii/S0010482506000424}
@ARTICLE{rahebi2013combination,
  author = {Rahebi, Javad and Hardala{\c{c}}, F{\i}rat},
  title = {Combination of Matched Filter and Gabor Filter for Retinal Vessel
	Extraction},
  journal = {Life Science Journal},
  year = {2013},
  volume = {10},
  number = {6s}
}

%line operators
@ARTICLE{ricci2007retinal,
  author = {Ricci, Elisa and Perfetti, Renzo},
  title = {Retinal blood vessel segmentation using line operators and support
	vector classification},
  journal = {Medical Imaging, IEEE Transactions on},
  year = {2007},
  volume = {26},
  pages = {1357--1365},
  number = {10},
  publisher = {IEEE}
}
@article{Nguyen2013multiline,
title = {An effective retinal blood vessel segmentation method using multi-scale line detection},
journal = {Pattern Recognition},
volume = {46},
number = {3},
pages = {703 -- 715},
year = {2013},
issn = {0031-3203},
doi = {http://dx.doi.org/10.1016/j.patcog.2012.08.009},
url = {http://www.sciencedirect.com/science/article/pii/S003132031200355X},
author = {Uyen T.V. Nguyen and Alauddin Bhuiyan and Laurence A.F. Park and Kotagiri Ramamohanarao}
}

@ARTICLE{staal2004ridge,
  author = {Staal, Joes and Abr{\`a}moff, Michael D and Niemeijer, Meindert and
	Viergever, Max A and van Ginneken, Bram},
  title = {Ridge-based vessel segmentation in color images of the retina},
  journal = {Medical Imaging, IEEE Transactions on},
  year = {2004},
  volume = {23},
  pages = {501--509},
  number = {4},
  publisher = {IEEE}
}
%connected components
@ARTICLE{walczyk2010comparative,
  author = {Walczyk, Robert and Armitage, Alistair and Binnie, David},
  title = {Comparative study on connected component labeling algorithms for
	embedded video processing systems.},
  year = {2010},
  publisher = {CSREA Press}
}

%local binary patterns
@INPROCEEDINGS{zabihi2010,
  author = {Zabihi, S.M. and Delgir, M. and Pourreza, H.-R.},
  title = {Retinal vessel segmentation using color image morphology and local
	binary patterns},
  booktitle = {Machine Vision and Image Processing (MVIP), 2010 6th Iranian},
  year = {2010},
  pages = {1-5},
  doi = {10.1109/IranianMVIP.2010.5941129}
}

%neural
@article{nekovei1995back,
  title={Back-propagation network and its configuration for blood vessel detection in angiograms},
  author={Nekovei, Reza and Sun, Ying},
  journal={Neural Networks, IEEE Transactions on},
  volume={6},
  number={1},
  pages={64--72},
  year={1995},
  publisher={IEEE}
}
%Unsupervised
@article{salem2007racal,
  title={Segmentation of retinal blood vessels using a novel clustering algorithm (RACAL) with a partial supervision strategy},
  author={Salem, Sameh A and Salem, Nancy M and Nandi, Asoke K},
  journal={Medical \& biological engineering \& computing},
  volume={45},
  number={3},
  pages={261--273},
  year={2007},
  publisher={Springer}
}
@inproceedings{salem2007hessian,
  title={Segmentation of retinal blood vessels based on analysis of the Hessian matrix and clustering algorithm},
  author={Salem, N and Salem, S and Nandi, A},
  booktitle={15th European Signal Processing Conference},
  pages={428--432},
  year={2007}
}
@ARTICLE{tolias1998fuzzycmeans,
author={Tolias, Y.A. and Panas, S.M.},
journal={Medical Imaging, IEEE Transactions on},
title={A fuzzy vessel tracking algorithm for retinal images based on fuzzy clustering},
year={1998},
volume={17},
number={2},
pages={263-273},
doi={10.1109/42.700738},
ISSN={0278-0062}
}

@article{kande2010fuzzy,
year={2010},
issn={0148-5598},
journal={Journal of Medical Systems},
volume={34},
number={5},
doi={10.1007/s10916-009-9299-0},
title={Unsupervised Fuzzy Based Vessel Segmentation In Pathological Digital Fundus Images},
url={http://dx.doi.org/10.1007/s10916-009-9299-0},
publisher={Springer US},
keywords={Fundus; Histogram matching; Matched filter; Retina},
author={Kande, GiriBabu and Subbaiah, P.Venkata and Savithri, T.Satya},
pages={849-858},
language={English}
}

%information retrieval
@BOOK{Manning:2008:IIR:1394399,
  title = {Introduction to Information Retrieval},
  publisher = {Cambridge University Press},
  year = {2008},
  author = {Manning, Christopher D. and Raghavan, Prabhakar and Sch\"{u}tze,
	Hinrich},
  address = {New York, NY, USA},
  isbn = {0521865719, 9780521865715}
}

@inproceedings{brahimi1998lossless,
  title={A lossless image compression algorithm using variable block size segmentation},
  author={Brahimi, Zahia and Saadi, KA and Baraka, N},
  year={1998},
  booktitle={Industrial Electronics Society, 1998. IECON'98. Proceedings of the 24th Annual Conference of the IEEE},
  volume={3},
  pages={1471--1476},
  organization={IEEE}
}

@misc{NikolicGabArea,
  title = {Calculating the area under a two-dimensional gaussian},
  author = {Nikolic, B. },
  url={http://www.mrao.cam.ac.uk/~bn204/_downloads/twodgaussian.pdf},
}

@article{mendonca2006segmentation,
  title={Segmentation of retinal blood vessels by combining the detection of centerlines and morphological reconstruction},
  author={Mendonca, Ana Maria and Campilho, Aurelio},
  journal={Medical Imaging, IEEE Transactions on},
  volume={25},
  number={9},
  pages={1200--1213},
  year={2006},
  publisher={IEEE}
}

