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@article{doi:10.1080/10255840903131878,
title = {{A review of algorithms for medical image segmentation and their applications to the female pelvic cavity}},
year = {2010},
journal = {Computer Methods in Biomechanics and Biomedical Engineering},
author = {Ma, Zhen and Tavares, João Manuel R S and Jorge, Renato Natal and Mascarenhas, T},
number = {2},
pages = {235--246},
volume = {13},
publisher = {Taylor {\&} Francis},
url = {https://doi.org/10.1080/10255840903131878},
doi = {10.1080/10255840903131878}
}
@article{doi:10.1146/annurev.bioeng.2.1.315,
title = {{Current Methods in Medical Image Segmentation}},
year = {2000},
journal = {Annual Review of Biomedical Engineering},
author = {Pham, Dzung L and Xu, Chenyang and Prince, Jerry L},
number = {1},
pages = {315--337},
volume = {2},
url = {https://doi.org/10.1146/annurev.bioeng.2.1.315},
doi = {10.1146/annurev.bioeng.2.1.315}
}
@article{Kronlage2017,
title = {{Large coverage MR neurography in CIDP: diagnostic accuracy and electrophysiological correlation}},
year = {2017},
journal = {Journal of Neurology},
author = {Kronlage, Moritz and B{\"{a}}umer, Philipp and Pitarokoili, Kalliopi and Schwarz, Daniel and Schwehr, Véronique and Godel, Tim and Heiland, Sabine and Gold, Ralf and Bendszus, Martin and Yoon, Min-Suk},
number = {7},
month = {7},
pages = {1434--1443},
volume = {264},
url = {https://doi.org/10.1007/s00415-017-8543-7},
doi = {10.1007/s00415-017-8543-7},
issn = {1432-1459}
}
@article{Mohassel2015,
title = {{Neurophysiology simplified for imagers}},
year = {2015},
journal = {Seminars in Musculoskeletal Radiology},
author = {Mohassel, Payam and Chaudhry, Vinay},
number = {2},
pages = {112--120},
volume = {19},
doi = {10.1055/s-0035-1545075},
issn = {1098898X},
keywords = {electromyography, myopathy, nerve conduction study, neuromuscular disease, neuropathy}
}
@article{Hughes466,
title = {{Peripheral neuropathy}},
year = {2002},
journal = {BMJ},
author = {Hughes, Richard A C},
number = {7335},
pages = {466--469},
volume = {324},
publisher = {BMJ Publishing Group Ltd},
url = {https://www.bmj.com/content/324/7335/466},
doi = {10.1136/bmj.324.7335.466},
issn = {0959-8138}
}
@article{scikit-image,
title = {{scikit-image: image processing in Python}},
year = {2014},
journal = {PeerJ},
author = {van der Walt, Stéfan and Sch{\"{o}}nberger, Johannes L. and Nunez-Iglesias, Juan and Boulogne, François and Warner, Joshua D. and Yager, Neil and Gouillart, Emmanuelle and Yu, Tony},
pages = {e453},
volume = {2},
url = {https://peerj.com/articles/453},
isbn = {2167-9843},
doi = {10.7717/peerj.453},
issn = {2167-8359},
pmid = {25024921},
arxivId = {1407.6245},
keywords = {Education, Image processing, Open source, Python, Reproducible research, Scientific programming, Visualization}
}
@article{Marr187,
title = {{Theory of edge detection}},
year = {1980},
journal = {Proceedings of the Royal Society of London - Biological Sciences},
author = {Marr, D. and Hildreth, E.},
number = {1167},
pages = {187--217},
volume = {207},
publisher = {The Royal Society},
url = {http://rspb.royalsocietypublishing.org/content/207/1167/187},
isbn = {0962-8452},
doi = {10.1098/rspb.1980.0020},
issn = {09628452},
pmid = {6102765},
arxivId = {arXiv:1011.1669v3}
}
@article{py06nimg,
title = {{user.guide 3 D active contour segmentation of anatomical structures: significantly imprved efficiency and reliability}},
year = {2006},
journal = {neuroImage},
author = {Yushkevich, PA; Piven J; Hazlett HC; Smith RG; Ho S, Gee JC; Gerig G},
number = {3},
pages = {2006},
volume = {31},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=16545965&retmode=ref&cmd=prlinks%5Cnpapers3://publication/doi/10.1016/j.neuroimage.2006.01.015},
doi = {http://dx.doi.org/10.1016/j.neuroimage.2006.01.015},
issn = {1053-8119}
}
@article{Cicek20163DAnnotation,
title = {{3D U-net: Learning dense volumetric segmentation from sparse annotation}},
year = {2016},
journal = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
author = {Cicek, Ozgun and Abdulkadir, Ahmed and Lienkamp, Soeren S. and Brox, Thomas and Ronneberger, Olaf},
month = {6},
pages = {424--432},
volume = {9901 LNCS},
url = {http://arxiv.org/abs/1606.06650},
isbn = {9783319467221},
doi = {10.1007/978-3-319-46723-8{\_}49},
issn = {16113349},
pmid = {17348934},
arxivId = {1606.06650},
keywords = {3D, Biomedical volumetric image segmentation, Convolutional neural networks, Fully-automated, Semi-automated, Sparse annotation, Xenopus kidney}
}
@article{BaxterJONATHANBAXTER2000ALearning,
title = {{A Model of Inductive Bias Learning}},
year = {2000},
journal = {Journal of Artificial Intelligence Research},
author = {Baxter JONATHANBAXTER, Jonathan},
pages = {149--198},
volume = {12}
}
@article{Dijkstra1959AGraphs,
title = {{A note on two problems in connexion with graphs}},
year = {1959},
journal = {Numerische Mathematik},
author = {Dijkstra, E. W.},
number = {1},
pages = {269--271},
volume = {1},
isbn = {0029-599X (Print) 0945-3245 (Online)},
doi = {10.1007/BF01386390},
issn = {0029599X},
pmid = {18215627}
}
@article{Lesage2009ASchemes,
title = {{A review of 3D vessel lumen segmentation techniques: Models, features and extraction schemes}},
year = {2009},
journal = {Medical Image Analysis},
author = {Lesage, David and Angelini, Elsa D and Bloch, Isabelle and Funka-Lea, Gareth},
number = {6},
month = {12},
pages = {819--845},
volume = {13},
publisher = {Elsevier},
url = {https://doi.org/10.1016/j.media.2009.07.011},
doi = {10.1016/j.media.2009.07.011},
issn = {1361-8415}
}
@article{Litjens2017AAnalysis,
title = {{A survey on deep learning in medical image analysis}},
year = {2017},
author = {Litjens, Geert and Kooi, Thijs and Bejnordi, Babak Ehteshami and Arindra, Arnaud and Setio, Adiyoso and Ciompi, Francesco and Ghafoorian, Mohsen and Laak, Jeroen A W M Van Der and Ginneken, Bram Van and S{\'{a}}nchez, Clara I},
number = {December 2012},
pages = {60--88},
volume = {42},
doi = {10.1016/j.media.2017.07.005},
arxivId = {1702.05747},
keywords = {Convolutional neural networks, Deep learning, Medica}
}
@article{BudaANetworks,
title = {{A systematic study of the class imbalance problem in convolutional neural networks}},
author = {Buda, Mateusz and Maki, Atsuto and Mazurowski, Maciej A},
keywords = {Class Imbalance, Convolutional Neural Networks, Deep Learning, Image Classification}
}
@article{Srinivas2016AVision,
title = {{A Taxonomy of Deep Convolutional Neural Nets for Computer Vision}},
year = {2016},
author = {Srinivas, Suraj and Sarvadevabhatla, Ravi Kiran and Mopuri, Konda Reddy and Prabhu, Nikita and Kruthiventi, Srinivas S S and Babu, R. Venkatesh},
url = {http://arxiv.org/abs/1601.06615%0Ahttp://dx.doi.org/10.3389/frobt.2015.00036},
isbn = {2296-9144},
doi = {10.3389/frobt.2015.00036},
issn = {2296-9144},
arxivId = {1601.06615}
}
@article{Kingma2014Adam:Optimization,
title = {{Adam: A Method for Stochastic Optimization}},
year = {2014},
author = {Kingma, Diederik P. and Ba, Jimmy},
pages = {1--15},
url = {http://arxiv.org/abs/1412.6980},
isbn = {9781450300728},
doi = {http://doi.acm.org.ezproxy.lib.ucf.edu/10.1145/1830483.1830503},
issn = {09252312},
pmid = {172668},
arxivId = {1412.6980}
}
@article{Baumgartner2017AnSegmentation,
title = {{An Exploration of 2D and 3D Deep Learning Techniques for Cardiac MR Image Segmentation}},
year = {2017},
author = {Baumgartner, Christian F. and Koch, Lisa M. and Pollefeys, Marc and Konukoglu, Ender},
pages = {1--8},
url = {http://arxiv.org/abs/1709.04496},
isbn = {9783319755410},
doi = {10.1007/978-3-319-75541-0},
arxivId = {1709.04496}
}
@article{Sobel1990AnOperator,
title = {{An isotropic 3x3 gradient operator}},
year = {1990},
journal = {Machine Vision for Three-Dimensional Scenes},
author = {Sobel, I},
number = {June},
pages = {376--379}
}
@article{Noble1998AnalysisInjuries,
title = {{Analysis of Upper and Lower Extremity Peripheral Nerve Injuries in a Population of Patients with Multiple Injuries}},
year = {1998},
journal = {Journal of Trauma and Acute Care Surgery},
author = {Noble, James and Munro, Catherine A and Prasad, Vannemreddy S S V and Midha, Rajiv},
number = {1},
volume = {45},
url = {https://journals.lww.com/jtrauma/Fulltext/1998/07000/Analysis_of_Upper_and_Lower_Extremity_Peripheral.25.aspx},
issn = {2163-0755}
}
@article{Oktay2018AnatomicallySegmentation,
title = {{Anatomically Constrained Neural Networks (ACNNs): Application to Cardiac Image Enhancement and Segmentation}},
year = {2018},
journal = {IEEE Transactions on Medical Imaging},
author = {Oktay, Ozan and Ferrante, Enzo and Kamnitsas, Konstantinos and Heinrich, Mattias and Bai, Wenjia and Caballero, Jose and Cook, Stuart A. and De Marvao, Antonio and Dawes, Timothy and O'Regan, Declan P. and Kainz, Bernhard and Glocker, Ben and Rueckert, Daniel},
number = {2},
pages = {384--395},
volume = {37},
isbn = {1558-254X (Electronic) 0278-0062 (Linking)},
doi = {10.1109/TMI.2017.2743464},
issn = {1558254X},
pmid = {28961105},
arxivId = {1705.08302},
keywords = {Shape prior, convolutional neural network, image super-resolution, medical image segmentation}
}
@article{Ambellan2018AutomatedInitiative,
title = {{Automated Segmentation of Knee Bone and Cartilage combining Statistical Shape Knowledge and Convolutional Neural Networks, Data from the Osteoarthritis Initiative}},
year = {2018},
journal = {1st Conference on Medical Imaging with Deep Learning},
author = {Ambellan, Felix and Tack, Alexander and Ehlke, Moritz and Zachow, Stefan},
number = {Midl},
pages = {1--10}
}
@article{Wang2017AutomaticNetworks,
title = {{Automatic Brain Tumor Segmentation using Cascaded Anisotropic Convolutional Neural Networks}},
year = {2017},
author = {Wang, Guotai and Li, Wenqi and Ourselin, Sebastien and Vercauteren, Tom},
pages = {1--12},
url = {http://arxiv.org/abs/1709.00382%0Ahttp://dx.doi.org/10.1007/978-3-319-75238-9_16},
isbn = {978-3-319-75238-9},
doi = {10.1007/978-3-319-75238-9{\_}16},
arxivId = {1709.00382},
keywords = {brain tumor, convolutional neural network, segmentation}
}
@article{SergeyIoffe2015BatchNormalization,
title = {{Batch Normalization}},
year = {2015},
journal = {Icml},
author = {Sergey Ioffe, Google and Christian Szegedy, Google},
number = {2},
pages = {137--141},
volume = {22},
url = {https://arxiv.org/pdf/1502.03167.pdf},
isbn = {9780874216561},
doi = {10.1007/s13398-014-0173-7.2},
issn = {10282092},
pmid = {15003161},
arxivId = {arXiv:1011.1669v3},
keywords = {Blechnaceae, Indonesia, New species, Stenochlaena}
}
@article{Navab2015BeyondNetwork,
title = {{Beyond Classification: Structured Regression for Robust Cell Detection Using Convolutional Neural Network}},
year = {2015},
journal = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
author = {Navab, Nassir and Hornegger, Joachim and Wells, William M. and Frangi, Alejandro F.},
pages = {358--365},
volume = {9351},
isbn = {9783319245737},
doi = {10.1007/978-3-319-24574-4},
issn = {16113349},
pmid = {23285570},
arxivId = {1505.04597}
}
@article{Kayalibay2017CNN-basedData,
title = {{CNN-based Segmentation of Medical Imaging Data}},
year = {2017},
author = {Kayalibay, Baris and Jensen, Grady and van der Smagt, Patrick},
url = {http://arxiv.org/abs/1701.03056},
arxivId = {1701.03056}
}
@article{Huttenlocher1993ComparingDistance,
title = {{Comparing Images Using the Hausdorff Distance}},
year = {1993},
journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
author = {Huttenlocher, Daniel P. and Klanderman, Gregory A. and Rucklidge, William J.},
number = {9},
pages = {850--863},
volume = {15},
isbn = {0162-8828 {\%}(},
doi = {10.1109/34.232073},
issn = {01628828},
keywords = {Distance transforms, Voronoi surface, model-based recognition}
}
@article{BalsigerContext-awareNeurography,
title = {{Context-aware Segmentation of Peripheral Nerves from Magnetic Resonance Neurography}},
author = {Balsiger, Fabian and Steindel, Carolin and El-koussy, Marwan and Arn, Mirjam and Valenzuela, Waldo and Reyes, Mauricio and Wagner, Benedikt and Scheidegger, Olivier},
number = {Midl 2018},
pages = {1--8}
}
@article{Ohana2014CurrentSystem,
title = {{Current and future imaging of the peripheral nervous system}},
year = {2014},
journal = {Diagnostic and Interventional Imaging},
author = {Ohana, M. and Moser, T. and Moussaou{\"{i}}, A. and Kremer, S. and Carlier, R. Y. and Liverneaux, P. and Dietemann, J. L.},
number = {1},
pages = {17--26},
volume = {95},
publisher = {Elsevier Masson SAS},
url = {http://dx.doi.org/10.1016/j.diii.2013.05.008},
isbn = {2211-5684 (Electronic)},
doi = {10.1016/j.diii.2013.05.008},
issn = {22115714},
pmid = {24144933},
keywords = {MRI, Neurography, Peripheral nervoussystem, Ultrasound}
}
@article{Prasoon2013DeepNetwork,
title = {{Deep Feature Learning for Knee Cartilage Segmentation Using a Triplanar Convolution Neural Network}},
year = {2013},
journal = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
author = {Prasoon, Adhish and Al., Et},
number = {PART 2},
pages = {599--606},
volume = {8150},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84885902026&partnerID=tZOtx3y1},
isbn = {978-3-642-40762-8},
doi = {10.1007/978-3-642-40763-5},
issn = {03029743},
pmid = {24505717}
}
@article{Lecun2015DeepLearning,
title = {{Deep learning}},
year = {2015},
journal = {Nature},
author = {Lecun, Yann and Bengio, Yoshua and Hinton, Geoffrey},
number = {7553},
pages = {436--444},
volume = {521},
isbn = {9780521835688},
doi = {10.1038/nature14539},
issn = {14764687},
pmid = {10463930},
arxivId = {arXiv:1312.6184v5}
}
@book{Goodfellow2016DeepLearning,
title = {{Deep Learning}},
year = {2016},
booktitle = {MIT Press},
author = {Goodfellow, Ian and Yoshua, Bengio and Aaron, Courville},
isbn = {9780262337434},
doi = {10.1142/S1793351X16500045},
issn = {1793-351X},
pmid = {10463930},
arxivId = {arXiv:1312.6184v5}
}
@article{Moeskops2017DeepModalities,
title = {{Deep Learning for Multi-Task Medical Image Segmentation in Multiple Modalities}},
year = {2017},
author = {Moeskops, Pim and Wolterink, Jelmer M. and van der Velden, Bas H. M. and Gilhuijs, Kenneth G. A. and Leiner, Tim and Viergever, Max A. and I{\v{s}}gum, Ivana},
number = {October},
pages = {478--486},
url = {http://arxiv.org/abs/1704.03379%0Ahttp://dx.doi.org/10.1007/978-3-319-46723-8_55},
isbn = {978-3-319-46723-8},
doi = {10.1007/978-3-319-46723-8{\_}55},
issn = {16113349 03029743},
pmid = {17348934},
arxivId = {1704.03379},
keywords = {age segmentation, brain mri, breast mri, cardiac cta, convolutional neural networks, deep learning, medical im-}
}
@article{WestonDeepEmbedding,
title = {{Deep Learning via Semi-Supervised Embedding}},
author = {Weston, Jason and Ratle, Frédéric and Mobahi, Hossein and Collobert, Ronan},
keywords = {deep learning, embedding, semi-supervised learning}
}
@article{Atzori2016DeepHands,
title = {{Deep learning with convolutional neural networks applied to electromyography data: A resource for the classification of movements for prosthetic hands}},
year = {2016},
journal = {Frontiers in Neurorobotics},
author = {Atzori, Manfredo and Cognolato, Matteo and M{\"{u}}ller, Henning},
number = {SEP},
pages = {1--10},
volume = {10},
doi = {10.3389/fnbot.2016.00009},
issn = {16625218},
pmid = {27656140},
arxivId = {1406.1231},
keywords = {Convolutional neural networks, Deep learning, Electromyography, Machine learning, Prosthetics, Rehabilitation robotics}
}
@article{He2015DeepRecognition,
title = {{Deep Residual Learning for Image Recognition}},
year = {2015},
author = {He, Kaiming and Zhang, Xiangyu and Ren, Shaoqing and Sun, Jian},
url = {http://arxiv.org/abs/1512.03385},
isbn = {978-1-4673-6964-0},
doi = {10.3389/fpsyg.2013.00124},
issn = {1664-1078},
pmid = {23554596},
arxivId = {1512.03385}
}
@incollection{Roth2015Deeporgan:Segmentation,
title = {{Deeporgan: Multi-level deep convolutional networks for automated pancreas segmentation}},
year = {2015},
booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
author = {Roth, Holger R. and Lu, Le and Farag, Amal and Shin, Hoo Chang and Liu, Jiamin and Turkbey, Evrim B. and Summers, Ronald M.},
isbn = {978-3-319-24552-2},
doi = {10.1007/978-3-319-24553-9{\_}68},
issn = {16113349},
pmid = {23285570},
arxivId = {1506.06448}
}
@article{Tetteh2018DeepVesselNet:Volumes,
title = {{DeepVesselNet: Vessel Segmentation, Centerline Prediction, and Bifurcation Detection in 3-D Angiographic Volumes}},
year = {2018},
author = {Tetteh, Giles and Efremov, Velizar and Forkert, Nils D. and Schneider, Matthias and Kirschke, Jan and Weber, Bruno and Zimmer, Claus and Piraud, Marie and Menze, Bjoern H.},
url = {http://arxiv.org/abs/1803.09340},
arxivId = {1803.09340}
}
@article{Dai2017DeformableNetworks,
title = {{Deformable Convolutional Networks}},
year = {2017},
journal = {Proceedings of the IEEE International Conference on Computer Vision},
author = {Dai, Jifeng and Qi, Haozhi and Xiong, Yuwen and Li, Yi and Zhang, Guodong and Hu, Han and Wei, Yichen},
pages = {764--773},
volume = {2017-Octob},
isbn = {9781538610329},
doi = {10.1109/ICCV.2017.89},
issn = {15505499},
pmid = {23459267},
arxivId = {1703.06211}
}
@article{He2014DelvingClassification,
title = {{Delving Deep into Rectifiers : Surpassing Human-Level Performance on ImageNet Classification}},
year = {2014},
author = {He, Kaiming},
isbn = {9781467383912},
doi = {10.1.1.725.4861},
issn = {15505499},
pmid = {7410480},
arxivId = {1502.01852v1}
}
@article{Huang2017DenselyNetworks,
title = {{Densely connected convolutional networks}},
year = {2017},
journal = {Proceedings - 30th IEEE Conference on Computer Vision and Pattern Recognition, CVPR 2017},
author = {Huang, Gao and Liu, Zhuang and Van Der Maaten, Laurens and Weinberger, Kilian Q.},
pages = {2261--2269},
volume = {2017-Janua},
isbn = {9781538604571},
doi = {10.1109/CVPR.2017.243},
issn = {0002-9645},
pmid = {211888},
arxivId = {1608.06993}
}
@article{Balsiger2016DevelopmentApproaches,
title = {{Development of Algorithms for Peripheral Nerve Segmentation using Machine Learning Approaches}},
year = {2016},
author = {Balsiger, Fabian},
number = {December}
}
@article{Jende2018DiabeticNeurography,
title = {{Diabetic neuropathy differs between type 1 and type 2 diabetes: Insights from magnetic resonance neurography}},
year = {2018},
journal = {Annals of Neurology},
author = {Jende, Johann M. E. and Groener, Jan B. and Oikonomou, Dimitrios and Heiland, Sabine and Kopf, Stefan and Pham, Mirko and Nawroth, Peter and Bendszus, Martin and Kurz, Felix T.},
url = {http://doi.wiley.com/10.1002/ana.25182},
doi = {10.1002/ana.25182},
issn = {03645134},
pmid = {29443416}
}
@article{Srivastava2014Dropout:Overfitting,
title = {{Dropout: A Simple Way to Prevent Neural Networks from Overfitting}},
year = {2014},
journal = {Journal of Machine Learning Research},
author = {Srivastava, Nitish and Hinton, Geoffrey and Krizhevsky, Alex and Sutskever, Ilya and Salakhutdinov, Ruslan},
pages = {1929--1958},
volume = {15},
isbn = {1532-4435},
doi = {10.1214/12-AOS1000},
issn = {15337928},
pmid = {23285570},
arxivId = {1102.4807},
keywords = {deep learning, model combination, neural networks, regularization}
}
@article{Martyn1997EpidemiologyNeuropathy,
title = {{Epidemiology of peripheral neuropathy}},
year = {1997},
journal = {Neurosurgery, and Psychiatry},
author = {Martyn, C N and Hughes, R A C},
pages = {310--318},
volume = {62},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1074084/pdf/jnnpsyc00004-0006.pdf}
}
@article{Selvan2018ExtractionNetworks,
title = {{Extraction of Airways using Graph Neural Networks}},
year = {2018},
author = {Selvan, Raghavendra and Kipf, Thomas and Welling, Max and Pedersen, Jesper H. and Petersen, Jens and de Bruijne, Marleen},
number = {Midl},
pages = {7--9},
url = {http://arxiv.org/abs/1804.04436},
arxivId = {1804.04436}
}
@article{Ren2017FasterNetworks,
title = {{Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks}},
year = {2017},
journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
author = {Ren, Shaoqing and He, Kaiming and Girshick, Ross and Sun, Jian},
number = {6},
pages = {1137--1149},
volume = {39},
isbn = {0162-8828 VO - PP},
doi = {10.1109/TPAMI.2016.2577031},
issn = {01628828},
pmid = {27295650},
arxivId = {1506.01497},
keywords = {Object detection, convolutional neural network, region proposal}
}
@article{Hu2016FastMask:Shot,
title = {{FastMask: Segment Multi-scale Object Candidates in One Shot}},
year = {2016},
author = {Hu, Hexiang and Lan, Shiyi and Jiang, Yuning and Cao, Zhimin and Sha, Fei},
url = {http://arxiv.org/abs/1612.08843},
isbn = {978-1-5386-0457-1},
doi = {10.1109/CVPR.2017.245},
arxivId = {1612.08843}
}
@article{Pohlen2017Full-resolutionScenes,
title = {{Full-resolution residual networks for semantic segmentation in street scenes}},
year = {2017},
journal = {Proceedings - 30th IEEE Conference on Computer Vision and Pattern Recognition, CVPR 2017},
author = {Pohlen, Tobias and Hermans, Alexander and Mathias, Markus and Leibe, Bastian},
pages = {3309--3318},
volume = {2017-Janua},
isbn = {9781538604571},
doi = {10.1109/CVPR.2017.353},
arxivId = {1611.08323}
}
@article{Long2015FullySegmentation,
title = {{Fully convolutional networks for semantic segmentation}},
year = {2015},
journal = {Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition},
author = {Long, Jonathan and Shelhamer, Evan and Darrell, Trevor},
pages = {3431--3440},
volume = {07-12-June},
isbn = {9781467369640},
doi = {10.1109/CVPR.2015.7298965},
issn = {10636919},
pmid = {16190471},
arxivId = {1411.4038}
}
@article{Sudre2017GeneralisedSegmentations,
title = {{Generalised dice overlap as a deep learning loss function for highly unbalanced segmentations}},
year = {2017},
journal = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
author = {Sudre, Carole H. and Li, Wenqi and Vercauteren, Tom and Ourselin, Sebastien and Jorge Cardoso, M.},
pages = {240--248},
volume = {10553 LNCS},
isbn = {9783319675572},
doi = {10.1007/978-3-319-67558-9{\_}28},
issn = {16113349},
arxivId = {1707.03237}
}
@article{Szegedy2014GoingConvolutions,
title = {{Going Deeper with Convolutions}},
year = {2014},
author = {Szegedy, Christian and Liu, Wei and Jia, Yangqing and Sermanet, Pierre and Reed, Scott and Anguelov, Dragomir and Erhan, Dumitru and Vanhoucke, Vincent and Rabinovich, Andrew and Hill, Chapel and Arbor, Ann},
pages = {1--9},
isbn = {9781467369640},
doi = {10.1109/CVPR.2015.7298594},
issn = {10636919},
pmid = {24920543},
arxivId = {1409.4842}
}
@article{Zotti2018GridNetSegmentation,
title = {{GridNet with automatic shape prior registration for automatic MRI cardiac segmentation}},
year = {2018},
journal = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
author = {Zotti, Clément and Luo, Zhiming and Humbert, Olivier and Lalande, Alain and Jodoin, Pierre Marc},
pages = {73--81},
volume = {10663 LNCS},
isbn = {9783319755403},
doi = {10.1007/978-3-319-75541-0{\_}8},
issn = {16113349},
arxivId = {1705.08943},
keywords = {Convolutional neural networks, Heart, MRI, Segmentation}
}
@article{Dauphin2014IdentifyingOptimization,
title = {{Identifying and attacking the saddle point problem in high-dimensional non-convex optimization}},
year = {2014},
author = {Dauphin, Yann and Pascanu, Razvan and Gulcehre, Caglar and Cho, Kyunghyun and Ganguli, Surya and Bengio, Yoshua},
pages = {1--14},
url = {http://arxiv.org/abs/1406.2572},
isbn = {1406.2572},
issn = {10495258},
arxivId = {1406.2572}
}
@article{Krizhevsky2012ImageNetNetworks,
title = {{ImageNet Classification with Deep Convolutional Neural Networks}},
year = {2012},
journal = {Advances In Neural Information Processing Systems},
author = {Krizhevsky, Alex and Sutskever, Ilya and Hinton, Geoffrey E},
pages = {1--9},
isbn = {9781627480031},
doi = {http://dx.doi.org/10.1016/j.protcy.2014.09.007},
issn = {10495258},
pmid = {7491034},
arxivId = {1102.0183}
}
@article{Russakovsky2015ImageNetChallenge,
title = {{ImageNet Large Scale Visual Recognition Challenge}},
year = {2015},
journal = {International Journal of Computer Vision},
author = {Russakovsky, Olga and Deng, Jia and Su, Hao and Krause, Jonathan and Satheesh, Sanjeev and Ma, Sean and Huang, Zhiheng and Karpathy, Andrej and Khosla, Aditya and Bernstein, Michael and Berg, Alexander C. and Fei-Fei, Li},
isbn = {0920-5691},
doi = {10.1007/s11263-015-0816-y},
issn = {15731405},
pmid = {16190471},
arxivId = {1409.0575},
keywords = {Benchmark, Dataset, Large-scale, Object detection, Object recognition}
}
@article{Sola1997ImportanceProblems,
title = {{Importance of input data normalization for the application of neural networks to complex industrial problems}},
year = {1997},
journal = {IEEE Transactions on Nuclear Science},
author = {Sola, J. and Sevilla, J.},
number = {3 PART 3},
pages = {1464--1468},
volume = {44},
isbn = {0018-9499},
doi = {10.1109/23.589532},
issn = {00189499},
keywords = {Network learning, Neural networks, Nuclear power plants, Power prediction system, Reactor pressure, Transients}
}
@article{Dimitrovski2015ImprovedFeatures,
title = {{Improved medical image modality classification using a combination of visual and textual features}},
year = {2015},
journal = {Computerized Medical Imaging and Graphics},
author = {Dimitrovski, Ivica and Kocev, Dragi and Kitanovski, Ivan and Loskovska, Suzana and D{\v{z}}eroski, Sašo},
pages = {14--26},
volume = {39},
isbn = {978-3-540-23105-9},
doi = {10.1016/j.compmedimag.2014.06.005},
issn = {18790771},
pmid = {24997992},
arxivId = {1102.0183},
keywords = {Feature fusion, Image modality classification, Visual image descriptors}
}
@article{Eaton-rosen2018ImprovingSegmentation,
title = {{Improving Data Augmentation for Medical Image Segmentation}},
year = {2018},
author = {Eaton-rosen, Zach and Bragman, Felix},
number = {Midl},
pages = {1--3}
}
@article{Gulcehre2013KnowledgeOptimization,
title = {{Knowledge Matters: Importance of Prior Information for Optimization}},
year = {2013},
author = {G{\"{u}}l{\c{c}}ehre, Çağlar and Bengio, Yoshua},
url = {http://arxiv.org/abs/1301.4083},
issn = {1532-4435},
arxivId = {1301.4083}
}
@article{Girdhar2016LearningObjects,
title = {{Learning a predictable and generative vector representation for objects}},
year = {2016},
journal = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
author = {Girdhar, Rohit and Fouhey, David F. and Rodriguez, Mikel and Gupta, Abhinav},
pages = {484--499},
volume = {9910 LNCS},
isbn = {9783319464657},
doi = {10.1007/978-3-319-46466-4{\_}29},
issn = {16113349},
pmid = {10463930},
arxivId = {1603.08637}
}
@article{2015LEARNINGMerced,
title = {{LEARNING SHAPE PRIORS FOR OBJECT SEGMENTATION VIA NEURAL NETWORKS Simon Safar Ming-Hsuan Yang University of California at Merced}},
year = {2015},
journal = {International Conference on Image Processing (ICIP)},
pages = {1835--1839},
isbn = {9781479983391}
}
@article{Du2010MagneticDisorders,
title = {{Magnetic resonance neurography for the evaluation of peripheral nerve, brachial plexus, and nerve root disorders}},
year = {2010},
journal = {Journal of Neurosurgery},
author = {Du, Rose and Auguste, Kurtis I. and Chin, Cynthia T. and Engstrom, John W. and Weinstein, Philip R.},
number = {2},
pages = {362--371},
volume = {112},
url = {http://thejns.org/doi/10.3171/2009.7.JNS09414},
isbn = {0022-3085},
doi = {10.3171/2009.7.JNS09414},
issn = {0022-3085},
pmid = {19663545}
}
@article{Chhabra2018MagneticReview,
title = {{Magnetic resonance neurography: current perspectives and literature review}},
year = {2018},
journal = {European Radiology},
author = {Chhabra, Avneesh and Madhuranthakam, Ananth J. and Andreisek, Gustav},
number = {2},
pages = {698--707},
volume = {28},
isbn = {1432-1084},
doi = {10.1007/s00330-017-4976-8},
issn = {14321084},
pmid = {28710579},
keywords = {DTI, MR neurography, MRI, MRN, Peripheral nerve}
}
@inproceedings{Lorensen1987MarchingAlgorithm,
title = {{Marching cubes: A high resolution 3D surface construction algorithm}},
year = {1987},
booktitle = {Proceedings of the 14th annual conference on Computer graphics and interactive techniques - SIGGRAPH '87},
author = {Lorensen, William E. and Cline, Harvey E.},
pages = {163--169},
url = {http://portal.acm.org/citation.cfm?doid=37401.37422},
isbn = {0897912276},
doi = {10.1145/37401.37422},
issn = {00978930},
pmid = {34}
}
@article{He2017MaskR-CNN,
title = {{Mask R-CNN}},
year = {2017},
journal = {Proceedings of the IEEE International Conference on Computer Vision},
author = {He, Kaiming and Gkioxari, Georgia and Doll{\'{a}}r, Piotr and Girshick, Ross},
month = {3},
pages = {2980--2988},
volume = {2017-Octob},
url = {http://arxiv.org/abs/1703.06870},
isbn = {9781538610329},
doi = {10.1109/ICCV.2017.322},
issn = {15505499},
pmid = {303902},
arxivId = {1703.06870}
}
@article{Dice1945MeasuresTh,
title = {{Measures of the Amount of Ecologic Association Between Species Author ( s ): Lee R . Dice Published by : Wiley Stable URL : http://www.jstor.org/stable/1932409 Accessed : 08-04-2016 13 : 33 UTC Your use of the JSTOR archive indicates your acceptance of th}},
year = {1945},
journal = {Ecology},
author = {Dice, Lee R.},
number = {3},
pages = {297--302},
volume = {26}
}
@article{Taha2015MetricsTool,
title = {{Metrics for evaluating 3D medical image segmentation: Analysis, selection, and tool}},
year = {2015},
journal = {BMC Medical Imaging},
author = {Taha, Abdel Aziz and Hanbury, Allan},
number = {1},
volume = {15},
publisher = {BMC Medical Imaging},
url = {http://dx.doi.org/10.1186/s12880-015-0068-x},
isbn = {1522-2586},
doi = {10.1186/s12880-015-0068-x},
issn = {14712342},
pmid = {26263899},
arxivId = {NIHMS150003},
keywords = {Evaluation metrics, Evaluation tool, Medical volume segmentation, Metric selection}
}
@article{Lin2014MicrosoftContext,
title = {{Microsoft COCO: Common objects in context}},
year = {2014},
journal = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
author = {Lin, Tsung Yi and Maire, Michael and Belongie, Serge and Hays, James and Perona, Pietro and Ramanan, Deva and Doll{\'{a}}r, Piotr and Zitnick, C. Lawrence},
number = {PART 5},
pages = {740--755},
volume = {8693 LNCS},
isbn = {978-3-319-10601-4},
doi = {10.1007/978-3-319-10602-1{\_}48},
issn = {16113349},
pmid = {16190471},
arxivId = {1405.0312}
}
@article{Zhang2017Mixup:Minimization,
title = {{mixup: Beyond Empirical Risk Minimization}},
year = {2017},
author = {Zhang, Hongyi and Cisse, Moustapha and Dauphin, Yann N. and Lopez-Paz, David},
pages = {1--13},
url = {http://arxiv.org/abs/1710.09412},
isbn = {221872068X},
arxivId = {1710.09412}
}
@article{Felisaz2017MRNeuropathy.,
title = {{MR Micro-Neurography and a Segmentation Protocol Applied to Diabetic Neuropathy.}},
year = {2017},
journal = {Radiology research and practice},
author = {Felisaz, P. F. and Maugeri, G. and Busi, V. and Vitale, R. and Balducci, F. and Gitto, S. and Leporati, P. and Pichiecchio, A. and Baldi, M. and Calliada, F. and Chiovato, L. and Bastianello, S.},
pages = {2761818},
volume = {2017},
url = {https://www.hindawi.com/journals/rrp/2017/2761818/%5Cnhttp://www.ncbi.nlm.nih.gov/pubmed/28567306%5Cnhttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5439248},
doi = {10.1155/2017/2761818},
issn = {2090-1941},
pmid = {28567306}
}
@article{Porz2014Multi-modalMachine,
title = {{Multi-modal glioblastoma segmentation: Man versus machine}},
year = {2014},
journal = {PLoS ONE},
author = {Porz, Nicole and Bauer, Stefan and Pica, Alessia and Schucht, Philippe and Beck, Jürgen and Verma, Rajeev Kumar and Slotboom, Johannes and Reyes, Mauricio and Wiest, Roland},
number = {5},
pages = {1--9},
volume = {9},
isbn = {10.1371/journal.pone.0096873},
doi = {10.1371/journal.pone.0096873},
issn = {19326203},
pmid = {24804720}
}
@article{Maes1997MultimodalityInformation,
title = {{Multimodality image registration by maximization of mutual information}},
year = {1997},
journal = {Medical Imaging, IEEE Transactions on},
author = {Maes, Frederik and Collignon, Andre and Vandermeulen, Dirk and Marchal, Guy and Suetens, Paul},
number = {2},
pages = {187--198},
volume = {16},
isbn = {0278-0062},
doi = {10.1109/42.563664},
issn = {0278-0062},
pmid = {9101328}
}
@article{Hodler2017MusculoskeletalImaging,
title = {{Musculoskeletal diseases 2017-2020: Diagnostic imaging}},
year = {2017},
journal = {Musculoskeletal Diseases 2017-2020: Diagnostic Imaging},
author = {Hodler, Juerg and Kubik-Huch, Rahel A. and von Schulthess, Gustav K.},
pages = {1--339},
isbn = {9783319540184},
doi = {10.1007/978-3-319-54018-4}
}
@article{Felisaz2016NerveMicro-neurography,
title = {{Nerve Fascicles and Epineurium Volume Segmentation of Peripheral Nerve Using Magnetic Resonance Micro-neurography}},
year = {2016},
journal = {Academic Radiology},
author = {Felisaz, Paolo Florent and Balducci, Francesco and Gitto, Salvatore and Carne, Irene and Montagna, Stefano and De Icco, Roberto and Pichiecchio, Anna and Baldi, Maurizia and Calliada, Fabrizio and Bastianello, Stefano},
number = {8},
pages = {1000--1007},
volume = {23},
publisher = {Elsevier Inc.},
url = {http://dx.doi.org/10.1016/j.acra.2016.03.013},
isbn = {1878-4046 (Electronic){\textbackslash}r1076-6332 (Linking)},
doi = {10.1016/j.acra.2016.03.013},
issn = {18784046},
pmid = {27209266},
keywords = {MRI, micro, nerve, neurography, segmentation}
}
@article{Rangavajla2014Non-InvasiveNerves,
title = {{Non-Invasive Imaging of Peripheral Nerves}},
year = {2014},
journal = {Cells Tissues Organs},
author = {Rangavajla, G and Mokarram, N and Masoodzadehgan, N and Pai, S B and Bellamkonda, R V},
number = {1},
pages = {69--77},
volume = {200},
isbn = {1169501206},
doi = {10.1007/s11695-012-0673-5.Conjugated},
issn = {01204157},
pmid = {26042227},
arxivId = {15334406},
keywords = {dti, imaging, mri, pet, pns, ultrasound}
}
@article{Mann1947OnOther,
title = {{On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other}},
year = {1947},
journal = {The Annals of Mathematical Statistics},
author = {Mann, H. B. and Whitney, D. R.},
number = {1},
pages = {50--60},
volume = {18},
url = {http://projecteuclid.org/euclid.aoms/1177730491},
isbn = {00034851},
doi = {10.1214/aoms/1177730491},
issn = {0003-4851},
pmid = {10226}
}
@article{Shapiro2004OnMeasures,
title = {{On Hausdorff Distance Measures}},
year = {2004},
journal = {Computer Vision Laboratory University of Massachusetts Amherst, MA},
author = {Shapiro, M.D. and Blaschko, M.B.},
pages = {1--21},
volume = {1003},
url = {http://www.cs.umass.edu/publication/docs/2004/UM-CS-2004-071.pdf},
keywords = {hausdorff, object recognition, spatially coherent matching}
}
@article{Caruana2000OverfittingStopping,
title = {{Overfitting in neural nets: Backpropagation, conjugate gradient, and early stopping}},
year = {2000},
journal = {the 13th International Conference on Neural Information Processing Systems},
author = {Caruana, Rich and Lawrence, Steve and Giles, Lee},
pages = {402--408},
isbn = {1049-5258},
doi = {10.1109/IJCNN.2000.857823},
issn = {10495258}
}
@article{Giraldo2015PeripheralClustering,
title = {{Peripheral nerve segmentation using Nonparametric Bayesian Hierarchical Clustering}},
year = {2015},
journal = {2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)},
author = {Giraldo, Juan J. and Alvarez, Mauricio A. and Orozco, Alvaro A.},
pages = {3101--3104},
url = {http://ieeexplore.ieee.org/document/7319048/},
isbn = {978-1-4244-9271-8},
doi = {10.1109/EMBC.2015.7319048},
issn = {1094-687X},
keywords = {Bayes methods, Biomedical imaging, Databases, Image segmentation, Mathematical model, Shape, Ultrasonic imaging, accidents, anesthesiology procedures, aqueous tissues, artifacts, assistance methodology, biomedical ultrasonics, chronic pain, clinical intervention, illness, image capturing process, image denoising, image processing, image segmentation, mean square error methods, mean squared error performance, median nerve, medical image processing, medical ultrasound images, muscle, muscles, neurophysiology, nonparametric Bayesian hierarchical clustering, pattern clustering, peripheral nerve segmentation method, peroneal nerve, soft structures, speckle, speckle noise, surgical interventions, true nerve structures, ulnar nerve, ultrasonic imaging}
}
@article{Paredes2015PeripheralModels,
title = {{Peripheral Nerve Segmentation Using Speckle Removal and Bayesian Shape Models}},
year = {2015},