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Recently there has been an increasing trend to use deep learning frameworks for both 2D consumer images and for 3D medical images.
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P. Thevenaz, T. Blu, and M. Unser · 2000
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Evaluation of Diffusion Techniques for Improved Vessel Visualization and Quantification in Three-Dimensional Rotational Angiography
E. Meijering, W. Niessen, J. Weickert, and M. Viergever · 2001
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E. P. Simoncelli and B. A. Olshausen · 2001
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Icasso: software for investigating the reliability of ICA estimates by clustering and visualization
J. Himberg and A. Hyvarinen · 2003
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Dictionary Learning Algorithms for Sparse Representation
K. Kreutz-Delgado, J. F. Murray, B. D. Rao, K. Engan, T.-W. Lee · 2003
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Local and reversible blood–brain barrier disruption by noninvasive focused ultrasound at frequencies suitable for trans-skull sonications
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Design of steerable filters for feature detection using canny-like criteria
M. Jacob and M. Unser · 2004
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A Review of Vessel Extraction Techniques and Algorithms
C. Kirbas and F. Quek · 2004
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Ridge based vessel segmentation in color images of the retina
J. J. Staal, M. D. Abramoff, M. Niemeijer, M. A. Viergever, and B. v. Ginneken · 2004
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Deep tissue two-photon microscopy
F. Helmchen and W. Denk · 2005
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Quantum dots spectrally distinguish multiple species within the tumor milieu in vivo
M. Stroh, J. P. Zimmer, D. G. Duda, T. S. Levchenko, K. S. Cohen · 2005
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Vessel enhancing diffusion: A scale space representation of vessel structures
R. Manniesing, M. A. Viergever, and W. J. Niessen · 2006
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On measuring the change in size of pulmonary nodules
A. Reeves, A. Chan, D. Yankelevitz, C. Henschke, B. Kressler · 2006
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Greedy layer-wise training of deep networks
Y. Bengio, P. Lamblin, D. Popovici, H. Larochelle, and others · 2007
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Image Denoising by Sparse 3-D Transform-Domain Collaborative Filtering
K. Dabov, A. Foi, V. Katkovnik, and K. Egiazarian · 2007
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Vessel Enhancing Diffusion Filter
A. Enquobahrie, L. Ibanez, E. Bullitt, and S. Aylward · 2007
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Automatic Centerline Extraction of Irregular Tubular Structures Using Probability Volumes from Multiphoton Imaging
A. Santamaría-Pang, C. M. Colbert, P. Saggau, and I. A. Kakadiaris · 2007
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A Proximal Iteration for Deconvolving Poisson Noisy Images Using Sparse Representations
F.-X. Dupe, J. Fadili, and J.-L. Starck · 2008
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Three Dimensional Curvilinear Structure Detection Using Optimally Oriented Flux
M. W. K. Law and A. C. S. Chung · 2008
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Altered morphology and 3d architecture of brain vasculature in a mouse model for Alzheimer’s disease
E. P. Meyer, A. Ulmann-Schuler, M. Staufenbiel, and T. Krucker · 2008
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The top ten causes of death-Fact sheet N310
W. H. Organization · 2008
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Fast High-Dimensional Filtering Using the Permutohedral Lattice
A. Adams, J. Baek, and M. A. Davis · 2009
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Image deblurring with Poisson data: from cells to galaxies
M. Bertero, P. Boccacci, G. Desiderà, and G. Vicidomini · 2009
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Learning rotational features for filament detection
G. Gonzalez, F. Fleurety, and P. Fua · 2009
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Learning Multiple Layers of Features from Tiny Images
A. Krizhevsky · 2009
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A review of 3d vessel lumen segmentation techniques: Models, features and extraction schemes
D. Lesage, E. D. Angelini, I. Bloch, and G. Funka-Lea · 2009
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Automated Analysis of Cellular Signals from Large-Scale Calcium Imaging Data
E. A. Mukamel, A. Nimmerjahn, and M. J. Schnitzer · 2009
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Standardized evaluation methodology and reference database for evaluating coronary artery centerline extraction algorithms
M. Schaap, C. T. Metz, T. van Walsum, A. G. van der Giessen, A. C. Weustink · 2009
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Bioimaging: Second window for in vivo imaging
A. M. Smith, M. C. Mancini, and S. Nie · 2009
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Correlations of Neuronal and Microvascular Densities in Murine Cortex Revealed by Direct Counting and Colocalization of Nuclei and Vessels
P. S. Tsai, J. P. Kaufhold, P. Blinder, B. Friedman, P. J. Drew · 2009
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Auto-Context and Its Application to High-Level Vision Tasks and 3d Brain Image Segmentation
Z. Tu and X. Bai · 2009
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Maximin affinity learning of image segmentation
S. Turaga, K. Briggman, M. Helmstaedter, W. Denk, and H. Seung · 2009
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Reproducible research in signal processing
P. Vandewalle, J. Kovacevic, and M. Vetterli · 2009
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Why Does Unsupervised Pre-training Help Deep Learning?
D. Erhan, Y. Bengio, A. Courville, P.-A. Manzagol, P. Vincent · 2010
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An Oriented Flux Symmetry Based Active Contour Model for Three Dimensional Vessel Segmentation
M. W. K. Law and A. C. S. Chung · 2010
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Metadata matters: access to image data in the real world
M. Linkert, C. T. Rueden, C. Allan, J.-M. Burel, W. Moore · 2010
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Image Denoising in Mixed Poisson-Gaussian Noise
F. Luisier, T. Blu, and M. Unser · 2010
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Optimal Inversion of the Anscombe Transformation in Low-Count Poisson Image Denoising
M. Makitalo and A. Foi · 2010
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Rectified linear units improve restricted boltzmann machines
V. Nair and G. E. Hinton · 2010
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Active learning literature survey
B. Settles · 2010
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Machine Learning in Medicine: A Primer for Physicians
A. K. Waljee and P. D. R. Higgins · 2010
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Near-infrared branding efficiently correlates light and electron microscopy
D. Bishop, I. Nikić, M. Brinkoetter, S. Knecht, S. Potz · 2011
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The DIADEM Data Sets: Representative Light Microscopy Images of Neuronal Morphology to Advance Automation of Digital Reconstructions
K. M. Brown, G. Barrionuevo, A. J. Canty, V. D. Paola, J. A. Hirsch · 2011
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Two-photon fluorescence microscopy study of cerebrovascular dynamics in ultrasound-induced blood–brain barrier opening
E. E. Cho, J. Drazic, M. Ganguly, B. Stefanovic, and K. Hynynen · 2011
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Automatic Multi-organ Segmentation Using Learning-Based Segmentation and Level Set Optimization
T. Kohlberger, M. Sofka, J. Zhang, N. Birkbeck, J. Wetzl · 2011
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Supervoxel-Based Segmentation of Mitochondria in EM Image Stacks With Learned Shape Features
A. Lucchi, K. Smith, R. Achanta, G. Knott, and P. Fua · 2011
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A constrained independent component analysis technique for artery–vein separation of two-photon laser scanning microscopy images of the cerebral microvasculature
H. Mehrabian, L. Lindvere, B. Stefanovic, and A. L. Martel · 2011
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Deep and fast live imaging with two-photon scanned light-sheet microscopy
T. V. Truong, W. Supatto, D. S. Koos, J. M. Choi, and S. E. Fraser · 2011
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Ultrasonic neuromodulation by brain stimulation with transcranial ultrasound
Y. Tufail, A. Yoshihiro, S. Pati, M. M. Li, and W. J. Tyler · 2011
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Label-free live brain imaging and targeted patching with third-harmonic generation microscopy
S. Witte, A. Negrean, J. C. Lodder, C. P. J. de Kock, G. Testa Silva · 2011
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Image Smoothing via L0 Gradient Minimization
L. Xu, C. Lu, Y. Xu, and J. Jia · 2011
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Blind Separation of Image Sources via Adaptive Dictionary Learning
V. Abolghasemi, S. Ferdowsi, and S. Sanei · 2012
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VMTK: Vascular Modeling Toolkit
L. Antiga and D. Steinman · 2012
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Better Mixing via Deep Representations
Y. Bengio, G. Mesnil, Y. Dauphin, and S. Rifai · 2012
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Deep Neural Networks Segment Neuronal Membranes in Electron Microscopy Images
D. Ciresan, A. Giusti, L. M. Gambardella, and J. Schmidhuber · 2012
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Learning Hierarchical Features for Scene Labeling
C. Farabet, C. Couprie, L. Najman, and Y. LeCun · 2012
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Choice-specific sequences in parietal cortex during a virtual-navigation decision task
C. D. Harvey, P. Coen, and D. W. Tank · 2012
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In vivo three-photon microscopy of subcortical structures within an intact mouse brain
N. G. Horton, K. Wang, D. Kobat, C. G. Clark, F. W. Wise · 2012
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Adaptive-weighted cubic B-spline using lookup tables for fast and efficient axial resampling of 3d confocal microscopy images
C. Indhumathi, Y. Cai, Y. Guan, M. Opas, and J. Zheng · 2012
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Characterization and adaptive optical correction of aberrations during in vivo imaging in the mouse cortex
N. Ji, T. R. Sato, and E. Betzig · 2012
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3d Convolutional Neural Networks for Human Action Recognition
S. Ji, W. Xu, M. Yang, and K. Yu · 2012
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Efficient Inference in Fully Connected CRFs with Gaussian Edge Potentials
P. Krähenbühl and V. Koltun · 2012
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ImageNet Classification with Deep Convolutional Neural Networks
A. Krizhevsky, I. Sutskever, and G. E. Hinton · 2012
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Automatic Segmentation of the Pulmonary Lobes From Chest CT Scans Based on Fissures, Vessels, and Bronchi
B. Lassen, E. van Rikxoort, M. Schmidt, S. Kerkstra, B. van Ginneken · 2012
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Mesh Processing in Medical-Image Analysis&# x2014; a Tutorial
J. A. Levine, R. R. Paulsen, and Y. Zhang · 2012
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Nonlocal Transform-Domain Filter for Volumetric Data Denoising and Reconstruction
M. Maggioni, V. Katkovnik, K. Egiazarian, and A. Foi · 2012
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Accurate and Efficient Linear Structure Segmentation by Leveraging Ad Hoc Features with Learned Filters
R. Rigamonti and V. Lepetit · 2012
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An artery-specific fluorescent dye for studying neurovascular coupling
Z. Shen, Z. Lu, P. Y. Chhatbar, P. O’Herron, and P. Kara · 2012
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Stacked Autoencoders for Unsupervised Feature Learning and Multiple Organ Detection in a Pilot Study Using 4d Patient Data
H.-C. Shin, M. Orton, D. Collins, S. Doran, and M. Leach · 2012
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Automated reconstruction of tree structures using path classifiers and Mixed Integer Programming
E. Turetken, F. Benmansour, and P. Fua · 2012
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On the Complexity of Neural Network Classifiers: A Comparison Between Shallow and Deep Architectures
M. Bianchini and F. Scarselli · 2013
Cited alongside, same era.
Fast Image Scanning with Deep Max-Pooling Convolutional Neural Networks
A. Giusti, D. C. Cireşan, J. Masci, L. M. Gambardella, and J. Schmidhuber · 2013
Cited alongside, same era.
I. J. Goodfellow, D. Warde-Farley, M. Mirza, A. Courville, and Y. Bengio · 2013
Cited alongside, same era.
Connectomic reconstruction of the inner plexiform layer in the mouse retina
M. Helmstaedter, K. L. Briggman, S. C. Turaga, V. Jain, H. S. Seung · 2013
Cited alongside, same era.
Some Improvements on Deep Convolutional Neural Network Based Image Classification
A. G. Howard · 2013
Learning Transferrable Knowledge for Semantic Segmentation with Deep Convolutional Neural Network
S. Hong, J. Oh, B. Han, and H. Lee · 2015
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Bidirectional Recurrent Convolutional Networks for Multi-Frame Super-Resolution
Y. Huang, W. Wang, and L. Wang · 2015
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Batch normalization: Accelerating deep network training by reducing internal covariate shift
S. Ioffe and C. Szegedy · 2015
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Matrix Backpropagation for Deep Networks with Structured Layers
C. Ionescu, O. Vantzos, and C. Sminchisescu · 2015
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Learning Sparse High Dimensional Filters: Image Filtering, Dense CRFs and Bilateral Neural Networks
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Cited alongside, same era.
Deep and Wide Multiscale Recursive Networks for Robust Image Labeling
G. B. Huang and V. Jain · 2013
Cited alongside, same era.
Retinal Vascular Caliber Measurements: Clinical Significance, Current Knowledge and Future Perspectives
M. K. Ikram, Y. T. Ong, C. Y. Cheung, and T. Y. Wong · 2013
Cited alongside, same era.
Standardized evaluation framework for evaluating coronary artery stenosis detection, stenosis quantification and lumen segmentation algorithms in computed tomography angiography
H. A. Kirişli, M. Schaap, C. T. Metz, A. S. Dharampal, W. B. Meijboom · 2013
Cited alongside, same era.
M. Lin, Q. Chen, and S. Yan · 2013
Cited alongside, same era.
Cerebral microvascular network geometry changes in response to functional stimulation
L. Lindvere, R. Janik, A. Dorr, D. Chartash, B. Sahota · 2013
Cited alongside, same era.
A fast learning algorithm for image segmentation with max-pooling convolutional networks
J. Masci, A. Giusti, D. Ciresan, G. Fricout, and J. Schmidhuber · 2013
Cited alongside, same era.
Drug delivery to the brain by focused ultrasound induced blood–brain barrier disruption: Quantitative evaluation of enhanced permeability of cerebral vasculature using two-photon microscopy
T. Nhan, A. Burgess, E. E. Cho, B. Stefanovic, L. Lilge · 2013
Cited alongside, same era.
V. Jampani, M. Kiefel, and P. V. Gehler · 2015
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Multi-Scale 3d Convolutional Neural Networks for Lesion Segmentation in Brain MRI
K. Kamnitsas, L. Chen, C. Ledig, D. Rueckert, and B. Glocker · 2015
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Machine Learning Approaches for Predicting Radiation Therapy Outcomes: A Clinician’s Perspective
J. Kang, R. Schwartz, J. Flickinger, and S. Beriwal · 2015
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Better reporting for better research: a checklist for reproducibility
A. Kenall, S. Edmunds, L. Goodman, L. Bal, L. Flintoft · 2015
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A. Kendall, V. Badrinarayanan, and R. Cipolla · 2015
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Vascular Flow Modelling Using Computational Fluid Dynamics
A. Keshmiri and K. Andrews · 2015
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Blind Depth-variant Deconvolution of 3d Data in Wide-field Fluorescence Microscopy
B. Kim and T. Naemura · 2015
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Two-Photon Absorbing Dyes with Minimal Autofluorescence in Tissue Imaging: Application to in Vivo Imaging of Amyloid-
D. Kim, H. Moon, S. H. Baik, S. Singha, Y. W. Jun · 2015
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Deeply-Recursive Convolutional Network for Image Super-Resolution
J. Kim, J. K. Lee, and K. M. Lee · 2015
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Variational Dropout and the Local Reparameterization Trick
D. P. Kingma, T. Salimans, and M. Welling · 2015
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Introducing Geometry in Active Learning for Image Segmentation
K. Konyushkova, R. Sznitman, and P. Fua · 2015
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Classifying and Segmenting Microscopy Images Using Convolutional Multiple Instance Learning
O. Z. Kraus, L. J. Ba, and B. Frey · 2015
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Human-level concept learning through probabilistic program induction
B. M. Lake, R. Salakhutdinov, and J. B. Tenenbaum · 2015
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Deep learning
Y. LeCun, Y. Bengio, and G. Hinton · 2015
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Recursive Training of 2d-3d Convolutional Networks for Neuronal Boundary Detection
K. Lee, A. Zlateski, A. Vishwanathan, and H. S. Seung · 2015
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Opinion: Reproducible research can still be wrong: Adopting a prevention approach
J. T. Leek and R. D. Peng · 2015
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Metadata management for high content screening in OMERO
S. Li, S. Besson, C. Blackburn, M. Carroll, R. K. Ferguson · 2015
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Efficient piecewise training of deep structured models for semantic segmentation
G. Lin, C. Shen, I. Reid, and A. v. d. Hengel · 2015
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An Ensemble of 2d Convolutional Neural Networks for Tumor Segmentation
M. Lyksborg, O. Puonti, M. Agn, and R. Larsen · 2015
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Improving Semi-Supervised Learning with Auxiliary Deep Generative Models
L. Maaløe, C. K. Sønderby, S. K. Sønderby, and O. Winther · 2015
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Weak Sinusoidal Electric Fields Entrain Spontaneous Ca Transients in the Dendritic Tufts of CA1 Pyramidal Cells in Rat Hippocampal Slice Preparations
K. Maeda, R. Maruyama, T. Nagae, M. Inoue, T. Aonishi · 2015
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Combinatorial Energy Learning for Image Segmentation
J. Maitin-Shepard, V. Jain, M. Januszewski, P. Li, J. Kornfeld · 2015
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OMERO and Bio-Formats 5: flexible access to large bioimaging datasets at scale
J. Moore, M. Linkert, C. Blackburn, M. Carroll, R. K. Ferguson · 2015
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Manipulating neuronal activity in the mouse brain with ultrasound: A comparison with optogenetic activation of the cerebral cortex
M. E. Moore, J. M. Loft, W. C. Clegern, and J. P. Wisor · 2015
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Gradient-based enhancement of tubular structures in medical images
R. Moreno and Ö. Smedby · 2015
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High quality surface reconstruction in radiotherapy: Cross-sectional contours to 3d mesh using wavelets
S. Moriconi, E. Scalco, S. Broggi, B. Avuzzi, R. Valdagni · 2015
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Active Learning for Delineation of Curvilinear Structures
A. Mosinska, R. Sznitman, P. Głowacki, and P. Fua · 2015
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Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks
M. G. Newberry, D. B. Ennis, and V. M. Savage · 2015
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Weakly- and Semi-Supervised Learning of a DCNN for Semantic Image Segmentation
G. Papandreou, L.-C. Chen, K. Murphy, and A. L. Yuille · 2015
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Automated quantification of neuronal networks and single-cell calcium dynamics using calcium imaging
T. P. Patel, K. Man, B. L. Firestein, and D. F. Meaney · 2015
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Predicting Alzheimer’s disease: a neuroimaging study with 3d convolutional neural networks
A. Payan and G. Montana · 2015
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From DIADEM to BigNeuron
H. Peng, E. Meijering, and G. A. Ascoli · 2015
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Tools and techniques for computational reproducibility
S. R. Piccolo, A. B. Lee, and M. B. Frampton · 2015
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Multiscale tensor anisotropic filtering of fluorescence microscopy for denoising microvasculature
V. Prasath, R. Pelapur, O. Glinskii, V. Glinsky, V. Huxley · 2015
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Driverseat: Crowdstrapping Learning Tasks for Autonomous Driving
P. Rajpurkar, T. Migimatsu, J. Kiske, R. Cheng-Yue, S. Tandon · 2015
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Semi-supervised Learning with Ladder Networks
A. Rasmus, M. Berglund, M. Honkala, H. Valpola, and T. Raiko · 2015
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Spectral Representations for Convolutional Neural Networks
O. Rippel, J. Snoek, and R. P. Adams · 2015
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U-Net: Convolutional Networks for Biomedical Image Segmentation
O. Ronneberger, P. Fischer, and T. Brox · 2015
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Neural networks in the future of neuroscience research
M. Rubinov · 2015
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Digital Topology and Geometry in Medical Imaging: A Survey
P. Saha, R. Strand, and G. Borgefors · 2015
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Automatic Morphological Reconstruction of Neurons from Multiphoton and Confocal Microscopy Images Using 3d Tubular Models
A. Santamaría-Pang, P. Hernandez-Herrera, M. Papadakis, P. Saggau, and I. A. Kakadiaris · 2015
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The ImageJ ecosystem: An open platform for biomedical image analysis
J. Schindelin, C. T. Rueden, M. C. Hiner, and K. W. Eliceiri · 2015
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Predicting Semantic Descriptions from Medical Images with Convolutional Neural Networks
T. Schlegl, S. M. Waldstein, W.-D. Vogl, U. Schmidt-Erfurth, and G. Langs · 2015
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A vascular perspective on neuronal migration
M. Segarra, B. C. Kirchmaier, and A. Acker-Palmer · 2015
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Robust and Fragile Aspects of Cortical Blood Flow in Relation to the Underlying Angioarchitecture
A. Y. Shih, C. Rühlmann, P. Blinder, A. Devor, P. J. Drew · 2015
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H.-C. Shin, L. Lu, L. Kim, A. Seff, J. Yao · 2015
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Projection onto the Manifold of Elongated Structures for Accurate Extraction
A. Sironi, V. Lepetit, and P. Fua · 2015
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Deep Feature Learning for EEG Recordings
S. Stober, A. Sternin, A. M. Owen, and J. A. Grahn · 2015
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Parallel Multi-Dimensional LSTM, With Application to Fast Biomedical Volumetric Image Segmentation
M. F. Stollenga, W. Byeon, M. Liwicki, and J. Schmidhuber · 2015
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Deep Learning in Diagnosis of Brain Disorders
H.-I. Suk, D. Shen, and A. D. N. Initiative · 2015
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Learning a Convolutional Neural Network for Non-uniform Motion Blur Removal
J. Sun, W. Cao, Z. Xu, and J. Ponce · 2015
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Rethinking the Inception Architecture for Computer Vision
C. Szegedy, V. Vanhoucke, S. Ioffe, J. Shlens, and Z. Wojna · 2015
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Metrics for evaluating 3d medical image segmentation: analysis, selection, and tool
A. A. Taha and A. Hanbury · 2015
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Acute two-photon imaging of the neurovascular unit in the cortex of active mice
C. H. T. Tran and G. R. Gordon · 2015
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Learning Spatiotemporal Features With 3d Convolutional Networks
D. Tran, L. Bourdev, R. Fergus, L. Torresani, and M. Paluri · 2015
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R. Vemulapalli, O. Tuzel, and M.-Y. Liu · 2015
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Quantum dots: bright and versatile in vitro and in vivo fluorescence imaging biosensors
K. D. Wegner and N. Hildebrandt · 2015
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An Iterative Convolutional Neural Network Algorithm Improves Electron Microscopy Image Segmentation
X. Wu · 2015
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Hybrid CNN and Dictionary-Based Models for Scene Recognition and Domain Adaptation
G.-S. Xie, X.-Y. Zhang, S. Yan, and C.-L. Liu · 2015
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Holistically-Nested Edge Detection
S. Xie and Z. Tu · 2015
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Deep Edge-Aware Filters
L. Xu, J. Ren, Q. Yan, R. Liao, and J. Jia · 2015
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Describing Videos by Exploiting Temporal Structure
L. Yao, A. Torabi, K. Cho, N. Ballas, C. Pal · 2015
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In vivo multi-photon luminescence imaging of cerebral vasculature and blood–brain barrier integrity using gold nanoparticles
H.-J. Yoon, E.-S. Lee, M. Kang, Y. Jeong, and J.-H. Park · 2015
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Stenosis map for volume visualization of constricted tubular structures: Application to coronary artery stenosis
J. Yun, Y. K. Kim, E. J. Chun, Y.-G. Shin, J. Lee · 2015
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