Local tracing of curvilinear structures in volumetric color images: Application to the Brainbow analysis

E. Bas1, D. Erdogmus1, R.W. Draft2, J.W. Lichtman2
1Department of Electrical and Computer Engineering, Northeastern University, 360 Huntington Ave., 409 Dana Research Center, Boston, MA 02148, United States
2Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, United States

Tài liệu tham khảo

Al-Kofahi, 2003, Median-based robust algorithms for tracing neurons from noisy confocal microscope images, IEEE Transactions on Information Technology in Biomedicine, 7, 302, 10.1109/TITB.2003.816564 Al-Kofahi, 2002, Rapid automated three-dimensional tracing of neurons from confocal image stacks, IEEE Transactions on Information Technology in Biomedicine, 6, 171, 10.1109/TITB.2002.1006304 R.E. Alley, Algorithm theoretical basis document for decorrelation stretch, Tech. Rep., 1996. Ascher, 1998 Ascoli, 2007, NeuroMorpho. Org: a central resource for neuronal morphologies, Journal of Neuroscience, 27, 9247, 10.1523/JNEUROSCI.2055-07.2007 Aykac, 2003, Segmentation and analysis of the human airway tree from three-dimensional X-ray CT images, IEEE Transactions on Medical Imaging, 22, 940, 10.1109/TMI.2003.815905 E. Bas, D. Erdogmus, Piecewise linear cylinder models for 3-dimensional axon segmentation, in: 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010. E. Bas, D. Erdogmus, Principal curve tracing, in: European Symposium on Artificial Neural Networks, April 2010b. Bauer, 2000, Distribution of points on a sphere with applications to star catalogs, Journal of Guidance, Control, and Dynamics, 10.2514/2.4497 Cai, 2006, Repulsive force based snake model to segment and track neuronal axons in 3d microscopy image stacks, Neuroimage, 32, 1608, 10.1016/j.neuroimage.2006.05.036 Cai, 2008, Using nonlinear diffusion and mean shift to detect and connect cross-sections of axons in 3d optical microscopy images, Medical Image Analysis, 12, 666, 10.1016/j.media.2008.03.002 Cherkassky, 1996, Shortest paths algorithms: theory and experimental evaluation, Mathematical Programming, 73, 129, 10.1007/BF02592101 Cohen, 1994, Automated tracing and volume measurements of neurons from 3d confocal fluorescence microscopy data, Microscopy, 173, 103, 10.1111/j.1365-2818.1994.tb03433.x Comaniciu, 2002, Mean shift: a robust approach toward feature space analysis, IEEE Transactions on Pattern Analysis and Machine Intelligence, 24, 603, 10.1109/34.1000236 Cruz, 2004, Non-linear model fitting to parameterize diseased blood vessels, 393 Dempster, 1977, Maximum likelihood from incomplete data via the EM algorithm, Journal of the Royal Statistical Society. Series B (Methodological), 39, 1, 10.1111/j.2517-6161.1977.tb01600.x Deschamps, 2001, Fast extraction of minimal paths in 3D images and applications to virtual endoscopy, Medical Image Analysis, 5, 10.1016/S1361-8415(01)00046-9 Eberly, 1996 Feng, 2000, Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP, Neuron, 28, 41, 10.1016/S0896-6273(00)00084-2 Fletcher, 1963, A rapidly convergent descent method for minimization, The Computer Journal, 6, 163, 10.1093/comjnl/6.2.163 Frangi, 1999, Model-based quantitation of 3-D magnetic resonance angiographic images, IEEE Transactions on Medical Imaging, 18, 946, 10.1109/42.811279 González, 2010, Delineating trees in noisy 2D images and 3D image-stacks, 2799 Hampel, 2011, Drosophila Brainbow: a recombinase-based fluorescence labeling technique to subdivide neural expression patterns, Nature Methods, 10.1038/nmeth.1566 Hastie, 1989, Principal curves, Journal of the American Statistical Association, 84, 502, 10.1080/01621459.1989.10478797 Kasthuri, 2003, The role of neuronal identity in synaptic competition, Nature, 424, 426, 10.1038/nature01836 Kégl, 2002, Learning and design of principal curves, IEEE Transactions on Pattern Analysis and Machine Intelligence, 22, 281, 10.1109/34.841759 Kitamura, 1988, Estimating the 3d skeletons and transverse areas of coronary arteries from biplane angiograms, IEEE Transactions on Medical Imaging, 7, 173, 10.1109/42.7779 Lee, 1991, Detecting boundaries in a vector field, IEEE Transactions on Signal Processing, 39, 1181, 10.1109/78.80971 Lee, 1994, Building skeleton models via 3-d medial surface axis thinning algorithms, Graphical Models and Image Processing, 56, 462, 10.1006/cgip.1994.1042 D. Lesage, E. Angelini, I. Bloch, G. Funka-Lea, Medial-based Bayesian tracking for vascular segmentation: application to coronary arteries in 3d CT angiography, in: 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2008, 2008, pp. 268–271. Lichtman, 2008, A technicolour approach to the connectome, Nature Reviews Neuroscience, 9, 417, 10.1038/nrn2391 Livet, 2007, Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system, Nature, 450, 56, 10.1038/nature06293 Lu, 2011, Neuronal tracing for connectomic studies, Neuroinformatics, 9, 159, 10.1007/s12021-011-9101-6 Meijering, 2010, Neuron tracing in perspective, Cytometry Part A, 77, 693, 10.1002/cyto.a.20895 Meijering, 2004, Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images, Cytometry Part A, 58A, 167, 10.1002/cyto.a.20022 R. Mikaël, P. Nikos, D. Rachid, Active shape models from a level set perspective, Tech. Rep. 4984, INRIA, 2003. <http://www-sop.inria.fr/rapports/sophia/RR-4984.html>. J. Miller, Relative critical sets in RR(N) and applications to image analysis. PhD dissertation, Dept. of Math., Univ. of NC, 1998. D. Nain, A. Yezzi, G. Turk, Vessel segmentation using a shape driven flow, in: Proc. of MICCAI’04, 2004, pp. 51–59. Osher, 1988, Fronts propagating with curvature dependent speed: algorithms based on Hamilton-Jacobi formulations, Journal of Computational Physics, 79, 12, 10.1016/0021-9991(88)90002-2 Ozertem, 2011, Locally defined principal curves and surfaces, Journal of Machine Learning Research, 12, 1249 Palágyi, 1998, A 3d 6-subiteration thinning algorithm for extracting medial lines, Pattern Recognition Letters, 19, 613, 10.1016/S0167-8655(98)00031-2 Peng, 2010, V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets, Nature Biotechnology, 10.1038/nbt.1612 Santamaría-Pang, 2007, Automatic centerline extraction of irregular tubular structures using probability volumes from multiphoton imaging, Medical Image Computing and Computer-Assisted Intervention – MICCAI, 2007, 486 Sato, 1998, 3d Multi-scale line filter for segmentation and visualization of curvilinear structures in medical images, Medical Image Analysis, 143, 10.1016/S1361-8415(98)80009-1 Schmitt, 2004, New methods for the computer-assisted 3d reconstruction of neurons, NeuroImage, 23, 1283, 10.1016/j.neuroimage.2004.06.047 Silverman, 1998 Streekstra, 2002, Analysis of tubular structures in three-dimensional confocal images, Network: Computation in Neural Systems, 13, 381, 10.1088/0954-898X/13/3/308 C. Tomasi and R. Manduchi, Bilateral filtering for gray and color images, in Proceedings 6th International Conference on Computer Vision, pp. 839–846, 1998. Tyrrell, 2007, Robust 3-d modeling of vasculature imagery using superellipsoids, IEEE Transactions on Medical Imaging, 26, 223, 10.1109/TMI.2006.889722 Vasilkoski, 2009, Detection of the optimal neuron traces in confocal microscopy images, Journal of Neuroscience Methods, 178, 197, 10.1016/j.jneumeth.2008.11.008 Waltz, 2006, An interior algorithm for nonlinear optimization that combines line search and trust region steps, Mathematical Programming, 107, 391, 10.1007/s10107-004-0560-5 J. Wang, X. Zhou, J. Lu, J. Lichtman, S.-F. Chang, S. Wong, Dynamic local tracing for 3d axon curvilinear structure detection from microscopic image stack, in: 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2007, 2007, pp. 81–84. Wink, 2004, Multiscale vessel tracking, IEEE Transactions on Medical Imaging, 23, 130, 10.1109/TMI.2003.819920 Zhang, 2008, 3d Axon structure extraction and analysis in confocal fluorescence microscopy images, Neural Computation, 20, 1899, 10.1162/neco.2008.05-07-519 Zhou, 2008, 3d Dendrite reconstruction and spine identification, 18 X. Zhu, Z. Xue, X. Gao, Y. Zhu, S.T. Wong, Voles: vascularity-oriented level set algorithm for pulmonary vessel segmentation in image guided intervention therapy, in: Proceedings of ISBI’09.