Anisotropic path searching for automatic neuron reconstruction

Medical Image Analysis

Volumn 15, Issue 5, 2011, Pages 680-689

  Xie, Jun ^a   Zhao, Ting ^a   Lee, Tzumin ^a   Myers, Eugene ^a   Peng, Hanchuan ^a  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Microscopy imaging; Neuron comparison; Neuron reconstruction

Indexed keywords

COMPARISON METHODS; COMPUTATIONALLY EFFICIENT; DATA SETS; MICROSCOPY IMAGING; NEURITES; NEURON RECONSTRUCTION; NEURONAL STRUCTURE; NOVEL METHODS; OPTIMALITY; PERFORMANCE EVALUATION; PRESYNAPTIC; STRUCTURE ANALYSIS; TEMPLATE-BASED METHOD; THREE-DIMENSIONAL MICROSCOPY; TOPOLOGICAL CONSTRAINTS; TRACING PROBLEM; WEIGHTED GRAPH;

ALGORITHMS;

NEURONS;

ALGORITHM; ANISOTROPIC PATH SEARCHING; ANISOTROPY; ARTICLE; CELL STRUCTURE; CONTROLLED STUDY; DROSOPHILA; IMAGE QUALITY; IMAGE RECONSTRUCTION; IMAGING SYSTEM; INTERMETHOD COMPARISON; NERVE CELL; NEUROANATOMICAL TRACT TRACING; NONHUMAN; OUTCOME ASSESSMENT; PRIORITY JOURNAL;

ALGORITHMS; ANIMALS; ANISOTROPY; DROSOPHILA; IMAGE ENHANCEMENT; IMAGE INTERPRETATION, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MICROSCOPY; NEURONS; PATTERN RECOGNITION, AUTOMATED;

EID: 80052165284     PISSN: 13618415     EISSN: 13618423     Source Type: Journal    
DOI: 10.1016/j.media.2011.05.013     Document Type: Article

References (29)

1. Aho A.V., Ullman J.D., Hopcroft J.E. Data Structures and Algorithms 1985, Addison-Wesley.
2. Al-kofahi K.A., Lasek S., Szarowski D.H., Pace C.J., Nagy G., Member S., Turner J.N., Roysam B. Rapid automated three-dimensional tracing of neurons from confocal image stacks. IEEE Transactions on Information Technology in Biomedicine 2002, 6:171-187.
3. Al-kofahi K.A., Can A., Lasek S., Szarowski D.H., Dowell-mesfin N., Shain W., Turner J.N., Roysam B. Median-based robust algorithms for tracing neurons from noisy confocal microscope images. IEEE Transactions on Information Technology in Biomedicine 2003, 7:302-317.
4. Al-Kofahi Y., Dowell-Mesfin N., Pace C., Shain W., Turner J.N., Roysam B. Improved detection of branching points in algorithms for automated neuron tracing from 3D confocal images. Cytometry Part A 2008, 73:36-43.
5. Bullitt E., Aylward S., Smith K., Mukherji S., Jiroutek M., Muller K. Symbolic description of intracerebral vessels segmented from magnetic resonance angiograms and evaluation by comparison with X-ray angiograms. Medical Image Analysis 2001, 5:157-169.
6. Can A., Shen H., Turner J.N., Tanenbaum H.L., Roysam B. Rapid automated tracing and feature extraction from retinal fundus images using direct exploratory algorithms. IEEE Transactions on Information Technology in Biomedicine 1999, 3:125-138.
7. Cohen A., Roysam B., Turner J. Automated tracing and volume measurements of neurons from 3D confocal fluorescence microscopy data. Journal of Microscopy 1994, 173:103-114.
8. Dijkstra E.W. A note on two problems in connection with graphs. Numerische Mathematic 1959, 269-271.
9. Evers J., Schmitt S., Sibila M., Duch C. Progress in functional neuroanatomy: precise automatic geometric reconstruction of neuronal morphology from confocal image stacks. Journal of Neurophysiology 2005, 93:2331-2342.
10. Felzenszwalb, P.F., Huttenlocher, D.P., 2004. Distance Transforms of Sampled Functions. Technical Report. Cornell Computing and Information Science.
11. Frangi A., Niessen W., Hoogeveen R., van Walsum T., Viergever M. Model-based quantitation of 3-D magnetic resonance angiographic images. IEEE Transactions on Medical Imaging 1999, 946-956.
12. He W., Hamilton T.A., Cohen A.R., Holmes T.J., Pace C., Szarowski D.H., Turner J.N., Roysam B. Automated three-dimensional tracing of neurons in confocal and brightfield images. Microscopy 2003, 9:296-310.
13. Jefferis G., Potter C., Chan A., Marin E., Rohlfing T., Maurer C., Luo L. Comprehensive maps of Drosophila higher olfactory centers: spatially segregated fruit and pheromone representation. Cell 2007, 128:1187-1203.
14. Johnson D.B. Efficient algorithms for shortest paths in sparse networks. Journal of the ACM 1977, 24:1-13.
15. Kass M., Witkin A., Terzopoulos D. Snakes: active contour models. International Journal on Computer Vision 1988, 321-331.
16. Kirbas C., Quek F. A review of vessel extraction techniques and algorithms. ACM Computing Surveys 2004, 36:81-121.
17. Koh I.Y.Y., Lindquist W.B., Zito K., Nimchinsky E.A., Svoboda K. An image analysis algorithm for dendritic spines. Neural Computation 2002, 14:1283-1310.
18. Meijering E., Jacob M., Sarria J.C., Steiner P., Hirling H., Unser M. Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images. Cytometry Part A 2004, 167-176.
19. Peng H., Ruan Z., Long F., Simpson J.H., Myers E. V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nature Biotechnology 2010, 28:348-353.
20. Quek F., Kirbas C. Vessel extraction in medical images by wave-propagation and traceback. Medical Imaging 2001, 20:117-131.
21. Schmitt S., Evers J., Duch C., Scholz M., Obermayer K. New methods for the computer-assisted 3-D reconstruction of neurons from confocal image stacks. NeuroImage 2004, 1283-1298.
22. Serra J., Soille P. Mathematical Morphology and Its Applications to Image Processing 1994, Kluwer Academic Publishers.
23. Shen H., Roysam B., Stewart C.V., Turner J.N., Tanenbaum H.L. Optimal scheduling of tracing computations for real-time vascular landmark extraction from retinal fundus images. IEEE Transactions on Information Technology in Biomedicine 2001, 5:77-91.
24. Vasilkoski Z., Stepanyants A. Detection of the optimal neuron traces in confocal microscopy images. Journal of Neuroscience Methods 2009, 178:197-204.
25. Xiong, G., Zhou, X., Ji, L., Degterev, A., Wong, S., 2006. Automated labeling of neurites in fluorescence microscopy images. In: Proceedings of 3rd IEEE International Symposium on Biomedical Imaging: Nano to Macro, pp. 534-537.
26. Yim P.J., Choyke P.L., Summers R.M. Gray-scale skeletonization of small vessels in magnetic resonance angiography. IEEE Transactions on Medical Imaging 2000, 19:568-576.
27. Zack G.W., Rogers W.E., Latt S.A. Automatic measurement of sister chromatid exchange frequency. Journal of Histochemistry & Cytochemistry 1977, 25:741-753.
28. Zana F., Klein J.C. Segmentation of vessel-like patterns using mathematical morphology and curvature evaluation. IEEE Transactions on Image Processing 2001, 10:1010-1019.
29. Zhang Y., Zhou X., Degterev A., Lipinski M., Adjeroh D., Yuan J., Wong S.T. Automated neurite extraction using dynamic programming for high-throughput screening of neuron-based assays. NeuroImage 2007, 35:1502-1515.