Detection of the optimal neuron traces in confocal microscopy images

Journal of Neuroscience Methods

Volumn 178, Issue 1, 2009, Pages 197-204

  Vasilkoski, Zlatko ^a   Stepanyants, Armen ^a  

^a NORTHEASTERN UNIVERSITY   (United States)

Author keywords

Axon; Confocal microscopy; Dendrite; Morphology; Optimization; Reconstruction; Skeleton

Indexed keywords

ALGORITHM; ANIMAL CELL; ARTICLE; CONFOCAL MICROSCOPY; CONTROLLED STUDY; DENDRITE; MONKEY; NERVE CELL; NERVE FIBER; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; THREE DIMENSIONAL IMAGING;

ALGORITHMS; ANIMALS; BRAIN; DENDRITES; HAPLORHINI; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROSCOPY, CONFOCAL; MODELS, NEUROLOGICAL; PYRAMIDAL CELLS;

EID: 59249101942     PISSN: 01650270     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jneumeth.2008.11.008     Document Type: Article

References (47)

1. Al-Kofahi K.A., Lasek S., Szarowski D.H., Pace C.J., Nagy G., Turner J.N., et al. Rapid automated three-dimensional tracing of neurons from confocal image stacks. IEEE Trans Inf Technol Biomed 6 (2002) 171-187
2. Ascoli G.A. Mobilizing the base of neuroscience data: the case of neuronal morphologies. Nat Rev Neurosci 7 (2006) 318-324
3. Ascoli G.A. Successes and rewards in sharing digital reconstructions of neuronal morphology. Neuroinformatics 5 (2007) 154-160
4. Binzegger T., Douglas R.J., and Martin K.A. A quantitative map of the circuit of cat primary visual cortex. J Neurosci 24 (2004) 8441-8453
5. Boyd S.P., and Vandenberghe L. Convex optimization (2004), Cambridge University Press, Cambridge, UK/ New York
6. Braitenberg V., and Schüz A. Cortex: statistics and geometry of neuronal connectivity. 2nd thoroughly rev. ed. (1998), Springer, Berlin/ New York
7. Briggman K.L., and Denk W. Towards neural circuit reconstruction with volume electron microscopy techniques. Curr Opin Neurobiol 16 (2006) 562-570
8. Cai H., Xu X., Lu J., Lichtman J., Yung S.P., and Wong S.T. Using nonlinear diffusion and mean shift to detect and connect cross-sections of axons in 3D optical microscopy images. Med Image Anal 12 6 (2008) 666-675
9. Can A., Shen H., Turner J.N., Tanenbaum H.L., and Roysam B. Rapid automated tracing and feature extraction from retinal fundus images using direct exploratory algorithms. IEEE Trans Inf Technol Biomed 3 (1999) 125-138
10. Cannon R.C., Turner D.A., Pyapali G.K., and Wheal H.V. An on-line archive of reconstructed hippocampal neurons. J Neurosci Methods 84 (1998) 49-54
11. Conchello J.A., and Lichtman J.W. Optical sectioning microscopy. Nat Methods 2 (2005) 920-931
12. Duan H., Wearne S.L., Morrison J.H., and Hof P.R. Quantitative analysis of the dendritic morphology of corticocortical projection neurons in the macaque monkey association cortex. Neuroscience 114 (2002) 349-359
13. Duan H., Wearne S.L., Rocher A.B., Macedo A., Morrison J.H., and Hof P.R. Age-related dendritic and spine changes in corticocortically projecting neurons in macaque monkeys. Cereb Cortex 13 (2003) 950-961
14. Elston G.N., and Rosa M.G. The occipitoparietal pathway of the macaque monkey: comparison of pyramidal cell morphology in layer III of functionally related cortical visual areas. Cereb Cortex 7 (1997) 432-452
15. Fiala J.C. Reconstruct: a free editor for serial section microscopy. J Microsc 218 (2005) 52-61
16. Frangi A.F., Niessen W.J., Hoogeveen R.M., van Walsum T., and Viergever M.A. Model-based quantitation of 3-D magnetic resonance angiographic images. IEEE Trans Med Imaging 18 (1999) 946-956
17. Jefferis G.S., Potter C.J., Chan A.M., Marin E.C., Rohlfing T., Maurer Jr. C.R., et al. Comprehensive maps of Drosophila higher olfactory centers: spatially segregated fruit and pheromone representation. Cell 128 (2007) 1187-1203
18. Kass M., Witkin A., and Terzopoulos D. Snakes: active contour models. Int J Comput Vis 1 (1988) 321-331
19. Kozloski J., Hamzei-Sichani F., and Yuste R. Stereotyped position of local synaptic targets in neocortex. Science 293 (2001) 868-872
20. Lee S., and Stevens C.F. General design principle for scalable neural circuits in a vertebrate retina. Proc Natl Acad Sci USA 104 (2007) 12931-12935
21. Lee T.C., Kashyap R.L., and Chu C.N. Building skeleton models via (3D) medial surface/axis thinning algorithms. CVGIP: Graph Models Image Process 56 (1994) 462-478
22. Li Y., Brewer D., Burke R.E., and Ascoli G.A. Developmental changes in spinal motoneuron dendrites in neonatal mice. J Comp Neurol 483 (2005) 304-317
23. Lichtman J.W., Livet J., and Sanes J.R. A technicolour approach to the connectome. Nat Rev Neurosci 9 (2008) 417-422
24. Livet J., Weissman T.A., Kang H., Draft R.W., Lu J., Bennis R.A., et al. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature 450 (2007) 56-62
25. Lubke J., Roth A., Feldmeyer D., and Sakmann B. Morphometric analysis of the columnar innervation domain of neurons connecting layer 4 and layer 2/3 of juvenile rat barrel cortex. Cereb Cortex 13 (2003) 1051-1063
26. Markram H. The blue brain project. Nat Rev Neurosci 7 (2006) 153-160
27. Meijering E., Jacob M., Sarria J.C., Steiner P., Hirling H., and Unser M. Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images. Cytometry A 58 (2004) 167-176
28. Micheva K.D., and Smith S.J. Array tomography: a new tool for imaging the molecular architecture and ultrastructure of neural circuits. Neuron 55 (2007) 25-36
29. Nimchinsky E.A., Hof P.R., Young W.G., and Morrison J.H. Neurochemical, morphologic, and laminar characterization of cortical projection neurons in the cingulate motor areas of the macaque monkey. J Comp Neurol 374 (1996) 136-160
30. Nimchinsky E.A., Young W.G., Yeung G., Shah R.A., Gordon J.W., Bloom F.E., et al. Differential vulnerability of oculomotor, facial, and hypoglossal nuclei in G86R superoxide dismutase transgenic mice. J Comp Neurol 416 (2000) 112-125
31. Palagyi K., and Kuba A. A 3D 6-subiteration thinning algorithm for extracting medial lines. Pattern Recognit Lett 19 (1998) 613-627
32. Russ J.C. The image processing handbook. 5th ed. (2007), CRC/Taylor and Francis, Boca Raton
33. Sato Y., Nakajima S., Shiraga N., Atsumi H., Yoshida S., Koller T., et al. Three-dimensional multi-scale line filter for segmentation and visualization of curvilinear structures in medical images. Med Image Anal 2 (1998) 143-168
34. Schmitt S., Evers J.F., Duch C., Scholz M., and Obermayer K. New methods for the computer-assisted 3-D reconstruction of neurons from confocal image stacks. Neuroimage 23 (2004) 1283-1298
35. Shepherd G.M., Stepanyants A., Bureau I., Chklovskii D., and Svoboda K. Geometric and functional organization of cortical circuits. Nat Neurosci 8 (2005) 782-790
36. Shikata H., Yin Z., Park Y., Kitaoka H., Sato Y., Johkoh T., et al. An algorithm for localizing branch points of pulmonary vessels for nonrigid registration of the lungs. Syst Comput Jpn 35 (2004) 1613-1623
37. Srinivasan R., Zhou X., Miller E., Lu J., Litchman J., and Wong S.T. Automated axon tracking of 3D confocal laser scanning microscopy images using guided probabilistic region merging. Neuroinformatics 5 (2007) 189-203
38. Stepanyants A., and Chklovskii D.B. Neurogeometry and potential synaptic connectivity. Trends Neurosci 28 (2005) 387-394
39. Stepanyants A., Tamás G., and Chklovskii D.B. Class-specific features of neuronal wiring. Neuron 43 (2004) 251-259
40. Stepanyants A., Hirsch J.A., Martinez L.M., Kisvárday Z.F., Ferecskó A.S., and Chklovskii D.B. Local potential connectivity in cat primary visual cortex. Cereb Cortex 18 (2008) 13-28
41. Stettler D.D., Das A., Bennett J., and Gilbert C.D. Lateral connectivity and contextual interactions in macaque primary visual cortex. Neuron 36 (2002) 739-750
42. Streekstra G.J., and van Pelt J. Analysis of tubular structures in three-dimensional confocal images. Network 13 (2002) 381-395
43. Wang J, Zhou X, Lu J, Lichtman J, Chang S-F, Wong STC. Dynamic local tracing for 3D axon curvilinear structure detection from microscopic image stack. In: IEEE, international symposium of biomedical imaging (ISBI). Washington, DC; 2007. p. 81-4, http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=04193227.
44. Wickersham I.R., Lyon D.C., Barnard R.J., Mori T., Finke S., Conzelmann K.K., et al. Monosynaptic restriction of transsynaptic tracing from single, genetically targeted neurons. Neuron 53 (2007) 639-647
45. Yamasaki T., Isokawa T., Matsui N., Ikeno H., and Kanzaki R. Reconstruction and simulation for three-dimensional morphological structure of insect neurons. Neurocomputing 69 (2006) 1043-1047
46. Zhou Y., and Toga A.W. Efficient skeletonization of volumetric objects. IEEE Trans Vis Comput Graph 05 (1999) 196-209
47. Zhou Y., Kaufman A., and Toga A.W. Three-dimensional skeleton and centerline generation based on an approximate minimum distance field. Vis Comput 14 (1998) 303-314