Rayburst sampling, an algorithm for automated three-dimensional shape analysis from laser scanning microscopy images

Nature Protocols

Volumn 1, Issue 4, 2006, Pages 2152-2161

  Rodriguez, Alfredo ^a   Ehlenberger, Douglas B ^a   Hof, Patrick R ^a   Wearne, Susan L ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL TISSUE; ARTICLE; BRANCHING MORPHOGENESIS; CELL FUNCTION; CELL SHAPE; CELL SIZE; CELL STRUCTURE; CELL SURFACE; CELL VOLUME; DENDRITIC SPINE; LASER MICROSCOPY; MONKEY; MORPHOMETRICS; NERVE CELL; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING;

ALGORITHMS; IMAGING, THREE-DIMENSIONAL; MICROSCOPY, CONFOCAL; NEURONS;

EID: 34248652917     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2006.313     Document Type: Article

References (40)

1. Vetter, P., Roth, A. & Häusser, M. Propagation of action potentials in dendrites depends on dendritic morphology. J. Neurophysiol. 85, 926-937 (2001).
2. Euler, T. & Denk, W. Dendritic processing. Curr. Opin. Neurobiol. 11, 415-422 (2001).
3. Stuart, G., Spruston, N. & Häusser, M. Dendrites (Oxford University Press, Oxford, 1999).
4. Rothnie, P., Kabaso, D., Hof, P.R., Henry, B.I. & Wearne, S.L. Functionally relevant measures of spatial complexity in neuronal dendritic arbors. J. Theor. Biol. 238, 506-526 (2004).
5. Mainen, Z.F. & Sejnowski, T.J. Influence of dendritic structure on firing pattern in model neocortical neurons. Nature 382, 363-366 (1996).
6. Krichmar, J.L., Nasuto, S.J., Scorcioni, R., Washington, S.D. & Ascoli, G.A. Effects of dendritic morphology on CA3 pyramidal cell electrophysiology: A simulation study. Brain Res. 941, 11-28 (2002).
7. Ascoli, G.A. Passive dendritic integration heavily affects spiking dynamics of recurrent networks. Neural Networks. 16, 657-663 (2003).
8. Häusser, M. & Mel, B.W. Dendrites: Bug or feature? Curr. Opin. Neurobiol. 13, 372-383 (2003).
9. Bloom, F.E., Young, W.G., Nimchinsky, E.A., Hof, P.R. & Morrison, J.H. Neuronal vulnerability and informatics in human disease. in Neuroinformatics - An Overview of the Human Brain Project (eds. Koslow, S.H. & Huerta, M.F.) 83-123 (Mahwah, Lawrence Erlbaum, 1997).
10. Streekstra, G.J., Smeulders, A.W.M. & van den Boomgaard, R. Scale dependent differential geometry for the measurement of center line and diameter in 3D curvilinear structures. in 6th European Conference on Computer Vision 2000 (Dublin, Ireland, 2000).
11. Streekstra, G.J. & van Pelt, J. Analysis of tubular structures in three-dimensional confocal images. Network Comput. Neural Systems 13, 381-395 (2002).
12. Dima, A., Scholz, M. & Obermayer, K. Semi-automatic quality determination of 3D confocal microscope scans of neuronal cells denoised by 3D-wavelet-shrinkage. In: H.H. Szu, ed., Wavelet Applications VI-Proceedings of the SPIE, 3723, 446-457 (1999).
13. Messerli, M. NeuronTracer Reference Manual V. 1.0##1-33 (Zurich, Bitplane AG, 2000).
14. Schmitt, S., Evers, J.F., Duch, C., Scholz, M. & Obermayer, K. New methods for the computer-assisted 3-D reconstruction of neurons from confocal image stacks. NeuroImage 23, 1283-1298 (2004).
15. He, W. et al. Automated three-dimensional tracing of neurons in confocal and brightfield images. Microsc. Microanal. 9, 296-310 (2003).
16. Al-Kofahi, K.A. et al. Rapid automated three-dimensional tracing of neurons from confocal image stacks. IEEE Trans. Inform. Tech. Biomed. 6, 171-187 (2003).
17. van Pelt, J., van Ooyen, A. & Uylings, H.B.M. The need for integrating neuronal morphology databases and computational environments in exploring neuronal structure and function. Anat. Embryol. 204 255-265 (2001).
18. Ashby, N. & Brittin, W.E. Thomson's problem. Am. J. Phys. 54 776-777 (1986).
19. Wearne, S.L. et al. New techniques for imaging, digitization and analysis of three-dimensional neuronal morphology on multiple scales. Neuroscience 136, 661-680 (2005).
20. Hill, S. Trilinear interpolation. in Graphics Gems IV (ed. Heckbert, P.S.). 521-525 (Academic Press, San Diego, 1994).
21. Scorcioni, R. & Ascoli, G.A. Algorithmic extraction of morphological statistics from electronic archives of neuroanatomy. in IWANN 2001, Lecture Notes in Computer Science (eds. Mira, J. & Prieto, A.) 30-37 (Springer-Verlag, Berlin, Heidelberg, 2001).
22. Weaver, C.M., Hof, P.R., Wearne, S.L. & Lindquist, W.B. Automated algorithms for multiscale morphometry of neuronal dendrites. Neural Comput. 16, 1353-1383 (2004).
23. Hines, M.L. The NEURON simulation program. in Neural Network Simulation Environments (ed. Skrzypek, J.) 147-163 (Kluwer, Norwell, MA, 1994).
24. Bower, J.M. & Beeman, D. The Book of Genesis: Exploring Realistic Neural Systems with the General Neural Simulation System 2nd edn. (Springer-Verlag, New York, NY, 1998).
25. Blum, H. A transformation for extracting new descriptors of shape. in Models for the Perception of Speech and Visual Form (ed. Wathen-Dunn, W.) 362-380 (MIT Pressm Cambridge, MA, 1967).
26. Koh, I.Y.Y., Lindquist, W.B., Zito, K., Nimchinsky, E.A. & Svoboda, K. An image analysis algorithmfor the fine structure of neuronal dendrites. Neural Comput. 14, 1283-1310 (2002).
27. Borgefors, G., Nystrom, I. & Sanniti Di Baja, G. Computing skeletons in three dimensions. Pattern Recognition 32, 1225-1236 (1999).
28. Peters, A., Palay, S.L. & Webster, H.D. The Fine Structure of the Nervous System (Oxford University Press, New York, 1991).
29. Jain, A.K. Fundamentals of Digital Image Processing (Prentice-Hall, Englewood Cliffs, NJ, 1989).
30. Rodriguez, A. et al. Automated reconstruction of 3D neuronal morphology from laser scanning microscopy images. Methods Companion Methods Enzymol. 30, 94-105 (2003).
31. Wu, C.-C., Reilly, J.F., Young, W.G., Morrison, J.H. & Bloom, F.E. High-throughput morphometric analysis of individual neurons. Cereb. Cortex 14, 543-554 (2004).
32. Hao, J. et al. Estrogen alters spine number and morphology in prefrontal cortex of aged female rhesus monkeys. J. Neurosci. 26, 2571-2578 (2006).
33. Cannon, R.C., Turner, D.A., Pyapali, G.K. & Wheal, H.V. An on-line archive of reconstructed hippocampal neurons. J. Neurosci. Methods 84, 49-54 (1998).
34. Hsiao, K. et al. Correlative memory deficits, Aβ elevation, and amyloid plaques in transgenic mice. Science 274, 99-102 (1996).
35. Duan, H., Wearne, S.L., Morrison, J.H. & Hof, P.R. Quantitative analysis of the dendritic morphology of corticocortical projection neurons in the macaque monkey association cortex. Neuroscience 114, 349-359 (2002).
36. Duan, H. et al. Age-related morphologic alterations in dendrites and spine densities of corticocortically projecting neurons in macaque monkeys. Cereb. Cortex 13, 950-961 (2003).
37. Perl, D.P. et al. Practical approaches to stereology in the setting of aging and disease-related brain banks. J. Chem. Neuroanat. 20, 7-19 (2000).
38. Hof, P.R., Nimchinsky, E.A. & Morrison, J.H. Neurochemical phenotype of corticocortical connections in the macaque monkey: Quantitative analysis of a subset of neurofilament protein-immunoreactive projection neurons in frontal, parietal, temporal and cingulate cortices. J. Comp. Neurol. 362, 109-133 (1995).
39. Nimchinsky, E.A., Hof, P.R., Young, W.G. & 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, 136-160 (1996).
40. Romijn, H.J. et al. Double immunolabeling of neuropeptides in the human hypothalamus as analyzed by confocal laser scanning fluorescence microscopy. J. Histochem. Cytochem. 47, 229-235 (1999).