Digital reconstructions of neuronal morphology: Three decades of research trends

Frontiers in Neuroscience

Volumn , Issue APR, 2012, Pages

  Halavi, Maryam ^a   Hamilton, Kelly A ^a   Parekh, Ruchi ^a   Ascoli, Giorgio A ^a  

^a George Mason University   (United States)

Author keywords

Data mining; Data sharing; Digital reconstruction; Literature mining; NeuroMorpho.Org; Neuron morphology; Potential connectivity; Three dimensional reconstruction

Indexed keywords

BRAIN REGION; DATA MINING; DIGITAL IMAGING; IMAGE RECONSTRUCTION; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MEDICAL RESEARCH; NERVE CELL NETWORK; PUBLICATION; REVIEW; SCIENTIFIC LITERATURE;

EID: 84862232853     PISSN: 16624548     EISSN: 1662453X     Source Type: Journal    
DOI: 10.3389/fnins.2012.00049     Document Type: Review

References (50)

1. Ascoli, G. A., Donohue, D. E., and Halavi, M. (2007). NeuroMorpho.Org - a central resource for neuronal morphologies. J. Neurosci. 27, 9247-9251.
2. Bas, E., and Erdogmus, D. (2011). Principal curves as skeletons of tubular objects: locally characterizing the structures of axons. Neuroinformatics 9, 181-191.
3. Blinkov, S. M., and Ivanitskii, G. R. (1968). Automatic analysis of brain cells. Vestn. Akad. Med. Nauk SSSR 23, 84-85.
4. Borst, A., and Haag, J. (1996). The intrinsic electrophysiological characteristics of fly lobula plate tangential cells: I. Passive membrane properties. J. Comput. Neurosci. 3, 313-336.
5. Cannon, R. C., Turner, D. A., Pyapali, G. K., and Wheal, H. V. (1998). An on-line archive of reconstructed hippocampal neurons. J. Neurosci. Methods 84, 49-54.
6. Capowski, J. J. (1976). Characteristics of neuroscience computer graphics displays and a proposed system to generate those displays. Comput. Graph. 10, 257-261.
7. Capowski, J. J. (1977). Computer-aided reconstruction of neuron trees from several serial sections. Comput. Biomed. Res. 10, 617-629.
8. Capowski, J. J. (1983). An automatic neuron reconstruction system. J. Neurosci. Methods 8, 353-364.
9. Capowski, J. J., and Réthelyi, M. (1982). Neuron reconstruction using a Quantimet image analyzing computer system. Acta Morphol. Acad. Sci. Hung. 30, 241-249.
10. Capowski, J. J., and Sedivec, M. J. (1981). Accurate computer reconstruction and graphics display of complex neurons utilizing state-of-the-art interactive techniques. Comput. Biomed. Res. 14, 518-532.
11. Chiang, A. S., Lin, C. Y., Chuang, C. C., Chang, H. M., Hsieh, C. H., Yeh, C. W., Shih, C. T., Wu, J. J., Wang, G. T., Chen, Y. C., Wu, C. C., Chen, G. Y., Ching, Y. T., Lee, P. C., Lin, C. Y., Lin, H. H., Wu, C. C., Hsu, H. W., Huang, Y. A., Chen, J. Y., Chiang, H. J., Lu, C. F., Ni, R. F., Yeh, C. Y., and Hwang, J. K. (2011). Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution. Curr. Biol. 21, 1-11.0
12. Chothani, P., Mehta, V., and Stepanyants, A. (2011). Automated tracing of neurites from light microscopy stacks of images. Neuroinformatics 9, 263-278.
13. De Schutter, E., and Bower, J. M. (1994). An active membrane model of the cerebellar Purkinje cell: I. Simulation of current clamps in slice. J. Neurophysiol. 71, 375-400.
14. DeVoogd, T. J., Chang, F. L., Floeter, M. K., Jencius, M. J., and Greenough, W. T. (1981). Distortions induced in neuronal quantification by camera lucida analysis: comparisons using a semi-automated data acquisition system. J. Neurosci. Methods 3, 285-294.
15. Donohue, D. E., and Ascoli, G. A. (2011). Automated reconstruction of neuronal morphology: an overview. Brain Res. Rev. 67, 94-102.
16. Freund, T. F., and Buzsáki, G. (1996). Interneurons of the hippocampus. Hippocampus 6, 347-470.
17. Garvey, C. F., Young, J. H. Jr., Coleman, P. D., and Simon, W. (1973). Automated three-dimensional dendrite tracking system. Electroencephalogr. Clin. Neurophysiol. 35, 199-204.
18. Gilbert, C. D., and Wiesel, T. N. (1983). Clustered intrinsic connections in cat visual cortex. J. Neurosci. 3, 1116-1133.
19. Gillette, T. A., Brown, K. M., and Ascoli, G. A. (2011). The DIADEM metric: comparing multiple reconstructions of the same neuron. Neuroinformatics 9, 233-245.
20. Glaser, E. M., and Van der loos, H. (1965). A semi-automatic computer-microscope for the analysis of neuronal morphology. IEEE Trans. Biomed. Eng. 12, 22-31.
21. Gonchar, Y., and Burkhalter, A. (1997). Three distinct families of GABAergic neurons in rat visual cortex. Cereb. Cortex 7, 347-358.
22. Halavi, M., Polavaram, S., Donohue, D. E., Hamilton, G., Hoyt, J., Smith, K. P., and Ascoli, G. A. (2008). NeuroMorpho.Org implementation of digital neuroscience: dense coverage and integration with the NIF. Neuroinformatics 6, 241-252.
23. Häusser, M., Spruston, N., and Stuart, G. J. (2000). Diversity and dynamics of dendritic signaling. Science 290, 739-744.
24. Johnson, E. M., and Capowski, J. J. (1983). A system for the three-dimensional reconstruction of biological structures. Comput. Biomed. Res. 16, 79-87.
25. Kozloski, J. (2011). Automated reconstruction of neural tissue and the role of large-scale simulation. Neuroinformatics 9, 133-142.
26. Larsen, P. O., and von Ins, M. (2010). The rate of growth in scientific publication and the decline in coverage provided by Science Citation Index. Scientometrics 84, 575-603.
27. Levinthal, C., Macagno, E., and Tountas, C. (1974). Computer-aided reconstruction from serial sections. Fed. Proc. 33, 2336-2340.
28. Liu, Y. (2011). The DIADEM and beyond. Neuroinformatics 9, 99-102.
29. Lu, J. (2011). Neuronal tracing for connectomic studies. Neuroinformatics 9, 159-166.
30. Luisi, J., Narayanaswamy, A., Galbreath, Z., and Roysam, B. (2011). The FARSIGHT trace editor: an open source tool for 3-D inspection and efficient pattern analysis aided editing of automated neuronal reconstructions. Neuroinformatics 9, 305-315.
31. Macagno, E. R., Levinthal, C., and Sobel, I. (1979). Three-dimensional computer reconstruction of neurons and neuronal assemblies. Annu. Rev. Biophys. Bioeng. 8, 323-351.
32. Macků, J., and Hradil, J. (1968). Model of the neuron and of neuron nets on computers. Sb. Ved. Pr. Lek. Fak. Karlovy Univerzity Hradci Kralove 11, 545-558.
33. Mazziotta, J. C., and Hamilton, B. L. (1977). Three-dimensional computer reconstruction and display of neuronal structure. Comput. Biol. Med. 7, 265-279.
34. Meijering, E. (2010). Neuron tracing in perspective. Cytometry A 77, 693-704.
35. Müller, H. M., Kenny, E. E., and Sternberg, P. W. (2004). Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol. 2, e309. doi: 10.1371/ journal.pbio.0020309
36. Narayanaswamy, A., Wang, Y., and Roysam, B. (2011). 3-D image pre-processing algorithms for improved automated tracing of neuronal arbors. Neuroinformatics 9, 219-231.
37. Peng, H., Long, F., and Myers, G. (2011). Automatic 3D neuron tracing using all-path pruning. Bioinformatics 27, i239-i247.
38. Schmitt, S., Evers, J. F., Duch, C., Scholz, M., and Obermayer, K. (2004). New methods for the computer-assisted 3-D reconstruction of neurons from confocal image stacks. Neuroimage 23, 1283-1298.
39. Scorcioni, R., Lazarewicz, M. T., and Ascoli, G. A. (2004). Quantitative morphometry of hippocampal pyramidal cells: differences between anatomical classes and reconstructing laboratories. J. Comp. Neurol. 473, 177-193.
40. Segev, I., and Rall, W. (1998). Excitable dendrites and spines: earlier theoretical insights elucidate recent direct observations. Trends Neurosci. 21, 453-460.
41. Senft, S. L. (2011). A brief history of neuronal reconstruction. Neuroinformatics 9, 119-128.
42. Simons, D. J., and Woolsey, T. A. (1984). Morphology of Golgi-Cox-impregnated barrel neurons in rat SmI cortex. J. Comp. Neurol. 230, 119-132.
43. Sobel, I., Levinthal, C., and Macagno, E. R. (1980). Special techniques for the automatic computer reconstruction of neuronal structures. Annu. Rev. Biophys. Bioeng. 9, 347-362.
44. Svoboda, K. (2011). The past, present, and future of single neuron reconstruction. Neuroinformatics 9, 97-98.
45. Türetken, E., González, G., Blum, C., and Fua, P. (2011). Automated reconstruction of dendritic and axonal trees by global optimization with geometric priors. Neuroinformatics 9, 279-302.
46. Valverde, F. (1976). Aspects of cortical organization related to the geometry of neurons with intra-cortical axons. J. Neurocytol. 5, 509-529.
47. Wang, Y., Narayanaswamy, A., Tsai, C. L., and Roysam, B. (2011). A broadly applicable 3-D neuron tracing method based on open-curve snake. Neuroinformatics 9, 193-217.
48. Yelnik, J., Percheron, G., Perbos, J., and François, C. (1981). A computer-aided method for the quantitative analysis of dendritic arborizations reconstructed from serial sections. J. Neurosci. Methods 4, 347-364.
49. Zhao, T., Xie, J., Amat, F., Clack, N., Ahammad, P., Peng, H., Long, F., and Myers, E. (2011). Automated reconstruction of neuronal morphology based on local geometrical and global structural models. Neuroinformatics 9, 247-261.
50. Zsuppán, F. (1984). A new approach to merging neuronal tree segments traced from serial sections. J. Neurosci. Methods 10, 199-204.