Mobilizing the base of neuroscience data: the case of neuronal morphologies (original) (raw)

References

  1. Human Brain Project [Online], (2006).
  2. Koslow, S. H. & Hirsch, M. D. Celebrating a decade of neuroscience databases: looking to the future of high-throughput data analysis, data integration, and discovery neuroscience. Neuroinformatics 2, 267–270 (2004).
    Article Google Scholar
  3. NIH Blueprint for Neuroscience Research [Online], (2006).
  4. Insel, T. R., Volkow, N. D., Li, T. K., Battey, J. F. Jr & Landis, S. C. Neuroscience networks: data-sharing in an information age. PLoS Biol. 1, e17 (2003).
    Article Google Scholar
  5. Koslow, S. H. Should the neuroscience community make a paradigm shift to sharing primary data? Nature Neurosci. 3, 863–865 (2000).
    Article CAS Google Scholar
  6. Eckersley, P. et al. Neuroscience data and tool sharing: a legal and policy framework for neuroinformatics. Neuroinformatics 1, 149–165 (2003).
    Article Google Scholar
  7. Ascoli, G. A., De Schutter, E. & Kennedy, D. N. An information science infrastructure for neuroscience. Neuroinformatics 1, 1–2 (2003).
    Article Google Scholar
  8. The neuroinformatics site [Online], (2006).
  9. Neuroscience Database Gateway [Online], (2006).
  10. Gardner, D. & Shepherd, G. M. A gateway to the future of neuroinformatics. Neuroinformatics 2, 271–274 (2004).
    Article Google Scholar
  11. Koslow, S. H. Sharing primary data: a threat or asset to discovery? Nature Rev. Neurosci. 3, 311–313 (2002).
    Article CAS Google Scholar
  12. Editorial. A debate over fMRI data sharing. Nature Neurosci. 3, 845–846 (2000).
  13. Van Horn, J. D., Grafton, S. T., Rockmore, D. & Gazzaniga, M. S. Sharing neuroimaging studies of human cognition. Nature Neurosci. 7, 473–481 (2004).
    Article CAS Google Scholar
  14. Martone, M. E. et al. The cell-centered database: a database for multiscale structural and protein localization data from light and electron microscopy. Neuroinformatics 1, 379–395 (2003).
    Article Google Scholar
  15. Becker, K. G. The sharing of cDNA microarray data. Nature Rev. Neurosci. 2, 438–440 (2001).
    Article CAS Google Scholar
  16. Geschwind, D. H. Sharing gene expression data: an array of options. Nature Rev. Neurosci. 2, 435–438 (2001).
    Article CAS Google Scholar
  17. Miles, M. F. Microarrays: lost in a storm of data? Nature Rev. Neurosci. 2, 441–443 (2001).
    Article CAS Google Scholar
  18. Bowden, D. M. & Dubach, M. F. NeuroNames 2002. Neuroinformatics 1, 43–59 (2003).
    Article Google Scholar
  19. Kotter, R. Online retrieval, processing, and visualization of primate connectivity data from the CoCoMac database. Neuroinformatics 2, 127–144 (2004).
    Article Google Scholar
  20. Bota, M., Dong, H. W. & Swanson, L. W. Brain architecture management system. Neuroinformatics 3, 15–48 (2005).
    Article Google Scholar
  21. Mirsky, J. S., Nadkarni, P. M., Healy, M. D., Miller, P. L. & Shepherd, G. M. Database tools for integrating and searching membrane property data correlated with neuronal morphology. J. Neurosci. Methods 82, 105–121 (1998).
    Article CAS Google Scholar
  22. Ascoli, G. A., Krichmar, J. L., Nasuto, S. J. & Senft, S. L. Generation, description and storage of dendritic morphology data. Phil. Trans. R. Soc. Lond. B 356, 1131–1145 (2001).
    Article CAS Google Scholar
  23. Capowski, J. J. Computer Techniques in Neuroanatomy (Plenum, New York, 1985).
    Google Scholar
  24. Glaser, J. R. & Glaser, E. M. Neuron imaging with Neurolucida — a PC-based system for image combining microscopy. Comput. Med. Imaging Graph. 14, 307–317 (1990).
    Article CAS Google Scholar
  25. Brown, K. M., Donohue, D. E., D'Alessandro, G. & Ascoli, G. A. A cross-platform freeware tool for digital reconstruction of neuronal arborizations from image stacks. Neuroinformatics 3, 343–360 (2005).
    Article Google Scholar
  26. Cannon, R. C., Wheal, H. V. & Turner, D. A. Dendrites of classes of hippocampal neurons differ in structural complexity and branching patterns. J. Comp. Neurol. 413, 619–633 (1999).
    Article CAS Google Scholar
  27. Li, Y., Brewer, D., Burke, R. E. & Ascoli, G. A. Developmental changes in spinal motoneuron dendrites in neonatal mice. J. Comp. Neurol. 483, 304–317 (2005).
    Article Google Scholar
  28. The NEURON Simulation Environment [Online], (2006).
  29. Senselab ModelDB [Online], (2006).
  30. Mainen, Z. F. & Sejnowski, T. J. Influence of dendritic structure on firing pattern in model neocortical neurons. Nature 382, 363–366 (1996).
    Article CAS Google Scholar
  31. 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).
    Article CAS Google Scholar
  32. Ascoli, G. A. Neuroanatomical algorithms for dendritic modelling. Network 13, 247–260 (2002).
    Article Google Scholar
  33. Stepanyants, A. & Chklovskii, D. B. Neurogeometry and potential synaptic connectivity. Trends Neurosci. 28, 387–394 (2005).
    Article CAS Google Scholar
  34. Markram, H. The blue brain project. Nature Rev. Neurosci. 7, 153–160 (2006).
    Article CAS Google Scholar
  35. Gardner, D. et al. Towards effective and rewarding data sharing. Neuroinformatics 1, 289–295 (2003).
    Article Google Scholar
  36. He, W. et al. Automated three-dimensional tracing of neurons in confocal and brightfield images. Microsc. Microanal. 9, 296–310 (2003).
    Article CAS Google Scholar
  37. Rodriguez, A. et al. Automated reconstruction of three-dimensional neuronal morphology from laser scanning microscopy images. Methods 30, 94–105 (2003).
    Article CAS Google Scholar
  38. 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).
    Article Google Scholar
  39. The NeuroMorpho.org inventory [Online], (2006).
  40. Turner, D. A., Cannon, R. C. & Ascoli, G. A. in Neuroscience Databases – A Practical Guide (ed. Kotter, R.) 81–98 (Elsevier, Amsterdam, 2002).
    Google Scholar
  41. Cannon, R. C., Howell, F. W., Goddard, N. H. & De Schutter, E. Non-curated distributed databases for experimental data and models in neuroscience. Network 13, 415–428 (2002).
    Article CAS Google Scholar
  42. Scorcioni, R., Lazarewicz, M. T. & Ascoli, G. A. Quantitative morphometry of hippocampal pyramidal cells: differences between anatomical classes and reconstructing laboratories. J. Comp. Neurol. 473, 177–193 (2004).
    Article Google Scholar
  43. Samsonovich, A. V. & Ascoli, G. A. Morphological homeostasis in cortical dendrites. Proc. Natl Acad. Sci. USA 103, 1569–1574 (2006).
    Article CAS Google Scholar
  44. Kennedy, D. N. The impact of neuroinformatics. Neuroinformatics 3, 287–292 (2005).
    Article Google Scholar
  45. Hines, M. L., Morse, T., Migliore, M., Carnevale, N. T. & Shepherd, G. M. ModelDB: A database to support computational neuroscience. J. Comput. Neurosci. 17, 7–11 (2004).
    Article Google Scholar
  46. International Consortium for Brain Mapping [Online], (2006).
  47. Mouse Brain Library [Online], (2006).
  48. Allen Brain Atlas [Online], (2006).
  49. BrainInfo [Online], (2006).
  50. The LNI neurophysiology database [Online], (2006).
  51. Synapse Web [Online], (2006).
  52. Cell Centered Database [Online], (2006).
  53. Computational Neurobiology and Imaging Center [Online], (2006).
  54. Computational Neuroscience on the Web [Online], (2006).
  55. Neuron_Morpho Plugin for ImageJ [Online], (2006).
  56. Cvapp: Neuron morphology and conversion tool [Online], (2006).
  57. L-Measure: Morphometric analysis of neuronal reconstructions [Online], (2006).
  58. Scorcioni, R. & Ascoli, G. A. Algorithmic extraction of morphological statistics from electronic archives of neuroanatomy. Lect. Notes Comp. Sci. 2084, 30–37 (2001).
    Article Google Scholar
  59. Ascoli, G. A. & Krichmar, J. L. L-Neuron: a modeling tool for the efficient generation and parsimonious description of dendritic morphology. Neurocomputing 32–33, 1003–1011 (2000).
    Article Google Scholar
  60. The GENESIS Simulation Environment [Online], (2006).
  61. Migliore, M., Ferrante, M. & Ascoli, G. A. Signal propagation in oblique dendrites of CA1 pyramidal cells. J. Neurophysiol. 94, 4145–4155 (2005).
    Article Google Scholar
  62. Samsonovich, A. V. & Ascoli, G. A. Statistical determinants of dendritic morphology in hippocampal pyramidal neurons: a hidden Markov model. Hippocampus 15, 166–183 (2005).
    Article Google Scholar

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