Neuronvisio: A graphical user interface with 3D capabilities for NEURON

Frontiers in Neuroinformatics

Volumn 6, Issue JUNE, 2012, Pages

  Mattioni, Michele ^a   Cohen, Uri ^b   Le Novère, Nicolas ^a  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^b HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

3D visualization; Electrophysiological model; Hdf storage; Matplotlib integration; Neuron model

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER MODEL; CYTOARCHITECTURE; HUMAN; IMAGE QUALITY; INFORMATION PROCESSING; INFORMATION RETRIEVAL; NERVE CELL; NERVE CELL NETWORK; NEUROANATOMY; NEUROIMAGING; NEUROSCIENCE; SIMULATION; THREE DIMENSIONAL IMAGING;

EID: 84863908861     PISSN: 16625196     EISSN: None     Source Type: Journal    
DOI: 10.3389/fninf.2012.00020     Document Type: Article

References (20)

1. Bower, J., and Beeman, D. (1998). The Book of GENESIS: Exploring Realistic Neural Models with the General NeuralSimulation System. NewYork: Springer-Verlag.
2. Carnevale, N. T., and Hines, M. L. (2006). The NEURON Book. Cambridge: Cambridge University Press.
3. Davison, A., Brüderle, D., Eppler, J., Kremkow, J., Muller, E., Pecevski, D., Perrinet, L., and Yger, P. (2008). PyNN: a common interface for neuronal network simulators. Front. Neuroinform. 2:11. doi:10.3389/neuro.11.011.2008
4. Dubois, P. F. (2007). Guest editor's introduction: python: batteries included. Comput. Sci. Eng. 9, 7-9.
5. Ermentrout, B., andMahajan, A. (2003). Simulating, analyzing, and animating dynamical systems: a guide to XPPAUT for researchers and students. Appl. Mech. Rev. 56, B53.
6. Gewaltig, M., and Diesmann, M. (2007). NEST (neural simulation tool). Scholarpedia J. 2, 1430.
7. Gleeson, P., Steuber, V., and Silver, R. (2007). Neuroconstruct: a tool for modelingnetworksofneuronsin3D space. Neuron 54, 219-235.
8. Goodman, D., and Brette, R. (2009). The brain simulator. Front. Neu-rosci. 3:2. doi:10.3389/neuro.01.026. 2009
9. Halavi, M., Polavaram, S., Donohue, D., Hamilton, G., Hoyt, J., Smith, K., and Ascoli, G. (2008). NeuroMorpho. Org implementation of digital neuroscience: dense coverage and integration with the NIF. Neuroinformatics 6, 241-252.
10. Hines, M., Davison, A., and Muller, E. (2009). NEURON and python. Front. Neuroinform. 3:1. doi:10.3389/neuro.11.001.2009
11. Hines, M., Morse, T., Migliore, M., Carnevale, N., and Shepherd, G. (2004). ModelDB: a database to support computational neuroscience. J. Comput. Neurosci. 17, 7-11.
12. Hunter, J. D. (2007). Matplotlib: a 2D graphics environment. Comput. Sci. Eng. 9, 90-95.
13. Izhikevich, E. (2003). Simple model of spiking neurons. IEEE Trans. Neural Netw. 14, 1569-1572.
14. Lapicque, L. (1907). Recherches quan-titatives sur l'excitation électrique des nerfs traitée comme une polarisation. J. Physiol. Pathol. Gen. 9, 620-635.
15. Mainen, Z., Joerges, J., Huguenard, J., and Sejnowski, T. (1995). A model of spike initiation in neocor-tical pyramidal neurons. Neuron 15, 1427-1439.
16. Perez, F., and Granger, B. (2007). IPython: asystem for interactive scientific computing. Comput. Sci. Eng. 9, 21-29.
17. Ray, S., and Bhalla, U. (2008). PyMOOSE: interoperable scripting in python for MOOSE. Front. Neuroinform. 2:6. doi: 10.3389/ neuro.11.006.2008
18. Sivakumaran, S., Hariharaputran, S., Mishra, J., and Bhalla, U. (2003). The database of quantitative cellular signaling: management and analysis of chemical kinetic models of signaling networks. Bioinformatics 19, 408-415.
19. The HDF Group. (2010). Hierarchical Data Format Version 5, 2000-2010. Available at: http://www.hdfgroup.org/HDF5
20. Varoquaux, G., Vaught, T., and Mill-man, J. (eds). (2008). "Mayavi: Making 3D DataVisualization Reusable, " in Proceedings of the 7th Python in Science Conference, Pasadena, 51-56.