A Software Tool for the Analysis of Neuronal Morphology Data

Overview

Journal Int Arch Med

Publisher iMedPub

Specialty General Medicine

Date 2014 Feb 18

PMID 24529393

Citations 7

Authors

Julia Ledderose

Luis Sencion

Humberto Salgado

Oscar Arias-Carrion

Mario Trevino

Affiliations

Soon will be listed here.

Abstract

Anatomy plays a fundamental role in supporting and shaping nervous system activity. The remarkable progress of computer processing power within the last two decades has enabled the generation of electronic databases of complete three-dimensional (3D) dendritic and axonal morphology for neuroanatomical studies. Several laboratories are freely posting their reconstructions online after result publication v.gr. NeuroMorpho.Org (Nat Rev Neurosci7:318-324, 2006). These neuroanatomical archives represent a crucial resource to explore the relationship between structure and function in the brain (Front Neurosci6:49, 2012). However, such 'Cartesian' descriptions bear little intuitive information for neuroscientists. Here, we developed a simple prototype of a MATLAB-based software tool to quantitatively describe the 3D neuronal structures from public repositories. The program imports neuronal reconstructions and quantifies statistical distributions of basic morphological parameters such as branch length, tortuosity, branch's genealogy and bifurcation angles. Using these morphological distributions, our algorithm can generate a set of virtual neurons readily usable for network simulations.

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References

da Fontoura Costa L, Zawadzki K, Miazaki M, Viana M, Taraskin S . Unveiling the neuromorphological space. Front Comput Neurosci. 2010; 4:150. PMC: 3001740. DOI: 10.3389/fncom.2010.00150. View

RALL W . Branching dendritic trees and motoneuron membrane resistivity. Exp Neurol. 1959; 1:491-527. DOI: 10.1016/0014-4886(59)90046-9. View

DeFelipe J . From the connectome to the synaptome: an epic love story. Science. 2010; 330(6008):1198-201. DOI: 10.1126/science.1193378. View

Bullitt E, Gerig G, Pizer S, Lin W, Aylward S . Measuring tortuosity of the intracerebral vasculature from MRA images. IEEE Trans Med Imaging. 2003; 22(9):1163-71. PMC: 2430603. DOI: 10.1109/TMI.2003.816964. View

Kaspirzhny A, Gogan P, Horcholle-Bossavit G, Tyc-Dumont S . Neuronal morphology data bases: morphological noise and assesment of data quality. Network. 2002; 13(3):357-80. View

Krichmar J, Nasuto S, Scorcioni R, Washington S, Ascoli G . Effects of dendritic morphology on CA3 pyramidal cell electrophysiology: a simulation study. Brain Res. 2002; 941(1-2):11-28. DOI: 10.1016/s0006-8993(02)02488-5. View

Stuart G, Spruston N, Sakmann B, Hausser M . Action potential initiation and backpropagation in neurons of the mammalian CNS. Trends Neurosci. 1997; 20(3):125-31. DOI: 10.1016/s0166-2236(96)10075-8. View

Mel B, Ruderman D, Archie K . Translation-invariant orientation tuning in visual "complex" cells could derive from intradendritic computations. J Neurosci. 1998; 18(11):4325-34. PMC: 6792789. View

Horcholle-Bossavit G, Gogan P, Ivanov Y, Korogod S, Tyc-Dumont S . The problem of the morphological noise in reconstructed dendritic arborizations. J Neurosci Methods. 2000; 95(1):83-93. DOI: 10.1016/s0165-0270(99)00159-4. View

10.

Halavi M, Hamilton K, Parekh R, Ascoli G . Digital reconstructions of neuronal morphology: three decades of research trends. Front Neurosci. 2012; 6:49. PMC: 3332236. DOI: 10.3389/fnins.2012.00049. View

11.

Meijering E, Jacob M, Sarria J, Steiner P, Hirling H, Unser M . Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images. Cytometry A. 2004; 58(2):167-76. DOI: 10.1002/cyto.a.20022. View

12.

Bradke F, Dotti C . Establishment of neuronal polarity: lessons from cultured hippocampal neurons. Curr Opin Neurobiol. 2000; 10(5):574-81. DOI: 10.1016/s0959-4388(00)00124-0. View

13.

van Ooyen A . Using theoretical models to analyse neural development. Nat Rev Neurosci. 2011; 12(6):311-26. DOI: 10.1038/nrn3031. View

14.

Sasaki T, Matsuki N, Ikegaya Y . Effects of axonal topology on the somatic modulation of synaptic outputs. J Neurosci. 2012; 32(8):2868-76. PMC: 6621900. DOI: 10.1523/JNEUROSCI.5365-11.2012. View

15.

Mainen Z, Sejnowski T . Influence of dendritic structure on firing pattern in model neocortical neurons. Nature. 1996; 382(6589):363-6. DOI: 10.1038/382363a0. View

16.

Kulik A, Vida I, Lujan R, Haas C, Lopez-Bendito G, Shigemoto R . Subcellular localization of metabotropic GABA(B) receptor subunits GABA(B1a/b) and GABA(B2) in the rat hippocampus. J Neurosci. 2003; 23(35):11026-35. PMC: 6741037. View

17.

Koene R, Tijms B, van Hees P, Postma F, de Ridder A, Ramakers G . NETMORPH: a framework for the stochastic generation of large scale neuronal networks with realistic neuron morphologies. Neuroinformatics. 2009; 7(3):195-210. DOI: 10.1007/s12021-009-9052-3. View

18.

Wong W, Wong R . Rapid dendritic movements during synapse formation and rearrangement. Curr Opin Neurobiol. 2000; 10(1):118-24. DOI: 10.1016/s0959-4388(99)00059-8. View

19.

Trevino M, Vivar C, Gutierrez R . Beta/gamma oscillatory activity in the CA3 hippocampal area is depressed by aberrant GABAergic transmission from the dentate gyrus after seizures. J Neurosci. 2007; 27(1):251-9. PMC: 6672272. DOI: 10.1523/JNEUROSCI.3815-06.2007. View

20.

Eilers J, Konnerth A . Dendritic signal integration. Curr Opin Neurobiol. 1997; 7(3):385-90. DOI: 10.1016/s0959-4388(97)80067-0. View