L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies

Abstract

L-Measure (LM) is a freely available software tool for the quantitative characterization of neuronal morphology. LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions. This report illustrates several LM protocols: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available at http://krasnow.gmu.edu/cn3 for either online use on any Java-enabled browser and platform or download for local execution under Windows and Linux.

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Figure 1: Representative collection of 15 neurons selected from NeuroMorpho.Org (all scale bars are 100 μm).
Figure 2
Figure 3: In the Function tab, users define the metrics to extract.
Figure 4: Examples of graphs from typical morphometric studies performed with L-Measure (LM) on reconstructed neurons available at NeuroMorpho.Org.
Figure 5: Input panel with statistical feature enabled (note 'Stat_tests' checkbox).
Figure 6: Function panel with statistical features enabled (note 'Stat_tests' checkbox).
Figure 7: The LMSearch panel allows users to find neuronal reconstructions with particular morphometric characteristics among arbitrarily large sets.

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Acknowledgements

This research was supported by NIH R01 grant NS39600 jointly funded by National Institute of Neurological Disorders and Stroke, National Institute for the Mentally Handicapped and National Science Foundation under the Human Brain Project.

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R.S. and S.P. contributed equally to this work.

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Correspondence to Giorgio A Ascoli.

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Scorcioni, R., Polavaram, S. & Ascoli, G. L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies. Nat Protoc 3, 866–876 (2008). https://doi.org/10.1038/nprot.2008.51

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