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 approximately 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.

Figure 1

Representative collection of 15 neurons selected from NeuroMorpho.Org (all scale bars are 100 μm). Ordered by row, from top left: (a) bipolar cell from rat neocortex (C130200-19), (b) parvalbumin cell from rat hippocampus (pv22c), (c) calretinin cell from rat hippocampus (cr10f), (d) climbing fiber from rat cerebellum (NMA), (e) dopaminergic cell from rat basal ganglia (Nigra11h941-1), (f) dorsal spinocerebellar tract cell from cat spinal cord (DSCT4), (g) ganglion cell from salamander retina (mp_ma_40984_gc2), (h) granule cell from rat hippocampus (411884b), (i) Martinotti cell from rat cerebral cortex (cellC150897B-I1), (j) medium spiny neuron from mouse basal forebrain (ACC1), (k) motoneuron from mouse spinal cord (ok_m215), (l) basket cell from rat neocortex (C040600B1), (m) pyramidal cell from cat neocortex (980804axden), (n) CA3 pyramidal cell from rat hippocampus (cell6zr), (o) Renshaw cell from cat spinal cord (renshawcell1).

Figure 2

In the Function tab users define the metrics to extract. Detailed definition of each metric is available in the Help panel (which also provides general usage information).

Figure 3

Examples of graphs from typical morphometric studies performed with LM on reconstructed neurons available at NeuroMorpho.Org. (a) Scatter plot of the overall number of branches in each cell vs. its total dendritic length. Straight lines represent linear fits. Inset shows frequency distribution of Branch Length for all Amaral CA3 group. (b) Distributions of surface area over relative path distance for apical and basal dendrites from CA3 pyramidal cell from Amaral archive. Each point is the average over 24 cells, error bars represent standard deviations. (c) Histograms of the number of basal branches (divided in internal, i.e. ending into a bifurcation, and terminal, i.e. ending into a tip) as a function of branch order (the number of bifurcations from the soma) for CA3 pyramidal cells l22t and c10861. (d) Scatter plot of diameter vs. bifurcation angle for each branch point within all 18 CA3 pyramidal neurons from young rats in Turner’s archive. Artificial noise uniformly distributed between −0.05 and 0.05 was added to all coordinate values for better visualization.

Figure 4

Input panel with statistical feature enabled (note “Stat_tests” checkbox). All cells from directory \ca3\Turner are loaded as Group1, while eight neurons from five different directories are pooled into Group2. The Input panel identifies the cells to be analyzed, while the Output tab determines if and where the results should be saved to disk.

Figure 5

Function panel with statistical features enabled (note “Stat_tests” checkbox). After the morphometric analysis conditions are set, extraction of measurements is initiated in the Go panel.

Figure 6

The LMSearch panel allows users to find neuronal reconstructions with particular morphometric characteristics among arbitrarily large sets. In this example, the search criteria indicate a Total Length greater than 18000 μm and a Total Volume greater than 2000 μm³. The resulting output consists of 13 neurons that satisfy these conditions over a total of 23 contained in AmaralOrigCA1 folder.