The definition of the soma is fuzzy, as there is no clear line demarcating the soma of the labeled neurons and the origin of the dendrites and axon. Thus, the morphometric analysis of the neuronal soma is highly subjective. This software provides a mathematical definition and an automatic segmentation method to delimit the neuronal soma. We applied this method to the characterization of pyramidal cells, which are the most abundant neurons in the cerebral cortex. Thus, this software is a means of characterizing pyramidal neurons in order to objectively compare the morphometry of the somata of these neurons in different cortical areas and species.
Optimal Wiring 
The way in which a neuronal tree expands plays an important role in its functional and computational characteristics. This software enables the user to analyze the wiring optimality of a three-dimensional neuron from its specification in .asc format. The software and a user manual are available for download by clicking the link below. It takes the branching points of the real three-dimensional neuronal reconstruction and it searches for the minimal wiring arborization structure that respects the branching points. The software is capable of processing wiring design problems with point clouds up to size 200. Both dendritic and axonal wiring can be analyzed.
Reconstruction files of pyramidal cells 
By clicking the link below the user can download the specification in .asc format of the 288 pyramidal cells analyzed in . The software for analyzing the wiring optimality is freely available above .