ClaytonBingham

Human-L5-Cortical-Neuron-Model

Human L5 Cortical Neuron Model

Evolutionary-Neuronal-Biophysics-Optimization

Evolutionary Neuronal Biophysics Optimization (ENBO) is unpublished work performed by Clayton Bingham, PhD in 2022 to support numerous related projects.

Human-Corticospinal-Tract-Biophysics-Estimation

Human-HDP-and-Zona-Incerta

This repository includes all the novel models and morphologies required to reproduce the data and results in

MacaqueHyperdirectPathway

This repository describes and makes available all anatomical data corresponding to the publication "Histology-driven model of the macaque motor hyperdirect pathway." accepted for publication in Brain Structure and Function (2021).

AttractedGrowthConeSearch

This script is used to support the addition of biologically realistic jitter to curves based on histological data. The basic principle of this method is to utilized hypothetical growth cones to control the meander angles which are added in the new line. This is preferable to random jitter which can add extreme meander angles and overlapping segments if not properly controlled. AGCS can be better used to control the parametric distribution of meander angles without disrupting the distribution of segment lengths beyond that which is reasonable.

nii2surface

nii2surface takes a nifti brain image stack, identifies a particular target voxel value (perhaps a label from an atlas) and creates a surface from the labeled voxels using Poisson Surface Reconstruction. If you use this class in your own work, kindly cite: "Bingham C.S., Parent M., McIntyre, C.C. Histology-Driven Model of the Macaque Hyperdirect Pathway. In Review."

Roots

Roots is a package designed to take experimentally determined morphometric data and return an artificial neuronal arbor which satisfies the user-defined parameters.

SWCToolkit

SWCToolkit is a package designed to facilitate virtual interaction with experimentally reconstructed morphologies documented in the standard SWC file format (i.e. neuromorpho). Originally this package was written to aid the construction of biologically realistic neural models for use in computational studies of extracellular electrical stimulation but it can be used for diverse neural modeling problems.

SWCVisualization

SWCVisualization is a package designed to facilitate virtual interaction with experimentally reconstructed morphologies documented in the standard SWC file format (i.e. neuromorpho). Originally this package was written to aid the construction of biologically realistic neural models for use in computational studies of extracellular electrical stimulation but it can be used for diverse neural modeling problems.

Neurospice

Neurospice v1.0 comprises a Python library to support automated construction of a mesh and field solution with user defined current sources as the input. This library could be used to support in silico estimation of Local Field Potentials where activated neuronal models are used to generate extracellular potentials.