NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

A unified framework for skeletonization, morphological analysis, and connectivity analysis.

A Python library which provides a collection of tools for the measurement, quantification, and visualization of neuron morphology.

Neuron geometry library for swc format.

The LCN-HippoModel is a biophysically realistic model of CA1 pyramidal cells aimed to get novel insights on firing dynamics in deep and superficial populations during the theta rhythm.

Make Vaa3D functions accessible for high-performance python computation.

Rolling release code for the nTracer ImageJ/Fiji plugin, as published in: Roossien DH, et. al, Bioinformatics 2019.

A ImageJ/Fiji plugin for the merging of multiple neuron traces between two images, as published in: Dizaji SA, Walker L, and Cai D, Journal of Neuroscience Methods 2019.

Publicly-released neuron tracing datasets from Cai Lab papers.

Enhanced G-Cut algorithm on automated segmentation of interweaving neurons

A toolkit for the correction and normalization of SWC files from neuron morphology experiments.

Fuzzy-Logic Based Detection and Characterization of Junctions and Terminations in Fluorescence Microscopy Images of Neurons

Morphological categorization of neurons in order to explore their functional features has drawn significant attention over past few decades. The enormous complexity in the structure of neurons poses a real challenge in the identification and analysis of similar and dissimilar neuronal cells. Existing methodologies often carry out strutural and geometrical simplifications, which substantially changes the morphological statistics. Using digitally-reconstructed neurons, we extend the work of Path2Path as ElasticP2P, which seamlessly integrates the graph-theoretic and differential-geometric frameworks. By decomposing a neuron into a set of paths, we derive graph metrics, which are path concurrence and path hierarchy. Next, we model each path as an elastic string to compute the geodesic distance between the paths of a pair of neurons. Later, we formulate the problem of finding the distance between two neurons as a path assignment problem with a cost function combining the graph metrics and the geodesic deformation of paths.

PhD dissertation: Methods for Automated Neuron Image Analysis candidate: Miroslav Radojevic Publisher: Erasmus University ISBN 978-94-6361-204-3

set of filament tracing metric computation utilities (for .swc files)

This macro analyse the branching of neurites in 2D microscopy images of neuronal cells

A generalized program to create artificial dendritic morphological data from a dataset of organic neuron morphologies. Adapted from Chou 2020: https://www.frontiersin.org/articles/10.3389/fncom.2020.00023/full