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 g…

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

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

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

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

Enhanced G-Cut algorithm on automated segmentation of interweaving neurons

Make Vaa3D functions accessible for high-performance python computation.

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

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

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.

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

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.

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

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

Neuron geometry library for swc format.

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