Computer-assisted Evaluation of Myelin formation (CEM) is a collection designed to automate myelin quantification. It requires use input to choose the best threshold values. The myelin is calculated as an overlap between neuronal signal and oligodendrocyte signal. Results are given as pixel counts and percents.

CEM runs as an imageJ plugin with an optional Matlab extension to remove cell bodies. More details are published at Kerman et al. 2015 Development. Supplemental Material includes a detailed user manual and the download link.




"The plugin analyzes fluorescence microscopy images of neurites and nuclei of dissociated cultured neurons. Given user-defined thresholds, the plugin counts neuronal nuclei, and traces and measures neurite length."[...]" NeuriteTracer is a fast simple-to-use ImageJ plugin for the analysis of outgrowth in two-dimensional fluorescence microscopy images of neuronal cultures. The plugin performed well on images from three different types of neurons with distinct morphologies."

This plugin requires parameter setting: Threshold levels and scale (see more details on the related publication)

Simple Tracing DF-Tracing


We have developed a novel approach, named DF-Tracing, to tackle this challenge. This method first extracts the neurite signal (foreground) from a noisy image by using anisotropic filtering and automated thresholding. Then, DF-Tracing executes a coupled distance-field (DF) algorithm on the extracted foreground neurite signal and reconstructs the neuron morphology automatically. Two distance-transform based “force” fields are used: one for “pressure”, which is the distance transform field of foreground pixels (voxels) to the background, and another for “thrust”, which is the distance transform field of the foreground pixels to an automatically determined seed point. The coupling of these two force fields can“push” a “rolling ball” quickly along the skeleton of a neuron, reconstructing the 3D cell morphology.

Simple Tracing - DT-fields



nctuTW is a "high-throughput computer method of reconstructing the neuronal structure of the fruit fly brain. The design philosophy of the proposed method differs from those of previous methods. We propose first to compute the 2D skeletons of a neuron in each slice of the image stack. The 3D neuronal structure is then constructed from the 2D skeletons. Biologists tend to use confocal microscopes for optimal images in a slice for human visualization; and images in two consecutive slices contain overlapped information. Consequently, a spherical object becomes oval in the image stack; that is, neurons in the image stack do not reflect the true shape of the neuron. This is the main reason we chose not to work directly on the 3D volume.

The proposed method comprises two steps. The first is the image processing step, which involves computing a set of voxels that is a superset of the 3D centerlines of the neuron. The shortest path graph algorithm then computes the centerlines. The proposed method was applied to process more than 16 000 neurons. By using a large amount of reconstructions, this study also demonstrated a result derived from the reconstructed data using the clustering technique." (Extracted from reference publication: https://doi.org/10.1371/journal.pcbi.1002658)

Illustrative image shows gold standard (top) and method results (bottom). 




By combining multiple image alignment and tracing into one program, Reconstruct (TM) allows images to be processed more efficiently. Tracing can be done directly on the transformed images and alignments can be asily modified. Reconstruct (TM) was developed from years of experience working with high magnification serial section images of brain tissue. (Extracted from User Manual)

"The original platform of the Reconstruct program allows a user to trace objects in serial sections by manually drawing the outline of each object on each section, which is time-consuming. We modified Reconstruct to enable semi-automatic tracing of axons using a region-growing algorithm called wildfire."




JFilament is an ImageJ plugin for segmentation and tracking of 2D and 3D filaments in fluorescenece microscopy images. The main algorithm used in Jfilament is "Stretching Open Active Contours" (SOAC). In order to use this method, the user must define seed points in the image where the SOAC method will begin.

JFilament also includes 2D "closed" active contours which can be used for tasks such as segmentation and tracking of cell boundaries.





ORION: Online Reconstruction and functional Imaging Of Neurons: segmentation and tracing of neurons for reconstruction.

A project to develop tools that explore single neuron function via sophisticated image analysis. ORION software bridges advanced optical imaging and compartmental modeling of neuronal function by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function. The goal of this project is to develop a computational and experimental framework to allow real-time mapping of functional imaging data (e.g., spatio-temporal patterns of dendritic voltages or intracellularions) to neuronal structure, during the very limited duration of an acute experiment.




The invention comprises a software tool, NeuronMetrics, which functions as a set of modules that run in the open-source program ImageJ. NeuronMetrics features a novel method for estimating neural “branch number” (a measure of the axonal complexity) from two-dimensional images. In addition, the tool features a novel method for modeling neural structure in large “gaps” that result from image artifacts.


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Neural Circuit Tracer


Neural Circuit Tracer (NCTracer) is open source software for automated and manual tracing of neurites from light microscopy stacks of images. NCTracer has more than one workflow available for neuron tracing. 

"The Neural Circuit Tracer is open source software built using Java (Sun Microsystems) and Matlab (MathWorks, Inc., Natick MA). It is based on the core of ImageJ (http://rsbweb.nih.gov/ij) and the graphic user interface has been developed by using Java Swings. The software combines anumber of functionalities of ImageJ with several newly developed functions for automated and manual tracing of neurites. The Neural Circuit Tracer is designed in a way
that will allow the users to add any plug-ins developed for ImageJ. More importantly, functions written in MatLab and converted into Java with Matlab JA toolbox can also be added to the Neural Circuit Tracer." 

Example of output from Neural Circuit Tracer



hIPNAT (hIPNAT: Image Processing for NeuroAnatomy and Tree-like structures) is a set of tools for the analysis of images of neurons and other tree-like morphologies. It is written for ImageJ, the de facto standard in scientific image processing. It is available through the ImageJ Neuroanatomy update site.

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