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NeuronJ specifications


Unique identifier OMICS_25913
Name NeuronJ
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Version 1.4.3
Stability Stable
Maintained Yes




No version available



  • person_outline Erik Meijering

Additional information

Publication for NeuronJ

NeuronJ citations


Absence of Wdr13 Gene Predisposes Mice to Mild Social Isolation – Chronic Stress, Leading to Depression Like Phenotype Associated With Differential Expression of Synaptic Proteins

PMCID: 5930177
PMID: 29743870
DOI: 10.3389/fnmol.2018.00133
call_split See protocol

[…] A1 neurons from 3-5 hippocampal sections for each mouse () were analyzed for dendritic branching. CA1 neurons were selected as described in previous reports (; ). Sholl analysis was carried out using NeuronJ plugin and Sholl Analysis plugin (v1.0) of ImageJ software. […]


Wide field corneal subbasal nerve plexus mosaics in age controlled healthy and type 2 diabetes populations

Sci Data
PMCID: 5914299
PMID: 29688226
DOI: 10.1038/sdata.2018.75
call_split See protocol

[…] Nerve fibers visible in all mosaics were traced using two approaches: manual and fully automated. An experienced observer manually traced the centerlines of all visible nerves using the NeuronJ tracing plugin for ImageJ (publicly available at in the acquired images, as previously described. The resulting manual tracings were checked for consistency and accu […]


A Novel Approach to Primary Cell Culture for Octopus vulgaris Neurons

Front Physiol
PMCID: 5891582
PMID: 29666582
DOI: 10.3389/fphys.2018.00220
call_split See protocol

[…] in 10 fields of view for each treatment was counted and measured using imageJ software. Neurite exhibiting at least half of the cell body length was counted as a neuronal process. Specifically, the “NeuronJ” plug-in (version 1.4.3) of NIH-ImageJ software (version 1.50 Meijering et al., ) was used to quantify the average neurite length of each neuron at different time points (day 1 and day 4). Eig […]


Dynamic cues for whisker based object localization: An analytical solution to vibration during active whisker touch

PLoS Comput Biol
PMCID: 5889188
PMID: 29584719
DOI: 10.1371/journal.pcbi.1006032

[…] the residual.Following behavioral sessions, the C2 whiskers were plucked and photographed at 6.3x magnification under a light macroscope. Whisker length and width was determined using ImageJ and the NeuronJ plugin. Total length includes the portion of the whisker embedded in the follicle. Whiskers were then weighed on a microgram balance. […]


AxonTracer: a novel ImageJ plugin for automated quantification of axon regeneration in spinal cord tissue

BMC Neurosci
PMCID: 5845359
PMID: 29523078
DOI: 10.1186/s12868-018-0409-0

[…] n the original image (Fig. e). To assess whether automated tracing and quantification by AxonTracer produces accurate measurements, we compared the results to semi-manual tracing by the ImageJ plugin NeuronJ [] (Fig. f). Quantification of regenerating axons with both methods was applied to the same images and showed no significant difference (n = 4, p = 0.84 by paired t test; Fig. g). Additional e […]


RNS60 exerts therapeutic effects in the SOD1 ALS mouse model through protective glia and peripheral nerve rescue

PMCID: 5833072
PMID: 29495962
DOI: 10.1186/s12974-018-1101-0

[…] For morphological analysis, we used Image J software ( with the NeuronJ plug in []. Cells were visualized by SMI32 staining and analyzed for the following parameters: total neurites extensions per neuron and number of neurites per neuron. Neurites were manually tr […]


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NeuronJ institution(s)
Departments of Medical Informatics and Radiology, Erasmus MC–University Medical Center Rotterdam, Rotterdam, The Netherlands; Institute for Biomedical Imaging, Optics, and Engineering, Swiss Federal Institute of Technology, Lausanne, Switzerland; Institute of Neurosciences, Swiss Federal Institute of Technology, Lausanne, Switzerland

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