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NeurphologyJ specifications


Unique identifier OMICS_06595
Name NeurphologyJ
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes


No version available


  • person_outline Eric Hwang

Publication for NeurphologyJ

NeurphologyJ citations


Mechano sensitization of mammalian neuronal networks through expression of the bacterial large conductance mechanosensitive ion channel

PMCID: 5897719
PMID: 29361543
DOI: 10.1242/jcs.210393

[…] quired on the DeltaVision Elite microscope (GE Healthcare Life Sciences) using a 20× air objective (PLN 20×/0.4, Olympus). The analysis was performed by running the morphology quantification software NeurphologyJ, an ImageJ plugin, as described by .Colocalization analysis was performed by using the Coloc2 Image plugin, by following the described procedure ().The viability plot was calculated as th […]


Abnormal Neural Progenitor Cells Differentiated from Induced Pluripotent Stem Cells Partially Mimicked Development of TSC2 Neurological Abnormalities

Stem Cell Reports
PMCID: 5390135
PMID: 28344003
DOI: 10.1016/j.stemcr.2017.02.020
call_split See protocol

[…] Neuron morphology, including soma size, neurite length, and neurite branching complexity, was automatically quantified using ImageJ (NIH) with the NeurphologyJ plug-in (). […]


Ran dependent TPX2 activation promotes acentrosomal microtubule nucleation in neurons

Sci Rep
PMCID: 5304320
PMID: 28205572
DOI: 10.1038/srep42297

[…] For neurite length analysis of P19 neurons, β-III-tubulin stained images were analyzed using ImageJ plug-in NeurphologyJ. For neurite length analysis of hippocampal neurons, neurites were manually traced with the ImageJ plugin NeuronJ 1.4.1. Only neurons expressing both EGFP and β-III-tubulin were analyzed. […]


The effect of fluorescent nanodiamonds on neuronal survival and morphogenesis

Sci Rep
PMCID: 4220284
PMID: 25370150
DOI: 10.1038/srep06919

[…] . After fixation and immunofluorescence staining, images of neurons were acquired using the automated fluorescence microscopy and the neurite length of hippocampal or DRG neurons was quantified using NeurphologyJ (). Surprisingly, FNDs provoked a dosage-dependent reduction in neurite length in both CNS hippocampal neurons () and PNS DRG neurons (). Furthermore, we discovered a striking morphologic […]


HCS Neurons: identifying phenotypic changes in multi neuron images upon drug treatments of high content screening

BMC Bioinformatics
PMCID: 3853092
PMID: 24564437
DOI: 10.1186/1471-2105-14-S16-S12

[…] Our original raw images were gray-scaled taken using fluorescence microscopy. We applied a preprocessing technique in the same way as reported previously in NeurphologyJ []. The four input parameters consisting of contrast, soma intensity, neurite width and particle cleanup value were set to 13, 288, 5 and 15, respectively. Examples of the original images […]


Chapter 17: Bioimage Informatics for Systems Pharmacology

PLoS Comput Biol
PMCID: 3635992
PMID: 23633943
DOI: 10.1371/journal.pcbi.1003043

[…] r AD therapy. shows an example of neurites and nuclei images acquired in . To quantitatively analyze neuron images, a number of publicly available software packages have been developed, for example, NeurphologyJ , NeuronJ , NeuriteTracer (Fiji plugin) , NeuriteIQ , NeuronMetrics , NeuronStudio , , NeuronJ , NeuronIQ , , and Vaa3D , . A review of software packages for neuron image analysis was als […]

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NeurphologyJ institution(s)
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan

NeurphologyJ review

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Anonymous user #1225's avatar image No country

Anonymous user #1225

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Dear All,

currently I am applying NeurphologyJ plugin (on ImageJ) in order to measure the projection length in neurons.
I follow the given instructions but in the last step of "Operation Instruction: Neurphology interactive application" I get the follow message "The source stacks must have the same number of images". Also I cannot see the "NeurphologyJHT in options at menu. Thus I cannot complete the analysis.
I am probably missing something or doing wrong.
do you have any ideas what I could do to fix it?

Thank you very much in advance,