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NeuronJ specifications

Information


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
Requirements
ImageJ
Maintained Yes

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Documentation


Maintainer


  • person_outline Erik Meijering <>

Additional information


https://imagescience.org/meijering/software/neuronj/manual/

Publication for NeuronJ

NeuronJ in pipeline

2009
PMCID: 2682575
PMID: 19479070
DOI: 10.1371/journal.pone.0005655

[…] inc., lexington, ma)., these software packages do not perform satisfactorily when dealing with image stacks in which multiple neural processes branch and intertwine with each other. for instance, neuronj works on 2d image only, but the complexity of fasciculated nerve fibers makes it necessary to distinguish individual processes by exploring the full 3d data set. moreover, when neural […]


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NeuronJ in publications

 (320)
PMCID: 5930177
PMID: 29743870
DOI: 10.3389/fnmol.2018.00133

[…] 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., human neuroblastoma cell line imr32 was cultured using dmem media supplemented with 10% fetal bovine serum and antibiotics. […]

PMCID: 5914299
PMID: 29688226
DOI: 10.1038/sdata.2018.75

[…] 6 gb ram)., 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 http://imagej.nih.gov/ij/) in the acquired images, as previously described. the resulting manual tracings were checked for consistency […]

PMCID: 5891582
PMID: 29666582
DOI: 10.3389/fphys.2018.00220

[…] 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). […]

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

[…] × 10 magnification. data were expressed as the ratio of the number of motor neurons to the total neurons., for morphological analysis, we used image j software (http://imagej.nih.gov/ij/) 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 […]

PMCID: 5835719
PMID: 29541019
DOI: 10.3389/fnmol.2018.00046

[…] 2000 reagent (invitrogen) according to the manufacturer’s instructions. the cell morphology was examined 36 h after transfection, and the neurite length was determined using imagej software (neuronj, national institutes of health, bethesda, md, united states). a single neurite was manually selected and traced semi-automatically to measure neurite length. neurons were deemed as bearing […]


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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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