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Simple Neurite Tracer specifications


Unique identifier OMICS_10496
Name Simple Neurite Tracer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes


No version available


  • person_outline Longair MH

Publication for Simple Neurite Tracer

Simple Neurite Tracer citations


GABAergic inhibition in dual transmission cholinergic and GABAergic striatal interneurons is abolished in Parkinson disease

Nat Commun
PMCID: 5897332
PMID: 29651049
DOI: 10.1038/s41467-018-03802-y

[…] ( without any additional pre-processing, dendrite and axon reconstructions, as well as morphological metric measurements were performed using the semi-automated “simple neurite tracer” plugin ( based on dendrites reconstructions, a sholl analysis was performed using “sholl analysis” plugin […]


An essential role for neuregulin 4 in the growth and elaboration of developing neocortical pyramidal dendrites

PMCID: 5866123
PMID: 29317193
DOI: 10.1016/j.expneurol.2018.01.002

[…] neurons were acquired with an axiovert 200 zeiss fluorescent microscope. neurite length and sholl analysis were carried out using fiji (imagej) software with the semi-automated plugin simple neurite tracer ()., brains were fixed overnight using 4% paraformaldehyde in 0.12 m phosphate-buffered saline (pbs) at 4 °c, washed in pbs and cryoprotected in 30% sucrose before being frozen […]


Gaze Stabilizing Central Vestibular Neurons Project Asymmetrically to Extraocular Motoneuron Pools

PMCID: 5700419
PMID: 28972121
DOI: 10.1523/JNEUROSCI.1711-17.2017

[…] unambiguously throughout its entirety to a distinct cell body; qualitatively, the asymmetry persisted among excluded fish. neurons were traced manually with the assistance of the imagej plugin simple neurite tracer (). cell bodies of the oculomotor and trochlear nuclei were localized manually using the fiji/imagej roi functionality (). superior oblique motoneurons were found in niv […]


Protocadherin αC2 is required for diffuse projections of serotonergic axons

Sci Rep
PMCID: 5698425
PMID: 29162883
DOI: 10.1038/s41598-017-16120-y

[…] were smoothed by the 3d gaussian lowpass filter function of imagej. all rfp(+) axons crossing both lines in one set of z-stack images (depth: 100 μm) were traced with the imagej plugin software, simple neurite tracer. for the statistical analysis, fisher’s exact test was used., sagittal sections of the olfactory bulb were also stained with the anti-sert antibody and dapi […]


Direct conversion of human fibroblasts to functional excitatory cortical neurons integrating into human neural networks

PMCID: 5622454
PMID: 28962665
DOI: 10.1186/s13287-017-0658-3

[…] was calculated by the software and used for analyzing the average cell soma size., neuronal morphology was assessed for three representative bmf-induced ictx cells and hctx and hstr neurons using simple neurite tracer plugin in fiji []. the outlined areas were filled out and then converted to 8-bit monochrome image in fiji., whole-cell patch-clamp recordings were performed with a heka double […]


3D Visualization of Individual Regenerating Retinal Ganglion Cell Axons Reveals Surprisingly Complex Growth Paths

PMCID: 5575138
PMID: 28856242
DOI: 10.1523/ENEURO.0093-17.2017

[…] rgcs from the retinal nerve fiber layer to the inner nuclear layer. images were tiled and reconstructed if a rgc’s dendrites extended out of field. dendrites were traced using imagej/fiji and the simple neurite tracer plugin (; ). linear sholl analysis was completed using the sholl analysis plugin for imagej/fiji (). sholl analysis data were analyzed as the average number of intersections […]

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Simple Neurite Tracer institution(s)
Institute of Neuroinformatics, Uni/ETH Zürich, Zürich, Switzerland; Department of Genetics, University of Cambridge, Cambridge, UK; Institute for Adaptive and Neural Computation, School of Informatics, The University of Edinburgh, Edinburgh, UK
Simple Neurite Tracer funding source(s)
EPSRC (with co-funding from the MRC and BBSRC) via the Doctoral Training Centre in Neuroinformatics at the University of Edinburgh; research grants from the BBSRC and EPSRC UK

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