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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


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  • person_outline Longair MH <>

Publication for Simple Neurite Tracer

Simple Neurite Tracer in publications

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 […]

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 […]

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 […]

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 […]

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 […]

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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