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Simple Neurite Tracer specifications

Information


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
Requirements
ImageJ
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Longair MH

Publication for Simple Neurite Tracer

Simple Neurite Tracer citations

 (81)
library_books

Cadherins Interact With Synaptic Organizers to Promote Synaptic Differentiation

2018
PMCID: 5936767
PMID: 29760652
DOI: 10.3389/fnmol.2018.00142

[…] resynaptic differentiation (“Presynaptic” in figures) was quantified by counting separated synapsin I-positive puncta on each cell. Neurite length was measured after tracing individual neurites using Simple Neurite Tracer-3.1.3 (Longair et al., ; source code is available from GitHub: https://github.com/fiji/Simple_Neurite_Tracer/). Neurite ramification (“Branch”) was counted when the neurite branc […]

call_split

Competition between microtubule associated proteins directs motor transport

2018
Nat Commun
PMCID: 5902456
PMID: 29662074
DOI: 10.1038/s41467-018-03909-2
call_split See protocol

[…] DA sensory neurons were collected for analysis from segment A3 or A4. Total dendrite length and number of branchpoints were determined from maximum Z-projections of the Z-stack image files using the Simple Neurite Tracer plugin for ImageJ Fiji. […]

library_books

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

2018
Nat Commun
PMCID: 5897332
PMID: 29651049
DOI: 10.1038/s41467-018-03802-y

[…] r (https://imagej.net/Image_Stitching). 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 (http://imagej.net/Simple_Neurite_Tracer). Based on dendrites reconstructions, a Sholl analysis was performed using “Sholl Analysis” plugin (http://imagej.net/Sholl_Analy […]

library_books

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

2018
PMCID: 5866123
PMID: 29317193
DOI: 10.1016/j.expneurol.2018.01.002

[…] escent-labelled 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 (). […]

library_books

Layer 5 Callosal Parvalbumin Expressing Neurons: A Distinct Functional Group of GABAergic Neurons

2018
PMCID: 5845545
PMID: 29559891
DOI: 10.3389/fncel.2018.00053

[…] hed together, when necessary. Image adjustment was performed in ImageJ for brightness/contrast corrections and pseudocoloring. Neurons were morphologically reconstructed in three dimensions using the Simple Neurite Tracer plugin for ImageJ (Longair et al., ). […]

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Kinesin 1 regulates cilia length through an interaction with the Bardet Biedl syndrome related protein CCDC28B

2018
Sci Rep
PMCID: 5813027
PMID: 29445114
DOI: 10.1038/s41598-018-21329-6
call_split See protocol

[…] FIJI and data was analyzed using Pyhton scripts. For each cilium, the 3D distal and proximal points were manually defined by the user using the ARL13B (red) channel. Based in these two 3D points, the Simple Neurite Tracer (SNT) plugin was used in FIJI, using default parameters, to build a simple path (curve) between them. This curve in the volume was find using two directional searches based on a […]

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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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