Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes

By Mark Longair, David Baker, J. Armstrong. Bioinform., 2011

933 citations recorded by the source corpus.

MOTIVATION Advances in techniques to sparsely label neurons unlock the potential to reconstruct connectivity from 3D image stacks acquired by light microscopy. We present an application for semi-automated tracing of neurons to quickly annotate noisy datasets and construct complex neuronal topologies, which we call the Simple Neurite Tracer. AVAILABILITY Simple Neurite Tracer is open source software, licensed under the GNU General Public Licence (GPL) and based on the public domain image processing software ImageJ. The software and further documentation are available via http://fiji.sc/Simple_Neurite_Tracer as part of the package Fiji, and can be used on Windows, Mac OS and Linux. Documentation and introductory screencasts are available at the same URL. CONTACT longair@ini.phys.ethz.ch; longair@ini.phys.ethz.ch.

Subfields: Biophysics, Structural Biology

View Paper: https://www.semanticscholar.org/paper/d75ec8768c39935e3161b7955a4ab1a834db42e2

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In Biophysics

Citations in the corpus

Psychedelics Promote Structural and Functional Neural Plasticity (2018, methodology): “Total dendrite length and the number of branch points were determined from maximum Z projections of the Z-stack image files using the Simple Neurite Tracer plugin for ImageJ Fiji (Longair et al., 2011).”
Image-Based Phenotyping of the Mature Arabidopsis Shoot System (2014, methodology): “The traits extracted with the proposed framework (PPFW ) are compared with traits from a semi-automatic analysis using Fiji Simple Neurite Tracer [19] (GT Fiji).”
SNT: a unifying toolbox for quantification of neuronal anatomy (2020, methodology): “A simple test for viability was performed as follows: the GRN is simulated for 100 time-steps with constant input values, with the following criteria assessed at the first and final time-step of the viability test: (1) all behavior regulating protein concentrations should change, (2) the GRN must bi”
The ImageJ ecosystem: an open platform for biomedical image analysis (2015, neutral): “Over time, projects such as the 3D Viewer, the Simple Neurite Tracer, and bUnwarpJ (Arganda!”
Purkinje cells directly inhibit granule cells in specialized regions of the cerebellar cortex (2016, methodology): “Stacks were stitched together to obtain large-area stacks, and cells were traced using ImageJ (NIH) with the Simple Neurite Tracer plug-in (Longair et al., 2011; Preibisch et al., 2009).”
Layer-Specific Organization of Local Excitatory and Inhibitory Synaptic Connectivity in the Rat Presubiculum (2017, methodology): “Selected cells were morphologically reconstructed using the Simple Neurite Tracer plug-in (Longair et al. 2011) in the Fiji distribution of ImageJ software (http://fiji.sc/) from confocal image stacks obtained with a 30× silicone-immersion objective (NA 1.05).”