2011/07/04 by Mark Longair, Dean A. Baker, J. Douglas Armstrong · 1,089 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · #Advanced Electron Microscopy Techniques and Applications #Advanced Fluorescence Microscopy Techniques #Artificial intelligence #Cell Image Analysis Techniques #Chemistry #Computer graphics (images) #Computer science #Construct (python library) #Data mining #Dataflow #Documentation #Neurite #Open source #Open source software #Operating system #Physics #Programming language #Simple (philosophy) #Software #TRACER #Tracing #Visualization
paper · pdf · doi:10.1093/bioinformatics/btr390
published in Bioinformatics 27(17), 2453-2454 (Oxford University Press)
openalex publication_date 2011/07/04 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
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/SimpleNeuriteTracer 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: [email protected]; [email protected].