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

TLDR

Advances in techniques to sparsely label neurons enable reconstruction of connectivity from 3D light‑microscopy image stacks. The authors present the Simple Neurite Tracer, a semi‑automated application for quickly annotating noisy datasets and building complex neuronal topologies. The open‑source software, licensed under the GPL and built on ImageJ, is distributed via the Fiji package and can be accessed on Windows, macOS, and Linux, with documentation and screencasts available at http://fiji.sc/Simple_Neurite_Tracer. Contact: [e-mail]; [e-mail].

Abstract

Abstract 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: [e-mail]; [e-mail]