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

Area of Science:

• Neuroscience
• Computational Biology
• Microscopy

Background:

• Advances in neuronal labeling techniques enable connectivity reconstruction from 3D light microscopy image stacks.
• Accurate reconstruction of neuronal topologies is crucial for understanding neural circuits.

Purpose of the Study:

• To present Simple Neurite Tracer, a novel application for semi-automated neuron tracing.
• To enable rapid annotation of noisy datasets and construction of complex neuronal topologies.

Main Methods:

• Development of an open-source software application based on ImageJ.
• Semi-automated tracing algorithms for annotating neuronal structures in 3D image stacks.
• Cross-platform compatibility (Windows, Mac OS, Linux).

Main Results:

• The Simple Neurite Tracer facilitates efficient and quick annotation of neuronal datasets.
• The software assists in constructing complex neuronal topologies from light microscopy data.

Conclusions:

• Simple Neurite Tracer is a valuable tool for neuroscientists studying neuronal connectivity.
• The open-source nature and availability on Fiji enhance its accessibility and utility.