Welcome to NeuronStudio. This program is designed to allow reconstruction of neuronal structures from confocal and multi-photon images. It is a self-contained software package that is free, easy to use, and available for 64-bit computers. NeuronStudio provides tools for manual, semi-manual, and automatic tracing of the dendritic arbor as well as manual and automatic detection and classification of dendritic spines. In addition, advanced 2D and 3D visualization techniques facilitate the verification of the reconstruction, as well as allowing accurate manual editing. The output of the program is compatible with standard compartment modeling and morphometric software applications. This documentation is intended to provide an introduction to the main features of the program and their use in constructing high-quality models.