ShuTu: Open-Source Software for Neuron Reconstruction

ShuTu (Chinese for "dendrite") is a software platform for semi-automated reconstruction of neuronal morphology. It is designed for neurons stained following patch-clamp recording and biocytin filling/staining. With an additional preprocessing step, it can also handle fluorescence images from confocal stacks. Even when there is only a single neuron in the imaged volume, automated reconstruction is tricky, because of background. Thus, ShuTu was developed to facilitate a two-step process: automated reconstruction, followed by manual correction. The software uses sophisticated algorithms to perform the automated reconstruction, as well as a convenient user interface to facilitate efficient completion of the reconstruction via manual annotation.