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. It can also handle fluorescence images from confocal stacks, however, by first inverting the images.
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: sophisticated algorithms perform the automated reconstruction, which is then superimposed on the images, along with a convenient user interface to facilitate efficient completion of the reconstruction via manual annotation.
A more detailed description of ShuTu can be found here (Frontiers in Neuroinformatics).
For more resources, including software downloads, go here (Dezhe Jin's ShuTu site).