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.
ShuTu was written by Dezhe Jin (Penn State University) and Ting Zhao (Janelia) in collaboration with Nelson Spruston (Janelia).
A more detailed description of ShuTu can be found here.
To install on Mac and Linux, download the zip file, and in a terminal and in the directory ShuTuMac or ShuTuUbuntu, type the commands
View source code and collaborate on Github.
Download images for practicing reconstruction.
Below are some additional images and reconstructions of the neurons described in the paper.