ShuTu: Open-Source Software for Neuron Reconstruction rat dente gyrus granule cell 63X

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.

Here we provide images of a rat dente gyrus granule cell for evaluting the software and practing reconstruction. The cell was filled and imaged by Ching-Lung Hsu at the Spruston Lab at Janelia. Two resolutions are provided, 63X and 100X. For quick evaluation, use this file 63X.