ShuTu: Rat CA1 pyramidal neuron 63X (Parts 1 - 12)
Here we provide images of a rat CA1 pyramidal neuron (63X) for practicing reconstruction using the ShuTu software platform. The cell was imaged by Ching-Lung Hsu in the Spruston Lab. Due to large sizes of the images files, the data for some neurons are split into multiple parts. After downloading and decompressing, the parts should be combined into one directory.
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.