ShuTu: Rat dentate gyrus granule cell 100X (compressed) Nelson Spruston Dezhe Jin Ting Zhao David Hunt Rachel Pearcy Ching-Lung Hsu 10.25378/janelia.5613184.v4 https://janelia.figshare.com/articles/dataset/ShuTu_an_Open-Source_Software_for_Neuron_Reconstruction_rat_dente_gyrus_granule_cell_100X_compressed_/5613184 <p>Here we provide images of a rat dentate gyrus granule cell (100X) for practicing reconstruction using the ShuTu software platform. The cell was filled and imaged by Ching-Lung Hsu in the Spruston Lab. Two resolutions are provided, 63X and 100X. For more accurate reconstruction, use 100X.</p><p>Currently this compressed file is set up only for Ubuntu. Due to agressive compression, the sharpness of the images is somewhat reduced. To decompress, first install <a href="http://www.openjpeg.org/">OpenJPEG</a> then decompress the images using the following commands:</p><p>sudo sh installOpenJpegForCompression.sh</p><p>python decompressToTiff.py ~/granuleCellCompress</p><p>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.</p> <p>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.</p> <p><br></p> <p><br></p> 2017-11-27 18:56:34 Dendritic morphology Neuroscience