TEM and array tomography images from Source data and images for "Single excitatory axons form clustered synapses onto CA1 pyramidal cell dendrites" by Bloss, Cembrowski, Karsh, Colonell, Fetter, and Spruston (2018).

<div>These are the raw images from Bloss et al. (2018), titled "Single excitatory axons from clustered synapses onto CA1 pyramidal cell dendrites"<br></div><div><br></div>Files include TEM micrographs, stacks of TEM micrographs, projections from array tomography volumes, and confocal laser microscopy images

ShuTu: Rat CA1 pyramidal neuron 63X (Parts 1 - 12)

<p>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.</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

Source data for "Single excitatory axons form clustered synapses onto CA1 pyramidal cell dendrites" by Bloss, Cembrowski, Karsh, Colonell, Fetter, and Spruston (2018).

These are the raw data from Bloss et al. (2018) titled "Single excitatory axons from clustered synapses onto CA1 pyramidal cell dendrites." <div><br></div><div>For the raw data, each sheet within the Excel file corresponds to a Figure or Supplementary Figure.</div

ShuTu: Rat dentate gyrus granule cell 63X

<p>Here we provide images of a rat dentate gyrus granule cell (63X) 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 quick evaluation, use this file 63X. <br></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

ShuTu: Video tutorial

<p>Here we provide a video tutorial for using the ShuTu software platform.</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><div><br></div

ShuTu: Mouse CA3 pyramidal neuron II 100X Parts 1 - 4

<p>Here we provide images of the mouse CA3 pyramidal neuron II (100X) for practicing reconstruction using the ShuTu software platform. The cell was imaged by David Hunt 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.</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

ShuTu: Rat dentate gyrus granule cell 100X (compressed)

<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

ShuTu: Mouse Purkinje cell confocal images 63X

<p>Here we provide images of the mouse Purkinje cell (63X) for practicing reconstruction using the ShuTu software platform. The cell was imaged by David Hunt in the Spruston Lab. </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

ShuTu: Rat dentate gyrus granule cell 100X

<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 this 100X fileset.<br></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