cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25378/janelia.5576071
title: Gruntman_2017_MatlabCode.zip

description: Data Analysis code, for Gruntman, et al. 2017
DOI: 10.25378/janelia.5576071.v1
title: Gruntman_2017_MatlabCode.zip

description: Data Analysis code, for Gruntman, et al. 2017
DOI: 10.25378/janelia.5576101.v1
title: Gruntman_2017_Data.zip

description: Data (17 cells) to accompany Gruntman, et al. 2017
DOI: 10.25378/janelia.5613190.v1
title: ShuTu: an Open-Source Software for Neuron Reconstruction rat dente gyrus granule cell 100X

description: 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.
<br>
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 more accurate reconstruction, use 100X.
DOI: 10.7284/150164
title: Meteorological Station data collected during research cruise RR2210 using a SIO MET-System instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.25378/janelia.5576101
title: Gruntman_2017_Data.zip

description: Data (17 cells) to accompany Gruntman, et al. 2017
DOI: 10.25378/janelia.5613169.v3
title: ShuTu: Rat dentate gyrus granule cell 63X

description: 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>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.<br><br>
DOI: 10.25378/janelia.5613184.v1
title: ShuTu: an Open-Source Software for Neuron Reconstruction rat dente gyrus granule cell 100X (compressed)

description: 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.
<br>
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 more accurate reconstruction, use 100X.
<br>
Currently this is set up only for Ubuntu. Due to agressive compression, the sharpness of the images is somewhat reduced. To decompress, first install OpenJPEG then decompress the images using the following commands:
sudo sh installOpenJpegForCompression.sh
python decompressToTiff.py ~/granuleCellCompress
DOI: 10.25378/janelia.5613184.v2
title: ShuTu: Open-Source Software for Neuron Reconstruction rat dente gyrus granule cell 100X (compressed)

description: 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.
<br>
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 more accurate reconstruction, use 100X.
<br>
Currently this is set up only for Ubuntu. Due to agressive compression, the sharpness of the images is somewhat reduced. To decompress, first install OpenJPEG then decompress the images using the following commands:
sudo sh installOpenJpegForCompression.sh
python decompressToTiff.py ~/granuleCellCompress
DOI: 10.25378/janelia.5613184.v3
title: ShuTu: Open-Source Software for Neuron Reconstruction rat dentate gyrus granule cell 100X (compressed)

description: 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.
<br>
Here we provide images of a rat dentate 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 more accurate reconstruction, use 100X.
<br>
Currently this is set up only for Ubuntu. Due to agressive compression, the sharpness of the images is somewhat reduced. To decompress, first install OpenJPEG then decompress the images using the following commands:
sudo sh installOpenJpegForCompression.sh
python decompressToTiff.py ~/granuleCellCompress
DOI: 10.25378/janelia.5613184.v4
title: ShuTu: Rat dentate gyrus granule cell 100X (compressed)

description: 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.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 OpenJPEG then decompress the images using the following commands:sudo sh installOpenJpegForCompression.shpython decompressToTiff.py ~/granuleCellCompressShuTu (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. <br> <br>
DOI: 10.25378/janelia.5613190.v2
title: ShuTu: Open-Source Software for Neuron Reconstruction rat dente gyrus granule cell 100X

description: 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.
<br>
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 more accurate reconstruction, use 100X.
DOI: 10.25378/janelia.5613190.v3
title: ShuTu: Open-Source Software for Neuron Reconstruction rat dentate gyrus granule cell 100X

description: 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. <br> Here we provide images of a rat dentate 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 more accurate reconstruction, use 100X.
DOI: 10.25378/janelia.5613190.v4
title: ShuTu: Rat dentate gyrus granule cell 100X

description: 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>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. <br>
DOI: 10.25378/janelia.5620687.v2
title: ShuTu: Open-Source Software for Neuron Reconstruction Mouse CA3 pyramidal neuron I 100X Parts 1 - 4

description: 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.<br>Here we provided the images and reconstructions of the neurons described in the paper. 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. <br> Mouse CA3 pyramidal neuron I, 100X (filled and imaged by David Hunt, the Spruston Lab, Janelia). This is the neuron discussed as the main example in the paper.
DOI: 10.25378/janelia.5623510.v3
title: ShuTu: Mouse CA3 pyramidal neuron II 100X Parts 1 - 4

description: 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.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. <br> <br>
DOI: 10.25378/janelia.5623621.v2
title: ShuTu: Open-Source Software for Neuron Reconstruction Mouse Purkinje Cell confocal images 63X

description: 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.
<br>
Here we provided the images and reconstructions of the neurons described in the paper.<br>Mouse Purkinje cell, confocal images, 63X (David Hunt).
DOI: 10.25378/janelia.5623621.v3
title: ShuTu: Mouse Purkinje Cell confocal images 63X

description: Here we provide the images for practicing reconstruction using the ShuTu software platform.Mouse Purkinje cell, confocal images, 63X (David Hunt in the Spruston lab.)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. <br> <br>
DOI: 10.25378/janelia.5623621.v4
title: ShuTu: Mouse Purkinje cell confocal images 63X

description: 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. 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.
<br>
<br>
DOI: 10.25378/janelia.5648308
title: Ring attractor dynamics in the Drosophila central brain: Processed data visual environment

description: Physiological data
DOI: 10.25378/janelia.5648308.v1
title: Ring attractor dynamics in the Drosophila central brain: Processed data visual environment

description: Physiological data
DOI: 10.25378/janelia.5648314
title: Ring attractor dynamics in the Drosophila central brain: Processed_data

description: Physiological data
DOI: 10.25378/janelia.5648317
title: Ring attractor dynamics in the Drosophila central brain: processed data

description: Physiological data
DOI: 10.25378/janelia.5648320
title: Ring attractor dynamics in the Drosophila central brain: Processed data powerbox-behavior

description: Physiological data
DOI: 10.25378/janelia.5648461
title: Ring attractor dynamics in the Drosophila central brain: Raw data visual environment

description: Physiological data
DOI: 10.25378/janelia.5648461.v1
title: Ring attractor dynamics in the Drosophila central brain: Raw data visual environment

description: Physiological data
DOI: 10.25378/janelia.5648470
title: Ring attractor dynamics in the Drosophila central brain: Raw data powerbox-behavior

description: Physiological data
DOI: 10.25378/janelia.5648470.v1
title: Ring attractor dynamics in the Drosophila central brain: Raw data powerbox-behavior

description: Physiological data
DOI: 10.25378/janelia.5648542
title: Ring attractor dynamics in the Drosophila central brain: Raw data powerbox bump shifting

description: Physiological data
DOI: 10.25378/janelia.5648542.v1
title: Ring attractor dynamics in the Drosophila central brain: Raw data powerbox bump shifting

description: Physiological data
DOI: 10.25378/janelia.5648545
title: Ring attractor dynamics in the Drosophila central brain: Raw data powerbox-flow

description: Physiological data
DOI: 10.25378/janelia.5648545.v1
title: Ring attractor dynamics in the Drosophila central brain: Raw data powerbox-flow

description: Physiological data
DOI: 10.25378/janelia.5708521
title: Figure 2 scripts and data

description: This zip file contains the Matlab code and data to recreate Figure 2 from "Simple integration of fast excitation and offset, delayed inhibition computes directional selectivity in Drosophila" by Gruntman et al 2018.<br>further information in the README.txt
DOI: 10.25378/janelia.5708527
title: Figure 5 Neuron simulation files

description: This .zip file contains the Neuron code to replicate Figure 5b (right column) and Supplementary Figure 6C (top row) of "Simple Integration of fast excitation, and offset delayed inihbition computes directional selectivity in Drosophila", by Gruntman et al 2018.
DOI: 10.25378/janelia.5782302
title: Central complex functional connectivity raw data

description: Each zip file contains a folder with the experiments for one day. Prairie microscopy format. Besides the data described in the paper, there is an anatomical stack for every fly (in the Z-series... folders, see labbook on the osf page for correspondances).<br>
DOI: 10.25378/janelia.5936218
title: Gen1 Color Depth MIPs

description: Color depth MIP files for Gen1 GAL4 and LexA brains and VNCs. Downloadable archives are publicly available at:<br>https://open.quiltdata.com/b/janelia-flylight-color-depth/tree/Color_Depth_MIPs_For_Download/ <br>For the construction of Janelia and VT GAL4 lines, see the below references.<br>
DOI: 10.25378/janelia.5936218.v1
title: Gen1 Color Depth MIPs

description: Color depth MIP files for Gen1 GAL4 and LexA brains and VNCs.<br>For the construction of Janelia and VT GAL4 lines, see the below references.<br><br>
DOI: 10.25378/janelia.6163622.v1
title: Recordings of ten thousand neurons in visual cortex during spontaneous behaviors

description: This dataset contains the ten thousand neuron data used in Stringer, Pachitariu et al, 2018a. A preprint of the paper is available on bioRxiv containing detailed information. The code to make the figures in the paper is available at <br>https://github.com/MouseLand/stringer-pachitariu-et-al-2018a<br>We encourage data users to fork this repository, or create their own repository inside MouseLand, where we will also be adding our future work. "Watching" the repository might  be a good idea, since any new information about the data, analyses of the data, or publications using it, will appear there.
DOI: 10.25378/janelia.6189089
title: Hunt_et.al_2018

description: A novel pyramidal cell type promotes sharp wave synchronization in the hippocampus
DOI: 10.25378/janelia.6189164
title: Hunt_et.al_2018

description: A novel pyramidal cell type promotes sharp wave synchronization in the CA3 region of the hippocampus
DOI: 10.25378/janelia.6189164.v1
title: Hunt_et.al_2018

description: A novel pyramidal cell type promotes sharp wave synchronization in the CA3 region of the hippocampus
DOI: 10.25378/janelia.6214019
title: Recordings of 10k neurons in V1 during drifting gratings

description: This data accompanies the following paper:<br>Robustness of spike deconvolution for calcium imaging of neural spikingMarius Pachitariu, Carsen Stringer, Kenneth D. HarrisbioRxiv 156786; doi: https://doi.org/10.1101/156786<br>where it is used to assess the performance of spike deconvolution algorithms. The code repository to reproduce the analyses in the paper is uploaded at <br>https://github.com/MouseLand/pachitariu-et-al-2018a<br><br>We recorded ~10,000 neurons simultaneously at 2.5Hz using calcium imaging. Visual stimuli were shown at approximately 1 Hz, with randomized inter-stimulus intervals. The stimuli were drifting gratings with 8 directions, 4 spatial frequencies and 3 temporal frequencies. Blank stimuli (gray screen) were also interleaved.
DOI: 10.25378/janelia.6252800
title: Software Guide (Full Version)

description: Preconfigured modules and example data for the practical software guide (full repository)<br>
DOI: 10.25378/janelia.6252938
title: Software Guide (Compact Version)

description: Preconfigured modules and example data for the practical software guide (compact repository)