2,097 Works

raw_data_imaging2_2.tar.gz

Sung Soo Kim, Ann M. Hermundstad, Sandro Romani, & Vivek Jayaraman
Two-photon imaging data for the following paper.

Generation of stable heading representations in diverse visual scenes
Sung Soo Kim+, Ann M. Hermundstad, Sandro Romani, L. F. Abbott, Vivek Jayaraman+
Nature (2019) 576:126-131

raw_data_imaging5_2.tar.gz

Sung Soo Kim, Ann M. Hermundstad, Sandro Romani, & Vivek Jayaraman
Two-photon imaging data for the following paper.

Generation of stable heading representations in diverse visual scenes
Sung Soo Kim+, Ann M. Hermundstad, Sandro Romani, L. F. Abbott, Vivek Jayaraman+
Nature (2019) 576:126-131

raw_data_imaging3.tar.gz

Sung Soo Kim, Ann M. Hermundstad, Sandro Romani, & Vivek Jayaraman
Two-photon imaging data for the following paper.

Generation of stable heading representations in diverse visual scenes
Sung Soo Kim+, Ann M. Hermundstad, Sandro Romani, L. F. Abbott, Vivek Jayaraman+
Nature (2019) 576:126-131

Kim_etal_Nature2019_simulation_codes.zip

Sung Soo Kim, Ann M. Hermundstad, Sandro Romani, & Vivek Jayaraman
Simulation codes (Matlab) for the following paper.

Generation of stable heading representations in diverse visual scenes
Sung Soo Kim+, Ann M. Hermundstad, Sandro Romani, L. F. Abbott, Vivek Jayaraman+
Nature (2019) 576:126-131

Generation of stable heading representations in diverse visual scenes

Sung Soo Kim, Ann M. Hermundstad, Sandro Romani, & Vivek Jayaraman
Many animals rely on an internal heading representation when navigating in varied environments. How this representation is linked to the sensory cues that define different surroundings is unclear. In the fly brain, heading is represented by 'compass' neurons that innervate a ring-shaped structure known as the ellipsoid body. Each compass neuron receives inputs from 'ring' neurons that are selective for particular visual features; this combination provides an ideal substrate for the extraction of directional information...

plasticity_codes_and_preprocessed_data.tar.gz

Sung Soo Kim, Ann M. Hermundstad, Sandro Romani, & Vivek Jayaraman
Analysis codes and pre-processed data to generate figures in the following paper.

Generation of stable heading representations in diverse visual scenes
Sung Soo Kim+, Ann M. Hermundstad, Sandro Romani, L. F. Abbott, Vivek Jayaraman+
Nature (2019) 576:126-131

raw_data_imaging4_2.tar.gz

Sung Soo Kim, Ann M. Hermundstad, Sandro Romani, & Vivek Jayaraman
Two-photon imaging data for the following paper.

Generation of stable heading representations in diverse visual scenes
Sung Soo Kim+, Ann M. Hermundstad, Sandro Romani, L. F. Abbott, Vivek Jayaraman+
Nature (2019) 576:126-131


raw_data_bhv.tar.gz

Sung Soo Kim, Ann M. Hermundstad, Sandro Romani, & Vivek Jayaraman
Raw behavior data of all flies for the following paper.

Generation of stable heading representations in diverse visual scenes
Sung Soo Kim+, Ann M. Hermundstad, Sandro Romani, L. F. Abbott, Vivek Jayaraman+
Nature (2019) 576:126-131

Simple integration paper data and code

Michael Reiser
Supplemental data and code for the manuscript: Simple integration of fast excitation and offset, delayed inhibition computes directional selectivity in Drosophila by Gruntman, Romani, and Reiser (2018)

ShuTu: Open-Source Software for Neuron Reconstruction rat dentate gyrus granule cell 100X

Nelson Spruston, , Ting Zhao, David Hunt, Rachel Pearcy &
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...

ShuTu: Mouse Purkinje Cell confocal images 63X

Nelson Spruston, David Hunt, , Ting Zhao, Rachel Pearcy &
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,...

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

Nelson Spruston, , , Ting Zhao, David Hunt & Rachel Pearcy
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...

Ring attractor dynamics in the Drosophila central brain: Raw data powerbox bump shifting

Sung Soo Kim
Physiological data

Software Guide (Compact Version)

Philipp Keller
Preconfigured modules and example data for the practical software guide (compact repository)

How far-out fundamental science has led to a revolution in brain imaging, with implications for the Loudoun County economy

Karel Svoboda
Slide deck from a "Science on Tap" public lecture given by Karel Svoboda at the Old Ox Brewery in Ashburn, VA on March 13, 2018. How the most far-out science benefits our economy.

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

Nelson Spruston, , Ting Zhao, David Hunt, Rachel Pearcy &
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...

ShuTu: an Open-Source Software for Neuron Reconstruction Mouse CA3 pyramidal neuron I 100X Parts 1 - 4

Nelson Spruston, David Hunt, , Ting Zhao, Rachel Pearcy &
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...

ShuTu: an Open-Source Software for Neuron Reconstruction Mouse Purkinje Cell confocal images 63X

Nelson Spruston, David Hunt, , Ting Zhao, Rachel Pearcy &
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...

ShuTu: an Open-Source Software for Neuron Reconstruction rat dente gyrus granule cell 100X

Nelson Spruston, , Ting Zhao, David Hunt, Rachel Pearcy &
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...

Ring attractor dynamics in the Drosophila central brain: Processed_data

Sung Soo Kim
Physiological data

Software Guide (Compact Version)

Philipp Keller
Preconfigured modules and example data for the practical software guide (compact repository)

Data S1A: Technical Drawings

Philipp Keller
Please contact innovation@janelia.hhmi.org or visit https://www.janelia.org/open-science/simview in order to obtain free access to this archive. The archive contains the blueprint of the adaptive multi-view light-sheet microscope for mouse imaging, including technical drawings for the microscope’s 77 types of custom mechanical components, assembly illustrations for the microscope’s 28 types of multi-part assemblies, and parts list of all custom and commercial mechanical microscope components

Whole-brain light-sheet imaging data

, Yu Mu, Aaron Kuan, Maxim Nikitchenko, Owen Randlett, Alex Chen, Jeffery Gavornik, Haim Sompolinsky, Florian Engert & Misha B. Ahrens
Supporting data for:
Brain-wide Organization of Neuronal Activity and Convergent Sensorimotor Transformations in Larval Zebrafish.
Xiuye Chen, Yu Mu, Yu Hu, Aaron T. Kuan, Maxim Nikitchenko, Owen Randlett, Alex B. Chen, Jeffery P. Gavornik, Haim Sompolinsky, Florian Engert, and Misha B. AhrensNeuron, 2018

Whole-brain light-sheet imaging data collected by Yu Mu in the Misha B. Ahrens lab at Janelia Research Campus (https://www.janelia.org/lab/ahrens-lab).Code by Xiuye Chen (Boston University and Harvard University, https://github.com/xiuyechen/ ) Contact: ahrensm@janelia.hhmi.org and xiuye.chen@gmail.com Data from...

MouseLight Neuron AA0381

Jayaram Chandrashekar, &
A vast neural tracing effort by a team of Janelia scientists has upped the number of fully-traced neurons in the mouse brain by a factor of 10. Researchers can now download and browse the data in three dimensions.
Inside the mouse brain, individual neurons zigzag across hemispheres, embroider branching patterns and, researchers have now discovered, can even spool out spindly fibers up to 45 centimeters long.
Scientists can see and explore these wandering neural traces in...

MouseLight Neuron AA0391

Jayaram Chandrashekar, &
A vast neural tracing effort by a team of Janelia scientists has upped the number of fully-traced neurons in the mouse brain by a factor of 10. Researchers can now download and browse the data in three dimensions.
Inside the mouse brain, individual neurons zigzag across hemispheres, embroider branching patterns and, researchers have now discovered, can even spool out spindly fibers up to 45 centimeters long.
Scientists can see and explore these wandering neural traces in...

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