Website for brain experimental data and other resources such as stimuli and analysis tools. Provides marketplace and discussion forum for sharing tools and data in neuroscience. Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS offers funding for new class of proposals focused on data sharing and other resources.

The accompanying neural data, sounds, and models are outlined in the publication: Fatemeh Khatami and Monty A. Escabí, Spiking network optimized for word recognition in noise predicts auditory system hierarchy. PLOS Comp. Bio (in press). The archive includes a MATLAB implementation of the auditory model from the above citation. The auditory model consists of a front end cochlear model that is connected to a hierarchical spiking neural network (HSNN). The HSNN contains inhibitory and excitatory connections between consecutive layers as outlined in the above manuscript. The original sounds used to test the network in a speech recognition task were derived from clean speech from the TIMIT Acoustic-Phonetic Continuous Speech Corpus (https://catalog.ldc.upenn.edu/LDC93S1). Here, edited speech sounds consisting of digits (“zero” to “nine”) that have added background noise and that were used in the study to test the network are included. The archive also includes neural data that was used to compare results from the auditory system to the auditory HSNN model. Neural data consists of recordings from auditory nerve (AN), inferior colliculus (IC), auditory thalamus (MGB) and cortex (A1).

These are processed and spike sorted recordings from olfactory bulb and piriform cortex under awake and anesthetized conditions. Documentation on the format of the files in this data can be found with a related dataset at https://crcns.org/data-sets/pcx/pcx-1/about-pcx-1

MATLAB scripts that use this data to produce the figures in the associated paper can be found at https://github.com/FranksLab/eLife2020-recurrents-stabilize

The Buzsaki Lab is proud to present a large selection of experimental data available for public access: https://buzsakilab.com/wp/database/. We publicly share more than a thousand sessions (about 40TB of raw and spike- and LFP-processed data) via our public data repository. The datasets are from freely moving rodents and include sleep-task-sleep sessions (3 to 24 hrs continuous recording sessions) in various brain structures, including metadata. We are happy to assist you in using the data. Our goal is that by sharing these data, other users can provide new insights, extend, contradict, or clarify our conclusions.

The databank contains electrophysiological recordings performed in freely moving rats and mice collected by investigators in the Buzsaki Lab over several years (a subset from head-fixed mice). Sessions have been collected with extracellular electrodes using high-channel-count silicon probes, with spike sorted single units, and intracellular and juxtacellular combined with extracellular electrodes. Several sessions include physiologically and optogenetically identified units. The sessions have been collected from various brain region pairs: the hippocampus, thalamus, amygdala, post-subiculum, septal region, and the entorhinal cortex, and various neocortical regions. In most behavioral tasks, the animals performed spatial behaviors (linear mazes and open fields), preceded and followed by long sleep sessions. Brain state classification is provided.

Getting started

The top menu “Databank” serves as a navigational menu to the databank. The metadata describing the experiments is stored in a relational database which means that there are many entry points for exploring the data. The databank is organized by projects, animal subjects, and sessions.

Accessing and downloading the datasets

We share the data through two services: our public Globus.org endpoint and our webshare: buzsakilab.nyumc.org. A subset of the datasets is also available at CRCNS.org. If you have an interest in a dataset that is not listed or is lacking information, please contact us. We pledge to make our data available immediately after publication.

Support

For support, please use our Buzsaki Databank google group. If you have an interest in a dataset that is not listed or is lacking information, please send us a request. Feel free to contact us, if you need more details on a given dataset or if a dataset is missing.

Preprocessed LFPs used in Gonzalez, J., Torterolo, P., & Tort, A. B. L. (2023). Mechanisms and functions of respiration-driven gamma oscillations in the primary olfactory cortex. eLife, 12, e83044. https://doi.org/10.7554/eLife.83044. The recordings obtained by decimating (low-pass filter and downsample) to 2000 Hz the original raw files available at: https://crcns.org/data-sets/pcx/pcx-1

Link Function: information

A virtual database cataloging numerous data set resources, including: BrainMaps.org, Cell Centered Database, Clinical Trials Network (CTN) Data Share, ClinicalTrials.gov, CRCNS, Gene Expression Omnibus, ArrayExpress, MPD - Mouse Phenome Database, BioSharing, Gene Weaver, XNAT Central, 1000 Functional Connectomes Project, Health.Data.gov, SciCrunch Registry, NIF Registry Automated Crawl Data, NeuroVault, OpenfMRI, Physiobank, RanchoBiosciences, YPED, Data.gov Science, and Research Data Catalog.

Please see the attached README for details.OverviewThis dataset contains a portion of the the pvc-7 dataset available on CRCNS.org in the form of a Mesmerize project (mesmerizelab.org). Please see the original dataset for information regarding the experiment. http://dx.doi.org/10.6080/K0C8276GWe are not affiliated with the authors of the original dataset who did the experiment. The purpose of this sub-dataset is to illustrate an application of Mesmerize.Opening the datasetThe dataset is compresed in tar archive with gzip compression. Decompression can take a while, you may get better performance if you read from a different filesystem than the one that you write to. I recommend using a fast filesystem to store the decompressed data since the image data is large.pigz should be faster for decompression compared to standard tar. For Ubuntu & Debian based distros you can install pigz through apt. For other distros please check your repositories.sudo apt install pigzOn Mac OSX you can install pigz through brew. See this: https://brewinstall.org/Install-pigz-on-Mac-with-Brew/Decompressing:pigz -dc pvc7_subdataset_mesmerize.tar.gz | tar -xfIf you cannot install pigz you can decompress with tar. This may take a long time.tar xvzf pvc7_subdataset_mesmerize.tar.gzThis will probably decompress into a directory called "share". Navigate to share/data/temp/kushal and you should see the project directory "pvc7_subdataset_mesmerize".Once decompressed, you can explore the dataset using Mesmerize. Simply open the Project Directory through the Mesmerize Welcome Window (the window that you are presented with when you launch Mesmerize). You will see the available analysis flowcharts and plots similar to this: http://www.mesmerizelab.org/Overview.html#welcome-windowDouble click on a flowchart or plot to open it. See the "Flowchart" and "Plots" sections below for details.You can explore individual project samples by using the Project Browser and double-clicking on the samples of interest. Note that the image sequence is large (~50GB) so make sure you have enough RAM available if you want to view it.

This dataset contains intracranial EEG recordings from one patient during single pulse electrical stimulation. These data were recorded at the Mayo Clinic in Rochester, MN, as part of the NIH Brain Initiative supported project R01 MH122258 "CRCNS: Processing speed in the human connectome across the lifespan".

The overarching goal of this project is to develop a large database of single pulse stimulation data and develop tools to advance our understanding of the human connectome across the lifespan.

Citing this dataset

This dataset is part of the paper on 'Basis profile curve identification to understand electrical stimulation effects in human brain networks' by Miller, Mueller and Hermes, 2021, https://www.biorxiv.org/content/10.1101/2021.01.24.428020v1.full. Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number R01MH122258. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The data was collected by Dora Hermes, Nick Gregg, Brian Lundstrom, Cindy Nelson, Gregg Worrell and Kai J. Miller. The BIDS formatting was performed by Dora Hermes and Gabriella Ojeda Valencia.

Format

It is formatted according to BIDS version 1.3.0

Details about the single pulse stimulation experiment

Patients were resting in the hospital bed, while single pulse stimulation was performed with a frequency of ~0.2 Hz. The stimulation had a duration of 200 microseconds, was biphasic and had an amplitude of 6mA. On the motor cortex stimulation amplitude was sometimes reduced to 1 or 2mA to minimize movement artifacts.

Contact

Please contact Dora Hermes (hermes.dora@mayo.edu) for questions.

Information

This dataset contains intracranial EEG (iEEG) recordings from 8 patients during single pulse electrical stimulation used in the publication of: Ojeda Valencia G, Gregg N, Huang H, Lundstrom B, Brinkmann B, Pal Attia T, Van Gompel J, Bernstein M, In MH, Huston J, Worrell G, Miller KJ, and Hermes D. 2023. Signatures of electrical stimulation driven network interactions in the human limbic system. Journal of Neuroscience (in press).

License

This dataset is made available under the Public Domain Dedication and License CC v1.0, whose full text can be found at https://creativecommons.org/publicdomain/zero/1.0/. We hope that all users will follow the ODC Attribution/Share-Alike Community Norms (http://www.opendatacommons.org/norms/odc-by-sa/); in particular, while not legally required, we hope that all users of the data will acknowledge by citing the following in any publication:

Ojeda Valencia G, Gregg N, Huang H, Lundstrom B, Brinkmann B, Pal Attia T, Van Gompel J, Bernstein M, In MH, Huston J, Worrell G, Miller KJ, and Hermes D. 2023. Signatures of electrical stimulation driven network interactions in the human limbic system. Journal of Neuroscience. DOI: https://doi.org/10.1523/JNEUROSCI.2201-22.2023

Task Description

Patients were resting in the hospital bed, while single pulse stimulation was performed. The stimulation had a duration of 200 microseconds, was biphasic and had an amplitude of 6mA. For subject 7 stimulation amplitude was sometimes reduced to 4mA to minimize interictal responses.

Code

Code to analyses these data is available at: https://github.com/MultimodalNeuroimagingLab/HAPwave

Dataset

This data is organized according to the Brain Imaging Data Structure specification (BIDS version 1.12.0). A community- driven specification for organizing neurophysiology data along with its metadata. For more information on this data specification, see https://bids-specification.readthedocs.io/en/stable/ Each subject has their own folder (e.g., ‘sub-01’) containing intracranial EEG (iEEG) recordings from 8 patients during single pulse electrical stimulation, as well as the metadata needed to understand the raw data and event timing.

Acknowledgements

This project was funded by the National Institute Of Mental Health of the National Institutes of Health Brain Initiative under Award Number R01 MH122258, “CRCNS: Processing speed in the human connectome across the lifespan". The overall goal of this project is to develop a large database of single pulse stimulation data and develop tools to advance our understanding of the human connectome across the lifespan. The data was collected by Dora Hermes, Nick Gregg, Brian Lundstrom, Cindy Nelson, Gabriela Ojeda Valencia, Gregg Worrell and Kai J. Miller. The BIDS formatting was performed by Dora Hermes and Gabriela Ojeda Valencia.

Contact

Please contact Dora Hermes (hermes.dora@mayo.edu) or Gabriela Ojeda Valencia (OjedaValencia.Alma@mayo.edu) for questions.

Basis Profile Curve identification in the human ventral temporal cortex

This dataset contains intracranial EEG recordings from five patients during single pulse electrical stimulation as described in:

• Huang, H., Gregg, N. M., Valencia, G. O., Brinkmann, B. H., Lundstrom, B. N., Worrell, G. A., ... & Hermes, D. (2023). Electrical stimulation of temporal and limbic circuitry produces distinct responses in human ventral temporal cortex. Journal of Neuroscience. DOI: https://doi.org/10.1523/JNEUROSCI.1325-22.2023

Please cite this work when using the data. These data were recorded at the Mayo Clinic in Rochester, MN, as part of the NIH Brain Initiative supported project R01 MH122258 "CRCNS: Processing speed in the human connectome across the lifespan". Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number R01MH122258 and by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number T32GM065841. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The data was collected by Harvey Huang, Dora Hermes, Nick Gregg, Brian Lundstrom, Cindy Nelson, Gregg Worrell and Kai J. Miller. The BIDS formatting was performed by Harvey Huang, Dora Hermes and Gabriela Ojeda Valencia.

Data can be analyzed using the Matlab code at: * https://github.com/hharveygit/VTCBPC_JNS_Manu

Format

Data are formatted according to BIDS version 1.9.9

Single pulse stimulation

The patient were resting in the hospital bed, while single pulse stimulation was performed with a frequency of ~0.2 Hz. The stimulation had a duration of 200 microseconds, was biphasic and had an amplitude of 6mA.

Contact

Please contact Dora Hermes (hermes.dora@mayo.edu) for questions.