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About hc-3

Information about the hc-3 data set.

Summary.

The data set contains recordings made from multiple hippocampal areas in Long-Evans rats, including: Cornu Ammonis: CA1 and CA3; dentate gyrus (DG), and entorhinal cortex: EC2, EC3, EC4, EC5.  The data was obtained during 442 recording sessions and includes responses of 7,737 neurons in eleven animals while they performed one of fourteen behaviors.  Total time for all experiments is 204.5 hours.   The raw (broadband) data was recorded at 20KHz, simultaneously from 31 to 127 channels.  The raw data was processed to extract the LFPs (Local Field Potentials) and detect spikes. Included in the data set are the following items:

  • Times and waveforms of detected potential spikes.
  • Results of spike sorting.
  • LFPs.
  • For many sessions, the coordinate and direction of the rats head and video files from which the positions were extracted.
  • Metadata tables giving properties of the neurons and characteristics of the recording sessions.

A fuller description of the data set is in crcns-hc3-data-description.pdf

Several publication based on some of the data are:

Theta oscillations provide temporal windows for local circuit computation in the entorhinal-hippocampal loop.
Mizuseki K, Sirota A, Pastalkova E, Buzsáki G., Neuron. 2009 Oct 29;64(2):267-80.
(http://www.ncbi.nlm.nih.gov/pubmed/19874793).

Hippocampal network dynamics constrain the time lag between pyramidal cells across modified environments.
Diba K, Buzsáki G., J Neurosci. 2008 Dec 10;28(50):13448-56.
(http://www.ncbi.nlm.nih.gov/pubmed/19074018).

The following publication describes this data set:

Neurosharing: large-scale data sets (spike, LFP) recorded from the hippocampal-entorhinal system in behaving rats [version 2]
Kenji Mizuseki, Kamran Diba, Eva Pastalkova, Jeff Teeters, Anton Sirota, György Buzsáki. F1000Research 2014, 3:98. doi: 10.12688/f1000research.3895.2

Format of the data.

The format of the data is described in crcns-hc3-data-description.pdf.  The data for each session is stored in a tar.gz file. The total size of the data is about 433 GB compressed. Not all of the data needs to be downloaded to use the data set.  Document crcns-hc3-data-description.pdf gives an overview of the data set and describes how to identify sessions of interest.  File crcns-hc3-session-cell-counts.zip contains lists that specify the number of cells from each region for each session and also lists which sessions have the most number of cells from each region.

How to download the data

Data may be downloaded from:
https://portal.nersc.gov/project/crcns/download/hc-3
A CRCNS.org account is required. See the download link for more instructions.

Getting help using the data.

If you have questions about using the data, post them on the forum for using data sets.

How to cite the data

Publications created through usage of the data should cite at least one of the publication given above and also cite the data set in the following recommended format:

Mizuseki, K., Sirota, A., Pastalkova, E., Diba, K., Buzsáki, G. (2013)
Multiple single unit recordings from different rat hippocampal and entorhinal regions while the animals were performing multiple behavioral tasks. CRCNS.org.
http://dx.doi.org/10.6080/K09G5JRZ

The above citation uses a Digital Object Identifier (DOI) which is assigned to the data set.  The DOI was created using DataCite (www.datacite.org) and the California Digital Library, "EZID" system (n2t.net/ezid/).

Documentation files

crcns-hc3-data-description.pdf (Read this first)
crcns-hc3-processing-flowchart.pdf
crcns-hc3-session-cell-counts.zip
crcns-hc3-metadata-tables.zip
crcns-hc3-channelorder.zip

Files for the hc-2 data set which are also relevant:
crcns-hc2-data-description.pdf
crcns-hc2-scripts-and-programs.pdf
crcns-hc2-shank_maps.pdf

Following is provided for reference, but should not normally be needed:
crcns-hc3-original-docs.zip

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