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About th-1

Information about the th-1 data set.

Summary.

The data set contains recordings made from multiple anterior thalamic nuclei, mainly the antero-dorsal (AD) nucleus, and subicular areas, mainly the post-subiculum (PoS), in freely moving mice. Thalamic and subicular electrodes yielding high number of the so-called Head-Direction (HD) cells were likely to be located in the AD nucleus and the PoS, respectively. Electrode placement was confirmed by histology.

The data was obtained during 42 recording sessions and includes responses of 720 neurons in the thalamus and 357 neurons in the PoS, in seven animals while they foraged for food in an open environment (53- x 46-cm).  Three animals were recorded simultaneously in the thalamus and the PoS (21 sessions). In the four other animals, electrodes were implanted in the anterior thalamus and in the pyramidal layer of the CA1 area of the hippocampus but only to record Local field Potentials (LFPs). The raw (broadband) data was recorded at 20KHz, simultaneously from 64 to 96 channels.  The raw data was processed to extract the LFPs and detect spikes. Included in the data set are the following items:

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

More information is given in document: crcns_th-1_data_description.pdf and in the following publication which is based on this dataset:

Internally organized mechanisms of the head direction sense. Peyrache A, Lacroix MM, Petersen PC, Buzsaki G, Nature Neuroscience. 2015

Format of the data.

The format of the data is the same as the hc-1, hc-2 and hc-3 data sets.   The data for each session is stored in a tar.gz file. The total size of the data is about 213 GB compressed. Not all of the data needs to be downloaded to use the data set.  A spreadsheet included in the docs folder in the data set downloads indicates which brain regions were recorded from within each session.

How to download the data.

The data must be downloaded from:

https://portal.nersc.gov/project/crcns/download/th-1

A CRCNS.org account is required.  This link allows bulk downloading of multiple files using the download script as described in the "Alternative download method" section on the download page.

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 the paper referenced above (Peyrache A. et al. 2015) and also cite the data set using the following:

Peyrache, A., Buzsáki, G. (2015)
Extracellular recordings from multi-site silicon probes in the anterior thalamus and subicular formation of freely moving mice. CRCNS.org.
http://dx.doi.org/10.6080/K0G15XS1

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_th-1_data_description.pdf

Files for other hc data set which are relevant:
crcns-hc3-data-description.pdf
crcns-hc3-processing-flowchart.pdf
crcns-hc2-data-description.pdf
crcns-hc2-processing-flowchart.pdf
crcns-hc2-scripts-and-programs.pdf

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