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About hc-1

Information about the data.

Summary.

The data consists of simultaneous intracellular and extracellular recordings in the hippocampus of anesthetized rats.  Experimental procedures as well as major results are described in:

Henze et al, J. Neurophysiology 84, 390-400 (2000) (http://www.ncbi.nlm.nih.gov/pubmed/10899213)
Harris et al, J. Neurophysiology 84, 401-414 (2000) ( http://www.ncbi.nlm.nih.gov/pubmed/10899214)

These data are useful as a benchmark for spike detection and sorting (see paper by Harris et al., for some of the methodology).

The data set is recorded from the CA1 hippocampal region. They contain recordings from the same neuron recorded both intracellularly and extracellularly.  Part of this data set has been already tested by various laboratories to test the uniquely developed unit clustering algorithms.  Currently, no widely accepted standards are available for the separation of single neurons or for the assessment of errors. Communicating information across laboratories without some standardized way is difficult, and the lack of quantification of clustering errors is often a source of interpretation problem of the original data. Our data set could be used as a benchmark for the development of improved data clustering tools.

Extracellular recordings were carried out partly with wire tetrodes for about half of the data set, while the remaining part with six-site linear silicon probes (see C. Gold, D. Henze, C. Koch and G. Buzsaki. On the Origin of the Extracellular Action Potential Waveform: A Modeling Study. J Neurophysiol. 2006 May;95(5):3113-28). Many of the neurons were also labeled with biocytin and reconstructed anatomically to allow for modeling under the constraints of physiological parameters (Gold et al., 2006).

Format of the data.

The data is organized into folders with each folder corresponding to an experiment with one cell.  The data is stored in a binary format which can be imported into Matlab and also into a program called Neuroscope (which is included in the download).  Total data size is about 21GB.  Not all the data needs to be downloaded initially.  Data d533101 and d561102 are known to be good and are enough to get started.  Details of the data format are in the crcns-hc1-data-description.pdf (which is also included in the download; in the download, the name of the file is README.txt).

How to download the data

Data may be downloaded from:
https://portal.nersc.gov/project/crcns/download/hc-1
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.  It is also possible to email questions to the data contributors.  Instructions for doing this are included with the download.  However, posting questions to the forum is preferable because then everyone can see the answers.

How to cite the data

Publications created through usage of the data should cite as least one of the two publications given above (Henze et al., J. Neurophysiology 84 (2000)), and also the data set using the following:

Henze, DA; Harris, KD; Borhegyi, Z; Csicsvari, J; Mamiya, A; Hirase, H; Sirota, A; Buzsáki, G (2009): Simultaneous intracellular and extracellular recordings from hippocampus region CA1 of anesthetized rats. CRCNS.org.
http://dx.doi.org/10.6080/K02Z13FP

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 file

crcns-hc1-data-description.pdf.
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