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About ssc-1

Information about the data including data types, experiments, format of the data.

Summary of the data

This dataset comprises calcium imaging data from vibrissal S1 in mice performing a pole localization task.  Briefly, the mouse uses a single whisker to localize a pole.  After a delay, it indicates the pole position by licking either right or left. Images were acquired using 2-photon imaging using a protein calcium sensor. The raw data consists of images. The processed data consists of fluorescence time series from multiple individual cells and simultaneously recorded behavioral variables, including whisker dynamics.

The data consists of:

  • Raw data:
    • Imaging stacks
    • Whisker videography
  • Processed calcium data:
    • masks of cell locations (Regions of interest, or ROIs)
    • raw fluorescence for each ROI
    • change in fluorescence for each ROI
    • algorithmically extracted calcium events for each ROI
  • Processed whisker video:
    • angle of the whisker
    • curvature of the whisker
    • times at which the whisker contacts the stimulus pole
  • Behavioral data:
    • Trial types
    • Trial timing
    • Trial outcomes  

The data is described in:

A Cellular Resolution Map of Barrel Cortex Activity during Tactile Behavior. Simon P. Peron, Jeremy Freeman, Vijay Iyer, Caiying Guo, Karel Svoboda. Neuron. 2015 May 6;86(3):783-99. doi: 10.1016/j.neuron.2015.03.027

A paper describing similar experiments is:
 

Flow of cortical activity underlying a tactile decision in mice. Guo ZV, Li N, Huber D, Ophir E, Gutnisky D, Ting JT, Feng G, Svoboda K.” Neuron. 2014 Jan 8;81(1):179-94. doi: 10.1016/j.neuron.2013.10.020.

 

Format of the data

The processed data and behavioral data for each session is stored in a separate mat (MATLAB file), with structures within the file used to organize the different data types.  Raw data calcium imaging stacks are stored in tif files, along with additional files that specify metadata about the images.  Raw whisker movement videos are in mp4 format.  Details are given in the documents linked to at the bottom of this page.  Data from five session is included.  Total size of the data is about 154 GB (compressed).  Almost all of that is raw data.  The five mat files take up about 600 MB.  A MatLab script which plots data from a trial is included. Data for additional sessions used for the Peron et. al. paper are in the ssc-2 data set.

Conditions for usage of this data in publications

If you publish any work using the data, please cite the Guo, et. al., publication above and also cite the data set in the following recommended format:

Simon Peron, Jeremy Freeman, Vijay Iyer, Karel Svoboda (2014);  Calcium imaging data from vibrissal S1 neurons in adult mice performing a pole localization task. CRCNS.org.
http://dx.doi.org/10.6080/K000001D

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 (ezid.cdlib.org).

How to download the data

Data may be downloaded from:
https://portal.nersc.gov/project/crcns/download/ssc-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, please post them on the forum for using data sets.

Documentation files

Svoboda_lab_data_format_general.pdf
crcns_ssc-1_data_description.pdf
meta_data_template_ks_08122014.xlsx

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