About ssc-2

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.  Volumetric calcium imaging in mice expressing GCaMP6s and nuclear red fluorescent proteins was used to sample activity in 75 % of superficial barrel cortex neurons across the relevant cortical columns, approximately 12,000 neurons per animal from eight animals, 137 total sessions, during performance of a single whisker object localization task.  The raw data consists of images of calcium activity and movies of whisker movement. The processed data consists of fluorescence time series from multiple individual cells and simultaneously recorded behavioral variables, including whisker dynamics.

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

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

Processed data and behavioral data for each session are stored in a single MATLAB file, with structures within the file used to organize the different data types.  These MATLAB files have been converted to the NWB format and the NWB formatted files are also available.  Raw data calcium imaging stacks are stored in .tif files.  Raw whisker movement videos are in mp4 format.  Details are given in the documents linked to at the bottom of this page.  Process data from all 137 sessions sessions is available (total size about 18 GB in Mat file format; 36 GB in NWB format).   Currently, raw data from the last session from each animal is available (total size about 269 GB) and raw data for five additional sessions in available in the ssc-1 data set.  Raw data from all remaining sessions will be added to this data set.   A MatLab script which plots data from a trial is included in the ssc-1 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, Caiying Guo, Karel Svoboda (2015);  Volumetric calcium imaging data recorded during performance of a single whisker object localization task, sampling activity in the majority of the relevant superficial barrel cortex neurons (75 %, 12,000 neurons per mouse). CRCNS.org.
http://dx.doi.org/10.6080/K0TB14TN

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-2
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-2_data_description.pdf