Dataset of "Distinct timescales of population coding across cortex"

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README.md

PPC_AC_2p_sound_localization

Dataset of "Distinct timescales of population coding across cortex"

This repository contains pre-processed behavioral data and neural data collected from mice performing sound localization task in a virtual reality (VR) environment. Neural data are recorded from PPC and AC using two-photon calcium imaging. Detailed information about data collection can be found in:

Runyan A. C., Piasini E., Panzeri S., Harvey C. D. 2017. Distinct timescales of population coding across cortex. Nature. doi: 10.1038/nature23020

Data contained in this repository were used in:

Valente M., Pica G., Runyan C. A., Morcos A. S., Harvey C. D., Panzeri S. 2020. Correlations enhance the behavioral readout of neural population activity in association cortex. BioRxiv. doi: https://doi.org/10.1101/2020.04.03.024133

Data are available in three different versions, that differ in how data is selected, organized and processed. In decreasing order of completeness:

Version 1 (area_ID_imaging_spk.mat)

This data version contains one .mat file for each session (AC/PPC, active/passive) for a total of 27 sessions (7 PPC active, 6 PPC passive, 7 AC active, 7 AC passive). Each .mat file contains neural variables, behavioral variables and stimulus identity.

  • Neural variables consist of deconvolved dF/F traces at the two-photon microscope sampling rate;
  • Behavioral variables consist of x-y position in the virtual T-maze, x-y running velocity and view angle in the VR system sampling rate;
  • Each trial has a different duration. Information about each trial timing and the match between imaging and VR acquisition is stored in the frame_timing_info field;
  • The stimulus identity is stored in the sound_location field (value = 1, 5, 3, 7, 8, 4, 6, 2 for stimuli from the extreme left to the extreme right).

Version 2 (area_ID_exp_data.mat)

This data version contains one .mat file for each one of the active sessions (AC/PPC) for a total of 14 sessions (7 PPC active, 7 AC active). Each .mat file contains neural variables, behavioral variables and stimulus identity.

  • Neural variables consist of deconvolved dF/F traces at the two-photon microscope sampling rate;
  • Behavioral variables consist of x-y position in the virtual T-maze, x-y running velocity and view angle and are re-sampled to match the imaging rate;
  • Each trial has a different duration. Information about each trial timing is stored in the frame_timing_info field;
  • Information about the stimuli is stored in the sound_location field (values ordered from 1 to 8 for stimuli from the extreme left to the extreme right).

Version 3 (aligned_data_simple.mat)

This version consists of a single .mat file containing a matlab struct with dimension equal to the number of active sessions (7 PPC active, 7 AC active). Each row of the structure refers to a single session and contains neural variables, behavioral variables and stimulus identity relative to that session.

  • Neural variables consist of the deconvolved dF/F traces at the two-photon microscope sampling rate. All trials have the same duration and are both aligned to the time of stimulus onset (r_aligned_stimulus) and to the time of choice (r_aligned_choice);
  • Behavioral variables consist of x-y position in the virtual T-maze and are re-sampled to match the imaging rate. All trials have the same duration and are both aligned to the first stimulus presentation (x_pos_aligned_stimulus, y_pos_aligned_stimulus) and to the turning frame (x_pos_aligned_choice, y_pos_aligned_choice);
  • The stimulus identity is stored in the sound_location field (values ordered from 1 to 8 for stimuli from the extreme left to the extreme right).
datacite.yml
Title Dataset of 'Distinct timescales of population coding across cortex'
Authors Runyan,Caroline;Department of Neurobiology, Harvard Medical School, Boston, MA, USA; Department of Neuroscience, Center for the Neural Basis of Cognition, University of Pittsburgh;ORCID:0000-0002-9066-4542
Valente,Martina;Neural Computation Laboratory, Istituto Italiano di Tecnologia, Rovereto, Italy; Center for Mind and Brain Sciences (CIMeC), University of Trento, Rovereto, Italy
Pica,Giuseppe;Neural Computation Laboratory, Istituto Italiano di Tecnologia, Rovereto, Italy;ORCID:0000-0002-4506-0600
Bondanelli,Giulio;Neural Computation Laboratory, Istituto Italiano di Tecnologia, Rovereto, Italy;ORCID:0000-0001-6781-4939
Moroni,Monica;Neural Computation Laboratory, Istituto Italiano di Tecnologia, Rovereto, Italy;ORCID:0000-0003-1852-7217
Harvey,Christopher D.;Department of Neurobiology, Harvard Medical School, Boston, MA, USA;ORCID:0000-0002-0520-7882
Panzeri,Stefano;Neural Computation Laboratory, Istituto Italiano di Tecnologia, Rovereto, Italy;ORCID:0000-0003-1700-8909
Description Behavioral data and two-photon calcium imaging neural data recorded from AC and PPC of awake mice performing a sound localization task in a virtual reality environment.
License Creative Commons Attribution-NonCommercial-ShareAlike 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/)
References Runyan, C., Piasini, E., Panzeri, S. et al. Distinct timescales of population coding across cortex. Nature 548, 92–96 (2017). [doi:10.1038/nature23020] (IsDescribedBy)
Valente, M., Pica, G., Runyan, C. A., Morcos, A. S., Harvey, C. D., Panzeri, S. (2020). Correlations enhance the behavioral readout of neural population activity in association cortex. bioRxiv: 2020.2004.2003.024133 [doi:10.1101/2020.04.03.024133] (IsReferencedBy)
Funding This work was supported by a Burroughs-Wellcome Fund Career Award at the Scientific Interface, the Searle Scholars Program, the New York Stem Cell Foundation, the Armenise-Harvard Foundation, the Alfred P. Sloan Research Foundation, a NARSAD Brain and Behavior Research Young Investigator Award, National Institutes of Health grants from the National Institute of Mental Health BRAINS program (R01-MH107620), the National Institute of Neurological Disorders and Stroke (R01-NS089521) and the BRAIN Initiative (R01 NS108410 and U19 NS107464), the Autonomous Province of Trento (Grandi Progetti ATTEND), and the Fondation Bertarelli.
Keywords Neuroscience
Sound localization
Two-photon calcium imaging
Behavior
Auditory Cortex
Posterior Parietal Cortex
Resource Type Dataset