Datasets from "Najafi, Farzaneh and Elsayed, Gamaleldin F and Pnevmatikakis, Eftychios and Cunningham, John P and Churchland, Anne K (2018) Inhibitory and excitatory populations in parietal cortex are equally selective for decision outcome in both novices and experts

Najafi, F., Elsayed, G. F., Pnevmatikakis, E., Cunningham, J. P., Churchland, A. K. (2018) Datasets from "Najafi, Farzaneh and Elsayed, Gamaleldin F and Pnevmatikakis, Eftychios and Cunningham, John P and Churchland, Anne K (2018) Inhibitory and excitatory populations in parietal cortex are equally selective for decision outcome in both novices and experts. [Dataset] (In Press)

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Abstract

This package contains data from the 4 mice included in "Najafi, Farzaneh and Elsayed, Gamaleldin F and Pnevmatikakis, Eftychios and Cunningham, John P and Churchland, Anne K (2018) Inhibitory and excitatory populations in parietal cortex are equally selective for decision outcome in both novices and experts." Each folder in "FN_dataSharing" belongs to a mouse discussed in the paper. Inside each "mouse" folder, there are folders for each session of experiment (imaging during decision making). Inside each "session" folder, two .mat files exist: 1) "post_*" file includes variables such as the activity of each neuron aligned on the choice ("firstSideTryAl"), trial outcomes ("outcomes"), stimulus rates ("stimrate"), animal's response side ("allResp_HR_LR"), etc. 2) "more_*" file includes variables such as which neurons are inhibitory ("inhibitRois_pix"), and what neurons have poor quality, hence excluded from analyses ("badROIs01"), etc.

Item Type: Dataset
Additional Information: This dataset is contained in a BagIt file created by BDBagIt.py which was archived using tar-gz and then split into 18 separate file that are under 4GB each. Total size of the dataset is: 69,978,355,808 (Just under 70TB). Use "cat FN_dataSharing.tgz-* | tar -xzf - " to reassemble and extract the files. BDBagIt may be used to verify the file contents, otherwise look in the FN_dataSharing/data directory. ******************************************************************* 2020-06-15 ADDENDUM Additional files were added on 15 June 2020 at the request of Farzaneh Najafi. These files are segregated from the initial dataset. The additional files may be accessed at: http://labshare.cshl.edu/shares/library/repository/39496/ Size: ~145 GB. Data format: mat files Description: This folder includes the output variables of the segmentation algorithm used in the paper (CNMF: https://github.com/flatironinstitute/CaImAn). More specifically, the subfolders are for each mouse used in the paper; inside each "mouse" folder are the "days" folders. The mat file inside each "day" folder includes all the outputs of the CNMF algorithm. The main variables inside the .mat are the following: S: inferred spikes; analyses in the paper were done using "S". C: temporal components: denoised and demixed fluorescence traces. A: spatial components, from which ROIs are computed. activity_man_eftMask_***: manually computed DF/F values on ROI masks derived from the CNMF algorithm. ******************************************************************* 2020-07-02 ADDENDUM Additional files were added on 1 July 2020 at the request of Farzaneh Najafi. These files are segregated and placed into the 2020-07-01 directory. The additional files may be accessed at: http://labshare.cshl.edu/shares/library/repository/39496/2020-07-01
Subjects: bioinformatics > genomics and proteomics > computers > computer software
organism description > animal behavior > decision making
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons
CSHL Authors:
Communities: CSHL labs > Churchland lab
Depositing User: Matt Covey
Date: 2018
Date Deposited: 23 Jul 2018 15:35
Last Modified: 01 Jul 2020 22:08
Related URLs:
URI: https://repository.cshl.edu/id/eprint/36980

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