V1_BCI

Data Summary

The data set contains processed data from neurons in primary visual cortex of mice during presentations of static sinusoidal gratings. Mice were trained in either BCI experiments or visual discrimination experiments. In addition, neuronal data during BCI experiments are also present in this dataset

Visual Stimulus

The visual stimuli consisted of 180 full-field static gratings of various orientation and spatial frequency. The stimulus set was generated and presented using Psychtoolbox-3 in MATLAB. The code to generate and present the stimulus is 'presentStaticGrating_Rapid.m'

'allsignals.mat' File

Each grating presentation session has a MATLAB data file, corresponding to the session named 'allsignals.mat'. We used the MATLAB version of the Suite2P, not the PYTHON version. Note: only the variables that were used in the analysis of the data are described here.

'data' variable contains the fluorescence intensity values of the cells as well as the frame at which each stimulus was presented. Each row represents a single 'file' recording. Each file of recording contains 4 repetitions through the 180 grating set.

[Variables saved in data]{.ul}

dF: neuropil-subtracted fluorescence trace of all the cells for each file. The dimension of the field is number of cells by number of frames. For details on neuropil subtraction, refer to https://www.biorxiv.org/content/10.1101/061507v2.

signal_decov: deconvolved events amplitude for each neuron.

usable_motionCorrection: If there was too much motion in the image, mark the frame. 1 means it is a usable frame, 0 means it is not.

usable_global: frame by frame information on whether a given frame has a large drop in signal, 1 means it is a usable frame, 0 means it is not.

usable_eyetracking: frame by frame information on whether the pupil was detected in a given frame. If not detected, the mouse was most likely blinking. 1 means it is a usable frame, 0 means it is not.

running_speed: speed of the locomotion.

usable_balltracking: frame by frame information on whether the mouse was in locomotive state. 1 means it is a usable frame, 0 means it is not.

usable_frames: A frame is usable if and only if it passes the four "usable" criteria. 1 means it is a usable frame, 0 means it is not.

stimOn: the frame at which a stimulus was presented. In each file, 720 stimuli were presented.

stimBlocks: the identity of the presented stimulus matching the presented frame information in 'stimOn'. The first column of this variable is the unique ID assigned to the stimulus. The second column is the orientation of the stimulus in degrees. The third column is the spatial frequency of the stimulus in cycles per degree.

'BCIData.mat' File

Data file containing BCI experiment data.

cellTrackingData: x-y coordinates of neuron location in pixels.

decoderData: Contains direct neuron activity as well as the frame at which the trial started and ended. Length of this variable is the number of trials.

suite2pData: suite2p fluorescence of all segmented neurons.

targetReachedProb: proportion of trials that the target was reached.

baselineData: Fluorescence data of all neurons in the field of view during baseline measurement.