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
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.
