README.md 2.2 KB
Dark Exposure Experiment Data
Data from each mouse is located in the directory corresponding to one of four conditions (Baseline 1, Baseline 2, PostDE, Recovery)
'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.