PrhNComm2024/README.md

Prh

Dataset description

Processed single cell calcium imaging data associated with manuscript titled "PERIRHINAL CORTEX LEARNS A PREDICTIVE MAP OF THE TASK ENVIRONMENT" (Lee, McLachlan et al. 2024, Nature Communications)

DATA ORGANIZATION

Processed calcium imaging data are stored as individual .mat files which correspond to an animal and session, found within the Animals directory and a zipped animal-specific subdirectory. For example, in ./Animals/pr023/pr023-19.mat, the animal name is pr023 and the session number is 19. Select sessions will be accompanied by whisker.mat files. Animal directories also contain a subdirectory named /in vivo registration/ which may contain A0 and A1 folders. A0/A1 refer to the imaging area. These folders contain ROIs and images used to align chronic recording sessions, following the same naming convention as the calcium imaging data files.

DATA STRUCTURE

within each .mat file, you may see the following variables saved: CaA0, CaA1, CaA2, licks, summary, trials.

CaA0/CaA1

these contain the calcium data for each of the areas (A0 or A1).
important fields:
CaA#.F_df_REF: the denoised RCaMP fluorescence traces.  an N by 1 cell where N is the number of trials session. each cell contains an M x P double array where M is the number of ROIs and P is the number of timepoints in the nth trial. 
CaA#.deconv_REF: the deconvolved calcium events.  an 1 by N cell where N is the number of trials session. each cell contains an M x P double array where M is the number of ROIs and P is the number of timepoints in the Nth trial. 
CaA#.trial_info: contains trial info necessary to link calcium recording with behavior data. 1 x N cell where N is the number of trials. CaA0.trialinfo{n}.matfile tells you the name of the nth trial which can be used to reference the correct trial in summary table (see summary table below)

CaA2

this contains fluorescence data for acetylcholine imaging experiments.
important fields:
CaA2.F: FdF of acetylcholine sensor GRAB-ACh3.0
CaA2.trial_info: contains trial info for linking recordings with behavior data, as above

trials

contains behavior task information. each row is trial. relevant columns:
timestamp: start time of trial. used to match trial to correct 2P recording (see summary table below). 
direction1: rotation direction and speed of sample stimulus (CW or CCW, 20 or 40)
direction2: rotation direction and speed of test stimulus (CW or CCW, 20 or 40)
decision: animal's decision for that trial (Hit, Miss, FA, or CR)

summary

summary.table contains information necessary to link calcium recording from CaA0/CaA1 to the trial data. relevant columns:
BhvStartTime: corresponds with "timestamp" columns of "trials"
'A0name': corresponds with CaA0.trialinfo{n}.matfile
'A1name': corresponds with CaA1.trialinfo{n}.matfile
in other words, use A0name to find correct calcium recording and BhvStarttime to find correct behavior data for the same trial.

whisker data files contain the variable whisker_dat, with mean angle, curvature, curve, and binary touch vectors for tracked whiskers in the corresponding trial