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Extend position tracking script with data accessed from NWB file #1

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Extend position tracking script with data accessed from NWB file #1

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f89ea82
demonstrate how to access the data from NWB
weiglszonja Oct 19, 2022
c0ffa0c
small refactor
weiglszonja Oct 19, 2022
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52 changes: 46 additions & 6 deletions f3+sf8/mouse_position_tracking.m
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Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,11 @@
% octant: current octant occupied by mouse (sfig 8)
% iT: extracted neural activity, truncated to overlap with behavioral data


%% Approach 1. Data accessed from original files
[parentdir,~,~] = fileparts(pwd);

%pos=readmatrix(fullfile(parentdir,'raw_data/','home_pos-speed-in_2021-07-26T13_50_50.csv'),'Delimiter',' ');
%pos = pos(:,2:3);

posT=readmatrix(fullfile(parentdir,'raw_data/','home_pos-speed-in_2021-07-26T13_50_50.csv'),'Delimiter',' ','OutputType','string');
caT=readmatrix(fullfile(parentdir,'raw_data/','invivo_2021-07-26T13_50_50.csv'),'Delimiter',' ','OutputType','string');
Expand All @@ -28,9 +29,52 @@
caT = str2double(extractBetween(caT,18,23))+60*str2double(extractBetween(caT,15,16))+3600*str2double(extractBetween(caT,12,13));
posT = str2double(extractBetween(posT(:,1),18,23))+60*str2double(extractBetween(posT(:,1),15,16))+3600*str2double(extractBetween(posT(:,1),12,13));

v = VideoReader(fullfile(parentdir,'raw_data/','home_arena_2021-07-26T13_50_50.avi'));

%pos = pos(:,2:3);
%% Approach 2. Data accessed from NWB File

% *MatNWB Setup*
% Start by setting up your MATLAB workspace. The code below clones the
% MatNWB repo to the current directory and adds the folder ontaining the
% MatNWB package to the MATLAB search path. MatNWB works by automatically
% creating API classes based on a defined schema. Running the generateCore() function
% generates these classes for the lastest schema version.

!git clone https://github.com/NeurodataWithoutBorders/matnwb.git
addpath('matnwb');
generateCore();

% Specify the full path to the NWB file
nwbfile_path = '.../ophys_2021-07-26T13_50_50.nwb';
% Use the nwbRead() function to load the NWB file.
nwbfile = nwbRead(nwbfile_path);

% The timestamps that are stored in NWB files are relative to the start
% time of the session and are in the unit of seconds.
% You can view the session start time by accessing the session_start_time
% attribute in nwbfile as:
% nwbfile.session_start_time

% Access the timestamps from the calcium imaging
caT = nwbfile.acquisition.get('TwoPhotonSeries').timestamps.load;

% Access the timestamps from the behavioral tracking video
posT = nwbfile.acquisition.get('Video: home_arena_2021-07-26T13_50_50').timestamps.load;
% The timestamps are adjusted to the imaging timestamps, i.e. the first
% timestamp in posT corresponds to caT(1) - posT(1) given the previous variables defined in Approach 1.

% Access the container for temporal weights
df_over_f = nwbfile.processing.get('ophys').nwbdatainterface.get('DfOverF');
% Access the temporal weights; when reading in MATLAB the first dimension is
% the number of cells, and second dimension is time.
T = df_over_f.roiresponseseries.get('RoiResponseSeries').data.load;
% To have the second dimension correspond to the number of cells, you can use transpose:
T = transpose(T);

% Access the filepath to the behavioral tracking video
v = VideoReader(nwbfile.acquisition.get('Video: home_arena_2021-07-26T13_50_50').external_file.load);

%%

xmin = 101;
xmax = 378;
Expand All @@ -49,10 +93,6 @@
red(3) = 4;
redlim = 1600;



v = VideoReader(fullfile(parentdir,'raw_data/','home_arena_2021-07-26T13_50_50.avi'));

v.CurrentTime = 64; %start at 1'04 to remove period of experimenter futzing

i=1;
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