Using the Coloc Function in EasyXT #Imaris #EasyXT #Coloc #Matlab #BIOP

ColocExamples.m

% Get EasyXT at:
% https://github.com/lacan/EasyXT
% The very first time you run it, use
% X = EasyXT('setup')
% To tell the XTension where the Imaris Executable file is.

% Disclaimer
% This code is provided as-is and hopefully will be of some use to people
% Olivier BURRI, Romain GUIET @ BIOP (EPFL - BioImaging & Optics Platform), July 2015

% NOTE: This code uses the great Matlab table() class. You need at least Matlab 2015a to run this, sorry...
% Start EasyXT, Imaris must be open
X = EasyXT;

% Choose Channels to colocalize. Channels is an nx2 array where the columns represent the two channels to colocalize. 
% It will run the colocalization n times, once for each combination of two channels
channels   = [1 2; 1 3]; % Colocalize channels 1 and 2, then 1 and 3

% Set the thresholds. Thresholds expects the same nx2 structure as the channels
thresholds = [20, 30; 20, 35]; % Ch1 thr: 20, Ch2 thr: 30, Ch1 thr: 20, Ch3 thr: 35

% Run the coloc
CCoeffs  = X.Coloc(channels, thresholds);

% Run the coloc independently for each slice
CCoeffsZ = X.Coloc(channels, thresholds, 'Independent Z', true);

% Run the coloc only within a mask
% Choose the mask, suppose it is a fourth channel
CCoeffsMask = X.Coloc(channels, thresholds, 'Mask Channel', 4, 'Mask Threshold', 121);

% Run the coloc and build a coloc channel
CCoeffs  = X.Coloc(channels, thresholds, 'Coloc Channel', true);

% Run the Coloc and get a Fluorogram
CCoeffs  = X.Coloc(channels, thresholds, 'Fluorogram', true);
% This will only give one fluorogram per channel pair and NOT for each independent slice.