Imaris Batch Channel Math with EasyXT #Imaris #EasyXT #Matlab

batchChannelMath.m

% Example of looping through a folder to process a series of images. 
% In this case, perform channel math.

% For convenience, this example uses EasyXT, but feel free to adapt it as needed.
% Get EasyXT Here: http://lacan.github.io/EasyXT/
% The ChannelMath method is borrowed from the XTension with the same name, made by Bitplane.

folder_name = uigetdir();
listing = dir(folder_name);

% Math expression you want to use
expression = {'sqrt(ch1 .* ch2)'};

% Extension of your image files
ext = '.lsm';


% Define save folder
savefolder_name = [folder_name '\save\'];
mkdir(savefolder_name);

%Start EasyXT(), Get it at: http://lacan.github.io/EasyXT/
X = EasyXT();

% Loop through the images
for i =1:size(listing,1)
    file = listing(i);
    if ~file.isdir && strcmp(file.name((end-3):end), ext)
        % Clear the scene and make a new one, just in case
        X.CreateNewScene();
        X.imarisApp.FileOpen([folder_name '\' file.name],'');
        
        % Call XTension or do some processing on the image
        X.ChannelMath(expression);
        app.FileSave([savefolder_name file.name(1:end-4) '.ims'], '');
        
    end
end