Example of usage of u-track with a microscopy file using Bio-Formats and an image onto an OMERO server

bf_tracking_example.m

% Create MovieData object from image file stored on disk
MD = MovieData.load(fullfile(path, 'myimage.dv'));

% Manipulate the movie, e.g. retrieve the first image of the first channel
I = MD.getChannel(1).loadImage(1);

% Remove all analysis performed on the movie
MD.reset(); 

% Set up single-particle tracking package
MD.addPackage(UTrackPackage(MD));
  
% Set up default single-particle detector and run detection step
MD.getPackage(1).createDefaultProcess(1);
MD.getPackage(1).getProcess(1).run();

% Set up default tracking and run tracking step
MD.getPackage(1).createDefaultProcess(2);
MD.getPackage(1).getProcess(2).run();

% Set up default tracking post-processing and run post-processing step
MD.getPackage(1).createDefaultProcess(3);
MD.getPackage(1).getProcess(3).run();

% Reload movie from MAT file stored on disk
MD = MovieData.load(fullfile(path, 'myimage', 'myimage.mat'));

% Re-run the detection step
MD.getPackage(1).getProcess(1).run();

% Load the detection output for the the first channel
movieInfo = MD.getPackage(1).getProcess(1).loadChannelOutput(1);

% Draw the first frame and the 
figure;
MD.getChannel(1).draw(1);  % draw the first image of the first channel
MD.getPackage(1).getProcess(1).draw(1, 1); % draw the output of the first frame/first channel for the detection process

omero_tracking_example.m

try
    % Create client and session
    [c, s] = loadOmero();

    % Read image id from config file
    imageID = str2double(c.getProperty('omero.imageid'));

    % Create MovieData object from remote OMERO image
    MD = MovieData.load(s, imageID);

    % Remove all analysis performed on the movie
    MD.reset();

    % Set up single-particle tracking package
    MD.addPackage(UTrackPackage(MD));
  
    % Set up default single-particle detector and run detection step
    MD.getPackage(1).createDefaultProcess(1);
    MD.getPackage(1).getProcess(1).run();

    % Set up default tracking and run tracking step
    MD.getPackage(1).createDefaultProcess(2);
    MD.getPackage(1).getProcess(2).run();

    % Set up default tracking post-processing and run post-processing step
    MD.getPackage(1).createDefaultProcess(3);
    MD.getPackage(1).getProcess(3).run();

    % Reload movie
    MD = MovieData.load(s, imageID);

    % Re-run the detection step
    MD.getPackage(1).getProcess(1).run();
catch err
    disp(err.message)
    c.closeSession();
    exit(2)
end

c.closeSession();