OMERO Matlab toolbox example for binary masks.

Segment_image_and_upload_masks.m

% Copyright (C) 2014 Glencoe Software, Inc.
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% loadOmero;
client = loadOmero('localhost');
session = client.createSession('user', 'pass');
client.enableKeepAlive(60);

image_id = 1;
z_plane = 0;
channel = 0;
time_point = 0;

images = getImages(session, image_id);
plane = getPlane(session, images, z_plane, channel, time_point);

% segment data
background = imopen(plane,strel('disk', 15));
equalised_illumination = plane - background;
increased_contrast = imadjust(equalised_illumination);
level = graythresh(increased_contrast);
bw = im2bw(increased_contrast, level);
bw = bwareaopen(bw, 50);
components = bwconncomp(bw, 4);

% create masks and save to OMERO image. 
stats = regionprops(components, 'PixelList');
for k=1:numel(stats)
    roi = omero.model.RoiI;
    x = stats(k).PixelList(:, 1);
    y = stats(k).PixelList(:, 2);
    %
    x0 = min(x);
    y0 = min(y);
    width = max(x) - x0 + 1;
    height = max(y) - y0 + 1;
    binary_mask = zeros(height, width);
    %
    for j = 1 : numel(x),
        x_position = x(j) - x0 + 1;
        y_position = y(j) - y0 + 1;
        binary_mask(y_position, x_position) = 1;
    end
    %
    mask = createMask(x0 - 1, y0 - 1, binary_mask);
    setShapeCoordinates(mask, z_plane, channel, time_point);
    mask.setFillColor(rint(2113863680));    %7DFF0000 - 50% red
    mask.setStrokeColor(rint(2113863680));  %7DFF0000 - 50% red
    mask.setTextValue(rstring('2014a'));
    %
    roi.addShape(mask);
    roi.setImage(omero.model.ImageI(images.getId.getValue, false));
    roi = session.getUpdateService().saveAndReturnObject(roi);
end