Integration of OMERO with 3rd Party Applications

java.lang.System.clearProperty('java.util.prefs.PreferencesFactory')
javaaddpath('/Applications/Micro-Manager1.4/ij.jar')
javaaddpath('/Applications/Micro-Manager1.4/plugins/Micro-Manager/MMCoreJ.jar')
javaaddpath('/Applications/Micro-Manager1.4/plugins/Micro-Manager/MMJ_.jar')
javaaddpath('/Applications/Micro-Manager1.4/plugins/Micro-Manager/bsh-2.0b4.jar')
javaaddpath('/Applications/Micro-Manager1.4/plugins/Micro-Manager/swingx-0.9.5.jar')
javaaddpath('/Applications/Micro-Manager1.4/plugins/Micro-Manager/swing-layout-1.0.4.jar')
javaaddpath('/Applications/Micro-Manager1.4/plugins/Micro-Manager/ome-xml.jar')
javaaddpath('/Applications/Micro-Manager1.4/plugins/Micro-Manager/loci-common.jar')
javaaddpath('/Applications/Micro-Manager1.4/plugins/Micro-Manager/scifio.jar')
javaaddpath('/Applications/Micro-Manager1.4/plugins/Micro-Manager/slf4j-api-1.7.1.jar')

OMERO Matlab Toolbox Configuration

inputdir=['/Users/bramalingam/OME/matlab/OMERO.matlab-5.1.0-ice35-b40'];
addpath(genpath(inputdir));
javaaddpath('/Users/bramalingam/OME/matlab/OMERO.matlab-5.1.0-ice35-b40/libs/omero_client.jar')
javaaddpath('/Users/bramalingam/OME/matlab/OMERO.matlab-5.1.0-ice35-b40/libs/ini4j.jar')
javaaddpath('/Users/bramalingam/OME/matlab/OMERO.matlab-5.1.0-ice35-b40/libs/bioformats_package.jar')

Config,Snap and Save Image

Micro-Manager : Load Microscope Configuration

import mmcorej.*;
mmc = CMMCore;
mmc.loadSystemConfiguration('/Applications/Micro-Manager1.4/MMConfig_demo.cfg');

Micro-Manager : Snap Image

mmc.snapImage();
img = mmc.getImage();

********************|Custom Written Analysis Scripts|*************

Bio-Formats: save image

proc0 = ImageUtils.makeProcessor(mmc, img);
imgp0 = ImagePlus('',proc0);
imgp0.show;
IJ.runPlugIn('loci.plugins.LociExporter', buffer.toString);

Upload Image and ...

OMERO: Create a Client and Session

client = loadOmero(host);
session = client.createSession(username, password);
client.enableKeepAlive(60);

OMERO: Upload_image.m

upload_image(path,session,username,password,ProjectName,DatasetName,host,importopt)

... add Metadata

Micro-Manager

devices = mmc.getLoadedDevices();
cvec =[];
for i=0:devices.size-1
    properties = mmc.getDevicePropertyNames(devices.get(i));
    cvec = [cvec ; {char(devices.get(i))} {'#'}];
    for j = 0:properties.size-1
        s = properties.get(j);
        v = mmc.getProperty(devices.get(i),s);
        cvec = [cvec ;  {char(s)} {char(v)}];
        imgp0.setProperty(char(s), char(v));
    end
end

OMERO: Key-Value pair Annotations

map = writeMapAnnotation(session, cvec(:,1)',cvec(:,2)');
link1 = linkAnnotation(session, map, 'image', imageId(1));
session.getUpdateService().saveAndReturnObject(link1);