Integration : Micromanager+Matlab+OMERO

micromanager_matlab_grid_calculator.m

function [img_grid] = grid_calculator(x,y,fs,nf,nwx,nwy,xwd,ywd)

%ex usage for a 96 well plate,9 fields being imaged with a interfield
%distance of 200 microns.

% img_grid = grid_calculator(0,0,200,9,12,8,9000,9000);

% x: Stage x position
% y: Stage y position
% fs: Intra-well field spacing
% nf: Number of fields per well
% nwx: number of wells in the x direction or number of columns in your plate (12 in the case of 96 wells).
% nwx: number of wells in the y direction or number of rows in your
% plate (12 in the case of 96 wells).
% xwd: Centroid to centroid distance between adjacent wells in the x
% direction (Inter column spacing).
% ywd: Centroid to centroid distance between adjacent wells in the y
% direction (Inter row spacing).


xgrid=(x-fs*nf):fs:(x+fs*nf);
ygrid=(y-fs*nf):fs:(y+fs*nf);

resvec=[];
for i=1:length(xgrid)
    xval=xgrid(i);
    for j=1:length(ygrid)
        yval=ygrid(j);
        resvec=[resvec ; xval yval x y ((x-xval)^2+(y-yval)^2)^0.5];
    end
end
[aa ii]=sort(resvec(:,5)); %#ok<*ASGLU>
img_grid=resvec(ii(1:nf),1:2);

xvec=repmat([0:xwd:(nwx-1)*xwd]',1,size(img_grid,1))';
xa1=repmat(img_grid(:,1),1,size(xvec,2));
xvec=xvec+xa1;
yvec=repmat(img_grid(:,2),1,size(xvec,2));

xvec=reshape(xvec,[],1);yvec=yvec(:);
yval=repmat([0:ywd:(nwy-1)*ywd]',1,size(yvec,1))';yval=yval(:);
rowvec=[xvec yvec];rowvec=repmat(rowvec,nwy,1);
img_grid=[rowvec(:,1) rowvec(:,2)+yval];

Micromanager_Matlab_OMERO.m

%Multiple sites imaging
%and image analysis(identifying cells with a circularity index>0.8)
%feedback, based on number of cells, change objective to check assay qc
%Author : Balaji.R

%Init
clear all;close all;

%Import packages
import mmcorej.*;
import org.micromanager.acquisition.AcquisitionWrapperEngine;
import org.micromanager.utils.ImageUtils;
import ij.IJ;
import ij.io.FileSaver;
import java.lang.StringBuffer;
import ij.ImagePlus;
import java.lang.StringBuffer;
import loci.formats.codec.CompressionType;

%OMERO Session
%Params
host= '';  %Host address
username = '';  %Username for OMERO
password = ''; %Password for OMERO
folder_depth_bioformats=10;
ProjectName = '';
DatasetName = '';

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

%Import type for Omero (1 for Symlink Transfer/inplace-import,2 for UploadRmFileTransfer, any other numeric value for
%regular upload)
importopt = 2;

%file locations
acqName = 'test-acq';

rootDirName = '/Applications/Micro-Manager1.4/test/';
mkdir(rootDirName)

%parameters
exposures = [10, 1000];
fields = 6;

%Create objects (Acquisition engine and core object)
mmc = CMMCore;

%load config
mmc.loadSystemConfiguration ('/Applications/Micro-Manager1.4/MMConfig_demo.cfg');

%Get config's of devices
stage=mmc.getXYStageDevice();
zdrive=mmc.getFocusDevice();

%Get position of X,Y and Z
X1= mmc.getXPosition(stage);
Y1= mmc.getYPosition(stage);
Z1=mmc.getPosition(zdrive); %Manually focus on the first field

%load camera properties
config_groups=mmc.getAvailableConfigGroups();

% read_rate=config_groups.get(5);
objective_turr=mmc.getAvailableConfigs(config_groups.get(4));
light_path=mmc.getAvailableConfigs(config_groups.get(3));
Gain_multipler=config_groups.get(2);
channels=mmc.getAvailableConfigs(config_groups.get(1));
camera_gain=config_groups.get(0);

%Set light path (To camera view)
mmc.setConfig(config_groups.get(3), light_path.get(1));

%stage movement in microns (Field spacing)
rval1=100;rval=X1;

%Image Output Directory and Suffix for Image Name
acqRoot = [pwd '/'];
BrightAcqName = 'Test.ome.tiff';

%Temporary Params
Wells={'A' 'B' 'C' 'D'};
Fields = {'F'};
cntr1=1;resvec=[];cellcntr=0;
for l=1:2
    
    %Move Stage
    mmc.setXYPosition(stage, rval, Y1);
    mmc.waitForDevice(stage);
    
    for k=1:3
        
        if k>1
            rval=rval1+mmc.getXPosition(stage);
        else
            rval=mmc.getXPosition(stage);
        end
        
        cntr=1;rvec=[];
        
        %Set Device/Config Group properties
        mmc.setPosition(zdrive,(Z1));
        mmc.setExposure(exposures(1));
        mmc.setConfig(config_groups.get(1), channels.get(0));
        
        mmc.setXYPosition(stage, rval, Y1);
        mmc.waitForDevice(stage);
        
        %Snap Image
        mmc.snapImage();
        img = mmc.getImage();
        width = mmc.getImageWidth();
        height = mmc.getImageHeight();
        
        %Saving image
        proc0 = ImageUtils.makeProcessor(mmc, img);
        imgp0 = ImagePlus('',proc0);
        
        %Extract Micro-Manager Device Properties
        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
        
        imgp0.show;
        cvec= [ cvec ; {'StageXPosition'} {num2str(mmc.getXPosition)};  {'StageYPosition'} {num2str(mmc.getYPosition)}; {'Z Position'} {num2str(mmc.getCurrentFocusScore)}];
        imgp0.setProperty('StageXPosition',char(mmc.getXPosition));
        imgp0.setProperty('StageYPosition',char(mmc.getYPosition));
        imgp0.setProperty('Z Position',char(mmc.getCurrentFocusScore));

        %Export Path
        path=[acqRoot Wells{1} '00' num2str(l) Fields{1} '00'  num2str(k) '_' BrightAcqName];
        
        %Bio-Formats Exporter
        buffer = StringBuffer();
        
        buffer.append(['outfile=' path]);
        buffer.append(' splitz=false');
        buffer.append(' splitc=false');
        buffer.append(' splitt=false');
        buffer.append([' compression=' char(CompressionType.UNCOMPRESSED.getCompression())]);
        buffer.append(' saveroi=true');
        
        IJ.runPlugIn('loci.plugins.LociExporter', buffer.toString);
        
        %Upload Image to the OMERO Server
        imageId = upload_image(path,session,username,password,ProjectName,DatasetName,host,importopt);
        
        %Upload Micro-Manager Device Properties as OMERO Key-Value pair Annotations
        map = writeMapAnnotation(session, cvec(:,1)',cvec(:,2)');
        link1 = linkAnnotation(session, map, 'image', imageId(1));
        session.getUpdateService().saveAndReturnObject(link1);
        
        imgp0.close;
        cntr1=cntr1+1;
        disp([mmc.getXPosition(),mmc.getYPosition()]);
        %     [seg_img clustidx]=kmeans(double(img(:)),3,'emptyaction','drop');
        %     idx1=find(clustidx==min(clustidx));
        %
        %     [aa numcells]=bwlabel(bwareaopen(reshape(seg_img==idx1,512,512),15));
        %     props = regionprops(aa, 'Area', 'Perimeter');
        %     areas = [props.Area];
        %     perims = [props.Perimeter];
        %     circularities = 4 * pi * areas ./ perims .^ 2; % formula for circularity index
        %
        %     remidx=find(circularities<=0.80);
        %     [finimg numcells]=bwlabel(~ismember(aa,[0 remidx]));
        %
        %     stagevec(k,:)=[rval Y1 Z1 numcells];
        
        %     cellcntr=cellcntr+numcells;
        %     imwrite(img,[rootDirName acqName '_field_'  num2str(k) '.tiff'],'Compression','none')
        %     if cellcntr>=70
        %         break
        %     end
        
    end
    
end
%Stitch all images together (QC View)
% montage(img1);imcontrast;

% figure;imagesc(stagevec(:,4));caxis([0 100])

% %Move stage to field with minimum cells and change objectives and snap an
% %image
% idx1=find(stagevec(:,4)==min(stagevec(:,4)));
% mmc.setXYPosition(stage, stagevec(idx1,1), Y1);
% mmc.waitForDevice(stage);
% %change objectives line
% curr_obj=objective_turr.get(0);
% mmc.setConfig(config_groups.get(4), curr_obj);
% mmc.snapImage();
% img = mmc.getImage();  % returned as a 1D array of signed integers in row-major order
% width = mmc.getImageWidth();
% height = mmc.getImageHeight();
%
% if mmc.getBytesPerPixel == 2
%     pixelType = 'uint16';
% else
%     pixelType = 'uint8';
% end
%
% img = typecast(img, pixelType);      % pixels must be interpreted as unsigned integers
% img = transpose(reshape(img, [width, height])); % image should be interpreted as a 2D array
% imshow(imadjust(img));title('10x image');

startup.m

clear all;close all;
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')
javaaddpath('/Applications/Micro-Manager1.4/plugins/bioformats_package.jar');

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')

strdiff.m

% Remove the occurances of string s2 from string s1
% Input: 
% s1 - big string 
% s2 - forbidded string to be removed
% 
% Output: 
% s - string containing s1 without s2
% 
function s = strdiff(s1, s2)

n = length(s2);

f = strfind(s1, s2); % find all occurances of 2nd string in 1st string

if(~isempty(f))
    bad_inds = f;
    for i=1:n-1
        bad_inds = union(bad_inds, f+i);
    end
    good_inds = setdiff(1:length(s1), bad_inds);
    s = s1(good_inds);
else % don't change the string
    s = s1;
end

upload_image.m

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


%Import Packages
import loci.formats.in.DefaultMetadataOptions;
import loci.formats.in.MetadataLevel;
import loci.common.*;
import omero.model.Dataset;
import omero.model.DatasetI;
import ome.services.blitz.repo.*;
import ome.formats.OMEROMetadataStoreClient;
import ome.formats.importer.*;
import ome.formats.importer.ImportConfig;
import ome.formats.importer.cli.ErrorHandler;
import ome.formats.importer.cli.LoggingImportMonitor;
import ome.formats.importer.transfers.*;
import ome.formats.importer.transfers.SymlinkFileTransfer;
import ome.formats.importer.transfers.UploadRmFileTransfer;
import java.util.prefs.*;

%Choose a dataset name, will be assigned to your imported dataset under the root user.
DataForImport = path;%Source Directory

%Logging (switch on)
loci.common.DebugTools.enableLogging('DEBUG');

%Configuration Object
config = ImportConfig();

%Set Config params
config.email.set('');
config.sendFiles.set(true);
config.sendReport.set(false);
config.contOnError.set(false);
config.debug.set(false);
config.hostname.set(host);


port = javaObject('java.lang.Integer',4064);
config.port.set(port);
config.username.set(username);
config.password.set(password);
config.targetClass.set('omero.model.Dataset');

%Check a project named ProjectName
projects = getProjects(session);
project = [];
for j=1:numel(projects)
    pjname=char(projects(j).getName.getValue());
    if ~isempty(strmatch(pjname,ProjectName,'exact'))
        project=projects(j);
        break
    end
end

if isempty(project)
    project = handle(createProject(session, ProjectName));
end

%Check datasetList under the Project to see if there are datasets with
%similar name
datasetsList = project.linkedDatasetList;
for i = 0:datasetsList.size()-1,
    d = datasetsList.get(i);
    dname = char(d.getName.getValue());
    
    if ~isempty(strmatch(dname,DatasetName,'exact'))
        dataset=d;
        break
    end
end

if (datasetsList.size()==0)
    dataset = createDataset(session, DatasetName, project.getId.getValue());
end

dataID = javaObject('java.lang.Long',dataset.getId().getValue());
config.targetId.set(dataID);

%Metadatastore Object
store = config.createStore();
store.logVersionInfo(config.getIniVersionNumber());
reader = OMEROWrapper(config);

%Library Object
if importopt == 1
    library = handle(ImportLibrary(store, reader, SymlinkFileTransfer));
elseif importopt == 2
    uploadRm = UploadRmFileTransfer;
    library = handle(ImportLibrary(store, reader,  uploadRm));
else    
    library = handle(ImportLibrary(store, reader));
end

handler = ErrorHandler(config);
library.addObserver(LoggingImportMonitor());

%Import
paths = DataForImport;
candidates = ImportCandidates(reader, paths, handler);
reader.setMetadataOptions(DefaultMetadataOptions(MetadataLevel.ALL));

% success = library.importCandidates(config, candidates);

containers = candidates.getContainers();
n = containers.size();
imageId = [];
for index=0:n-1
    ic = containers.get(index);
    ic.setTarget(dataset);
    pixels = library.importImage(ic,index,0,n);
    imageId = [imageId ; pixels.get(0).getImage.getId.getValue];
end
if importopt == 2
   uploadRm.afterTransfer(handler.errorCount,toJavaList(paths));
end
%Logout and close session
store.logout();