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OMERO Matlab language bindings

See Developing OMERO clients and OME-Remote Objects, for an introduction to Object.

Installing the OMERO.matlab toolbox

  • Download the latest released version from the download page . For the latest build, go here, and download the OMERO.matlab zip file.
  • Unzip the directory anywhere on your system.
  • In Matlab, move to the newly unzipped directory and run loadOmero;.
  • The Matlab files are now on your path, and the necessary jars are on your java classpath. You can change directories and still have access to OMERO.

Once OMERO.matlab is installed, the typical workflow is:

  1. Creating a connection
  2. Keeping your session alive
  3. Creating an unencrypted session (optional)
  4. Do some work (load objects, work with them, upload to the server...)
  5. Closing your connection
  6. Unloading OMERO (optional)

As a quickstart example, the following lines create a secure connection to a server, read a series of images and close the connection.

client = loadOmero(servername, port);
session = client.createSession(user, password);
client.enableKeepAlive(60);
images = getImages(session, ids);
client.closeSession();

Configuring the OMERO.matlab connection

Creating a connection

As described under Working with OMERO, there are several ways to configure your connection to an OMERO server. OMERO.matlab comes with a few conveniences for making this work.

If you run client = loadOmero; (i.e. loadOmero with a return value), then OMERO.matlab will try to configure the omero.client object for you. First, it checks the ICE_CONFIG environment variable. If set, it will let the omero.client constructor initialize itself. Otherwise, it looks for the file ice.config in the current directory. The OMERO.matlab toolbox comes with a default ice.config file pointing at localhost, which you can edit for your server.

Alternatively, you can pass the same parameters to loadOmero; that you would pass to omero.client:

>> omero_client_1 = loadOmero('localhost');
>> omero_client_2 = omero.client('localhost');

Or, if you want a session created directly, the following are equivalent:

>> [client1, session1] = loadOmero('localhost');
>> client2 = loadOmero('localhost');
>> session2 = client2.createSession()

Keeping your session alive

For executing any long running task, you will need a background thread which keeps your session alive. If you are familiar with Matlab Timers you can use omeroKeepAlive.m directly or modify it to your liking.

>> [c,s] = loadOmero;
>> t = omeroKeepAlive(c); % Creates a 60-second timer and starts it
>> ...
>> delete(t);             % Disables the keep-alive

Alternatively, you can use the Java-based enableKeepAlive method, but it is not configurable from within Matlab:

c.enableKeepAlive(60); % Calls session.keepAlive() every 60 seconds
c.closeSession();      % Close session to end the keep-alive

Creating an unencrypted session

If you want to speed up the data transfer, you can create and use an unencrypted session as:

unsecureClient = client.createClient(false);
sessionUnencrypted = unsecureClient.getSession();

Closing your connection

When you are done with OMERO, it is critical that you close your connection to save resources:

client.closeSession();
clear client1;
clear session1;

If you created an unencrypted session, you will need to close the unsecure session as well:

client.closeSession();
unsecureClient.closeSession();

Unloading OMERO

Then if you would like, you can unload OMERO as well:

unloadOmero();

You may see the following warning when unloading OMERO:

>> unloadOmero()
Warning: Objects of omero/client class exist - not clearing java
> In javaclasspath>doclear at 377
  In javaclasspath>local_javapath at 194
  In javaclasspath at 105
  In javarmpath at 48
  In unloadOmero at 75

===============================================================
While unloading OMERO, found java objects left in workspace.
Please remove with 'clear <name>' and then run 'unloadOmero'
again.  Printing all objects...
===============================================================

  Name      Size            Bytes  Class           Attributes

  c         1x1                    omero.client

Closing session(s) for 1 found client(s): c

This means that there is still an OMERO.matlab object in your workspace. If not listed, use whos to find such objects, and clear to remove them. After that, run unloadOmero() again:

>> clear c
>> unloadOmero()

Warning

You should also unload OMERO before installing a new version of OMERO.matlab or calling loadOmero again.

If you need to create another session without unloading/loading OMERO again, use the omero.client object directly:

>> [c,s] = loadOmero(arg1,arg2);
>> c = omero.client(arg3,arg4);
>> s = c.createSession();

Reading data

The IContainer service provides methods to load the data management hierarchy in OMERO – projects, datasets, etc. A list of examples follows, indicating how to load projects, datasets, screens, etc.

  • Projects

The projects owned by the user currently logged in can be retrieved using the getProjects function:

projects = getProjects(session)

If the project identifiers are known, they can be specified as:

projects = getProjects(session, ids)

If the projects contains datasets, the datasets will automatically be loaded:

for j = 1 : numel(projects)
    datasetsList = projects(j).linkedDatasetList;
    for i = 0:datasetsList.size()-1,
        d = datasetsList.get(i);
    end
end

If the datasets contains images, the images will automatically be loaded:

imageList = projects(1).linkedDatasetList.get(0).linkedImageList;

To avoid loading the whole graph (projects, datasets, images), pass false as a second optional argument. Only datasets will be loaded:

unloadedProjects = getProjects(session, ids, false)
  • Datasets

The datasets owned by the user currently logged in can be retrieved using the getDatasets function:

datasets = getDatasets(session)

If the dataset identifiers are known, they can be specified as:

datasets = getDatasets(session, ids)

If the datasets contain images, the images will automatically be loaded:

imageList = datasets(1).linkedImageList;

To avoid loading the images, pass false as a second optional argument:

unloadedDatasets = getDatasets(session, ids, false)
  • Images

All the images owned by the user currently logged in can be retrieved using the getImages function:

images = getImages(session)

If the image identifiers are known, they can be specified as:

images = getImages(session, ids)

Alternately, all the images contained in projects or datasets can be returned by specifying the parent type and identifiers as:

projectImages = getImages(session, 'project', projectIds)
datasetImages = getImages(session, 'dataset', datasetsIds)

The Image-Pixels model implies you need to use the pixels objects to access valuable data about the image:

pixels = image.getPrimaryPixels();
sizeZ = pixels.getSizeZ().getValue(); % The number of z-sections.
sizeT = pixels.getSizeT().getValue(); % The number of timepoints.
sizeC = pixels.getSizeC().getValue(); % The number of channels.
sizeX = pixels.getSizeX().getValue(); % The number of pixels along the X-axis.
sizeY = pixels.getSizeY().getValue(); % The number of pixels along the Y-axis.
  • Screens

The screens owned by the user currently logged in can be retrieved using the getScreens function:

screens = getScreens(session)

If the screen identifiers are known, they can be specified as:

screens = getScreens(session, ids)

Note that the wells are not loaded. The plate objects can be accessed using:

for j = 1 : numel(screens),
platesList = screens(j).linkedPlateList;
for i = 0:platesList.size()-1,
    plate = platesList.get(i);
    plateAcquisitionList = plate.copyPlateAcquisitions();
    for k = 0:plateAcquisitionList.size()-1,
        pa = plateAcquisitionList.get(i);
    end
end
  • Plates

The plates owned by the user currently logged in can be retrieved using the getPlates function:

plates = getPlates(session)

If the plate identifiers are known, they can be specified as:

plates = getPlates(session, ids)
  • Wells

Given a plate identifier, the wells can be loaded using the findAllByQuery method:

wellList = session.getQueryService().findAllByQuery(
['select well from Well as well '...
'left outer join fetch well.plate as pt '...
'left outer join fetch well.wellSamples as ws '...
'left outer join fetch ws.plateAcquisition as pa '...
'left outer join fetch ws.image as img '...
'left outer join fetch img.pixels as pix '...
'left outer join fetch pix.pixelsType as pt '...
'where well.plate.id = ', num2str(plateId)], []);
for j = 0:wellList.size()-1,
    well = wellList.get(j);
    wellsSampleList = well.copyWellSamples();
    well.getId().getValue()
    for i = 0:wellsSampleList.size()-1,
        ws = wellsSampleList.get(i);
        ws.getId().getValue()
        pa = ws.getPlateAcquisition();
    end
end

Raw data access

You can retrieve data, plane by plane or retrieve a stack.

  • Plane

The plane of an input image at coordinates (z, c, t) can be retrieved using the getPlane function:

plane = getPlane(session, image, z, c, t);

Alternately, the image identifier can be passed to the function:

plane = getPlane(session, imageID, z, c, t);
  • Tile

The tile of an input image at coordinates (z, c, t) originated at (x, y) and of dimensions (w, h) can be retrieved using the getTile function:

tile = getTile(session, image, z, c, t, x, y, w, h);

Alternately, the image identifier can be passed to the function:

tile = getTile(session, imageID, z, c, t, x, y, w, h);
  • Stack

The tile of an input image at coordinates (c, t) can be retrieved using the getStack function:

stack = getStack(session, image, c, t);

Alternately, the image identifier can be passed to the function:

stack = getStack(session, imageID, c, t);
  • Hypercube

This is useful when you need the pixels intensity.

%Create the store to load the stack. No access via the gateway
store = session.createRawPixelsStore();
store.setPixelsId(pixelsId, false); %Indicate the pixels set you are working on

% offset values in each dimension XYZCT
offset = java.util.ArrayList;
offset.add(java.lang.Integer(0));
offset.add(java.lang.Integer(0));
offset.add(java.lang.Integer(0));
offset.add(java.lang.Integer(0));
offset.add(java.lang.Integer(0));

size = java.util.ArrayList;
size.add(java.lang.Integer(sizeX));
size.add(java.lang.Integer(sizeY));
size.add(java.lang.Integer(sizeZ));
size.add(java.lang.Integer(sizeC));
size.add(java.lang.Integer(sizeT));

% indicate the step in each direction, step = 1, will return values at index 0, 1, 2.
% step = 2, values at index 0, 2, 4 etc.
step = java.util.ArrayList;
step.add(java.lang.Integer(1));
step.add(java.lang.Integer(1));
step.add(java.lang.Integer(1));
step.add(java.lang.Integer(1));
step.add(java.lang.Integer(1));
% Retrieve the data
store.getHypercube(offset, size, step);
% close the store
store.close();

Thumbnails

  • Single thumbnails

The cache thumbnail of an input image can be retrieved using the getThumbnail function:

thumbnail = getThumbnail(session, image, width, height);

Alternately, the image identifier can be passed to the function:

thumbnail = getThumbnail(session, imageID, width, height);

Note

The width or height arguments are optional and will be set to 48 pixels if not specified.

To preserve the aspect ratio of the retrieved thumbnail, use the getThumbnailByLongestSide function:

thumbnail = getThumbnailByLongestSide(session, image, size);

or alternately using the image identifier:

thumbnail = getThumbnailByLongestSide(session, imageID, size);
  • Thumbnail set

A set of cached thumbnails can be retrieved from a list of input images using the getThumbnailSet function:

thumbnailSet = getThumbnailSet(session, images, width, height);

To preserve the aspect ratio of the retrieved thumbnails, use the getThumbnailByLongestSideSet function:

thumbnailSet = getThumbnailSetByLongestSide(session, images, size);

Annotations

  • Reading annotations

If the identifier of a tag annotation is known, the annotation can be retrieved from the server using the getTagAnnotations function:

tagAnnotations = getTagAnnotations(session, tagIds);

See also

getFileAnnotations
Utility function to retrieve file annotations by identifier
getCommentAnnotations
Utility function to retrieve comment annotations by identifier
getXmlAnnotations
Utility function to retrieve xml annotations by identifier

To retrieve the tag annotations linked to a given object, an image for instance, use the getImageTagAnnotations function:

tagAnnotations = getImageTagAnnotations(session, imageIds);

See also

getImageFileAnnotations, getImageCommentAnnotations, getImageFileAnnotations
Utility function to retrieve annotations linked to images
getDatasetTagAnnotations, getDatasetFileAnnotations, getDatasetCommentAnnotations, getDatasetFileAnnotations
Utility function to retrieve annotations linked to datasets
getProjectTagAnnotations, getProjectFileAnnotations, getProjectCommentAnnotations, getProjectFileAnnotations
Utility function to retrieve annotations linked to projects
getScreenTagAnnotations, getScreenFileAnnotations, getScreenCommentAnnotations, getScreenFileAnnotations
Utility function to retrieve annotations linked to screens
getPlateTagAnnotations, getPlateFileAnnotations, getPlateCommentAnnotations, getPlateFileAnnotations
Utility function to retrieve annotations linked to plates
  • Reading file annotations

The content of a file annotation can be downloaded locally on disk using the getFileAnnotationContent function:

getFileAnnotationContent(session, fileAnnotation, target_file);

Alternately, if only the file annotation identifier is known:

getFileAnnotationContent(session, faid, target_file);

Writing data

  • Create a Dataset and link it to an existing project.
dataset = omero.model.DatasetI;
dataset.setName(omero.rtypes.rstring(char('name dataset')));
dataset.setDescription(omero.rtypes.rstring(char('description dataset')));

%link Dataset and Project

link = omero.model.ProjectDatasetLinkI;
link.setChild(dataset);
link.setParent(omero.model.ProjectI(projectId, false));

session.getUpdateService().saveAndReturnObject(link);
  • Create a tag (tag annotation) and link it to an existing project.
tag = omero.model.TagAnnotationI;
tag.setTextValue(omero.rtypes.rstring(char('name tag')));
tag.setDescription(omero.rtypes.rstring(char('description tag')));

%link tag and project
link = omero.model.ProjectAnnotationLinkI;
link.setChild(tag);
link.setParent(omero.model.ProjectI(projectId, false));

session.getUpdateService().saveAndReturnObject(link);
  • Create a file annotation and link to an image.

To attach a file to an object e.g. an image, few objects need to be created:

  1. an OriginalFile
  2. a FileAnnotation
  3. a link between the Image and the FileAnnotation.
% To retrieve the image see above.
iUpdate = session.getUpdateService(); % service used to write object

% create the original file object.
%read local file
file = java.io.File(fileToUpload);
name = file.getName();
absolutePath = file.getAbsolutePath();
path = absolutePath.substring(0, absolutePath.length()-name.length());

originalFile = omero.model.OriginalFileI;
originalFile.setName(omero.rtypes.rstring(name));
originalFile.setPath(omero.rtypes.rstring(path));
originalFile.setSize(omero.rtypes.rlong(file.length()));
originalFile.setSha1(omero.rtypes.rstring(generatedSha1));
originalFile.setMimetype(omero.rtypes.rstring(fileMimeType));

% now save the originalFile object
originalFile = iUpdate.saveAndReturnObject(originalFile);

% Initialize the service to load the raw data
rawFileStore = session.createRawFileStore();
rawFileStore.setFileId(originalFile.getId().getValue());

%  open file and read it

%code for small file.
fid = fopen(fileToUpload);
byteArray = fread(fid,[1, file.length()], 'uint8');
rawFileStore.write(byteArray, 0, file.length());
fclose(fid);


originalFile = rawFileStore.save();
% Important to close the service
rawFileStore.close();
% now, you have an original File in the database and raw data uploaded.
% You now need to link the Original file to the image using the File annotation object. That's the way to do it.
fa = omero.model.FileAnnotationI;
fa.setFile(originalFile);
fa.setDescription(omero.rtypes.rstring(description)); % The description set above e.g. PointsModel
fa.setNs(omero.rtypes.rstring(NAME_SPACE_TO_SET)) % The name space you have set to identify the file annotation.

% save the file annotation.
fa = iUpdate.saveAndReturnObject(fa);

% now link the image and the annotation
link = omero.model.ImageAnnotationLinkI;
link.setChild(fa);
link.setParent(image);
% save the link back to the server.
iUpdate.saveAndReturnObject(link);

% To attach to a Dataset use omero.model.DatasetAnnotationLinkI;

How to use OMERO tables

  • Create a table. In the following example, a table is created with 2 columns.
name = char(java.util.UUID.randomUUID());
columns = javaArray('omero.grid.Column', 2)
columns(1) = omero.grid.LongColumn('Uid', 'testLong', []);
valuesString = javaArray('java.lang.String', 1);
columns(2) = omero.grid.StringColumn('MyStringColumn', '', 64, valuesString);

%create a new table.
table = session.sharedResources().newTable(1, name);

%initialize the table
table.initialize(columns);
%add data to the table.
data = javaArray('omero.grid.Column', 2);
data(1) = omero.grid.LongColumn('Uid', 'test Long', [2]);
valuesString = javaArray('java.lang.String', 1);
valuesString(1) = java.lang.String('add');
data(2) = omero.grid.StringColumn('MyStringColumn', '', 64, valuesString);
table.addData(data);
file = table.getOriginalFile(); % if you need to interact with the table
  • Read the contents of the table.
of = omero.model.OriginalFileI(file.getId(), false);
tablePrx = session.sharedResources().openTable(of);

%read headers
headers = tablePrx.getHeaders();
for i=1:size(headers, 1),
    headers(i).name; % name of the header
    %do something
end

% Depending on size of table, you may only want to read some blocks.
cols = [0:size(headers, 1)-1]; % The number of columns you wish to read.
rows = [0:tablePrx.getNumberOfRows()-1]; % The number of rows you wish to read.
data = tablePrx.slice(cols, rows); % read the data.
c = data.columns;
for i=1:size(c),
    column = c(i);
    %do something
end
tablePrx.close(); % Important to close when done.

ROIs

To learn about the model see developers/roi.html. Note that annotation can be linked to ROI.

  • Creating ROI

This example creates an ROI with a rectangular shape and attach it to an image:

% First create a rectangular shape.
rectangle = createRectangle(0, 0, 10, 20);
% indicate on which plane to attach the shape
setShapeCoordinates(rectangle, 0, 0, 0);

% First create an ellipse shape.
ellipse = createEllipse(0, 0, 10, 20);
% indicate on which plane to attach the shape
setShapeCoordinates(ellipse, 0, 0, 0);

% Create the roi.
roi = omero.model.RoiI;
% Attach the shapes to the roi, several shapes can be added.
roi.addShape(rectangle);
roi.addShape(ellipse);

% Link the roi and the image
roi.setImage(omero.model.ImageI(imageId, false));
% save
iUpdate = session.getUpdateService();
roi = iUpdate.saveAndReturnObject(roi);
% Check that the shape has been added.
numShapes = roi.sizeOfShapes;
for ns = 1:numShapes
   shape = roi.getShape(ns-1);
end

See also

ROI utility functions
OMERO.matlab functions for creating and managing Shape and ROI objects.
  • Retrieving ROIs linked to an image
service = session.getRoiService();
roiResult = service.findByImage(imageId, []);
rois = roiResult.rois;
n = rois.size;
shapeType = '';
for thisROI  = 1:n
    roi = rois.get(thisROI-1);
    numShapes = roi.sizeOfShapes; % an ROI can have multiple shapes.
    for ns = 1:numShapes
        shape = roi.getShape(ns-1); % the shape
        if (isa(shape, 'omero.model.Rect'))
           %handle rectangle
           rectangle = shape;
           rectangle.getX().getValue()
        elseif (isa(shape, 'omero.model.Ellipse'))
           ellipse = shape;
           ellipse.getCx().getValue()
        elseif (isa(shape, 'omero.model.Point'))
           point = shape;
           point.getX().getValue();
        elseif (isa(shape, 'omero.model.Line'))
           line = shape;
           line.getX1().getValue();
        end
    end
end
  • Removing a shape from ROI
// Retrieve the roi linked to an image
service = session.getRoiService();
roiResult = service.findByImage(imageId, []);
n = rois.size;
for thisROI  = 1:n
    roi = rois.get(thisROI-1);
    numShapes = roi.sizeOfShapes; % an ROI can have multiple shapes.
    for ns = 1:numShapes
        shape = roi.getShape(ns-1); % the shape
        % remove the shape
        roi.removeShape(shape);
    end
    %Update the roi.
    roi = iUpdate.saveAndReturnObject(roi);
end

Deleting data

It is possible to delete projects, datasets, images, ROIs etc. and objects linked to them depending on the specified options (see Deleting in OMERO). For example, images of known identifiers can be deleted from the server using the deleteImages function:

deleteImages(session, imageIds);

See also

deleteProjects, deleteDatasets, deleteScreens, deletePlates
Utility functions to delete objects

Rendering images

  • Initialize the rendering engine and render an image.
% See load section to find out how to load pixels.
% Create rendering engine.
pixelsId = pixels.getId().getValue(); % see Load data section
re = session.createRenderingEngine();
re.lookupPixels(pixelsId);
% Check if default required.
if (~re.lookupRenderingDef(pixelsId))
    re.resetDefaults();
    re.lookupRenderingDef(pixelsId);
end
% start the rendering engine
re.load();

% render a Plane as compressed. Possible to render it uncompressed.
pDef = omero.romio.PlaneDef;
pDef.z = re.getDefaultZ();
pDef.t = re.getDefaultT();
pDef.slice = omero.romio.XY.value;

% Number of channels.
sizeC = pixels.getSizeC().getValue()-1;
if (sizeC == 0)
    re.setActive(0, 1);
else
    for k = 0:sizeC,
        re.setActive(k, 0);
        values = re.renderCompressed(pDef);
        stream = java.io.ByteArrayInputStream(values);
        image = javax.imageio.ImageIO.read(stream);
        stream.close();
        figure(k+1);
        imshow(JavaImageToMatlab(image));
        %make all the channels active.
        for i = 0:sizeC,
           re.setActive(i, 1);
        end
    end
end

% All channels active and save the image as a JPEG.
figure(pixels.getSizeC().getValue()+2);
values = re.renderCompressed(pDef);
stream = java.io.ByteArrayInputStream(values);
image = javax.imageio.ImageIO.read(stream);
stream.close();
imshow(JavaImageToMatlab(image));
%file = [imagename '.jpg'];
%fid = fopen(file, 'wb');
%fwrite(fid, values, 'int8');
%fclose(fid);
%delete(file);

%Close the rendering engine.
re.close();

Creating Image

The following example shows how to create an image from an image already in OMERO. A similar approach can be applied when uploading an image.

% See above how to load the pixels


sizeZ = pixels.getSizeZ().getValue() % The number of z-sections.
sizeT = pixels.getSizeT().getValue(); % The number of timepoints.
sizeC = pixels.getSizeC().getValue(); % The number of channels.
sizeX = pixels.getSizeX().getValue();
sizeY = pixels.getSizeY().getValue();

% Initialize the raw pixels store

pixelsId = pixels.getId().getValue()
store = session.createRawPixelsStore();
store.setPixelsId(pixelsId, false);

map = java.util.HashMap;
for z = 0:sizeZ-1,
  for t = 0:sizeT-1,
    planeC1 = store.getPlane(z, 0, t);
    map.put(linearize(z, t, sizeZ), planeC1); % linearize does sizeZ*t+z
  end
end

% Close to free space.
store.close();

% Retrieve the pixels type of the source image

proxy = session.getPixelsService();
l = proxy.getAllEnumerations('omero.model.PixelsType');
original = pixels.getPixelsType().getValue().getValue();
for j = 0:l.size()-1,
    type = l.get(j);
    if (type.getValue().getValue() == original)
        break;
    end
end

% Create the new image
description = char(['Source Image ID: ' int2str(image.getId().getValue())]);
name = char(['newImageFrom' int2str(image.getId().getValue())]);
idNew = proxy.createImage(sizeX, sizeY, sizeZ, sizeT, java.util.Arrays.asList(java.lang.Integer(0)), type, name, description);


%Load the new image.
list = iContainer.getImages('omero.model.Image', java.util.Arrays.asList(java.lang.Long(idNew.getValue())), omero.sys.ParametersI());
if (list.size == 0)
   exception = MException('OMERO:CreateImage', 'Image Id not valid');
   throw(exception);
end

imageNew = list.get(0);

%load the dataset hosting the source image and link it to the new image.
param = omero.sys.ParametersI();
param.noLeaves(); % indicate to load the images.
% load the dataset
results = session.getContainerService().loadContainerHierarchy('omero.model.Dataset', java.util.Arrays.asList(datasetId), param);
if (results.size == 0)
   exception = MException('OMERO:CreateImage', 'Dataset Id not valid');
   throw(exception);
end
dataset = results.get(0);
link = omero.model.DatasetImageLinkI;
link.setChild(omero.model.ImageI(imageNew.getId().getValue(), false));
link.setParent(omero.model.DatasetI(dataset.getId().getValue(), false));

session.getUpdateService().saveAndReturnObject(link);


%Copy the data.
pixelsNewList = imageNew.copyPixels();
pixelsNew = pixelsNewList.get(0);
pixelsNewId = pixelsNew.getId().getValue()
store = session.createRawPixelsStore();
store.setPixelsId(pixelsNewId, false);

for z = 0:sizeZ-1,
   for t = 0:sizeT-1,
      index = linearize(z, t, sizeZ);
      store.setPlane(map.get(index), z, 0, t); % copy the raw data
   end
end

%save the data
store.save();

%close
store.close();