Open Microscopy Environment

Hello,
I have a long history in Matlab but I haven't had any luck successfully opening an image from the server, and the information on the website is not very clear. Does anyone have a step by step tutorial, or can point me to the right area of the API?

Thank You,
Damien

Dear Damien,

With OMERO.matlab-4.4.4-ice33-b3099 installed and after correct initialization of the variables, the code example below should:
1. initiate the toolbox and connect to the server
2. load the image imageID using the ContainerService
3. retrieve the first plane of the image using the RawPixelsStore service

Code: Select all

server = xxx;
username = xxx;
password = xxx;
imageID = xxx;

% Load the OMERO.matlab toolbox
loadOmero;

% Create a client and a session
client = omero.client(server);
session = client.createSession(username, password);
omeroKeepAlive(client);

% Create a list of image IDs to be retrieved
ids = java.util.ArrayList();
imageId = java.lang.Long(imageID);
ids.add(imageId);

% Load images by IDs using container service
proxy = session.getContainerService();
list = proxy.getImages('omero.model.Image', ids, omero.sys.ParametersI());
image = list.get(0);

% Create raw pixels store to read the planes
pixels = image.getPrimaryPixels();
store = session.createRawPixelsStore();
store.setPixelsId(pixels.getId().getValue(), false);

% Read the first plane and convert it into double matrix
plane = store.getPlane(0, 0, 0);
I = double(toMatrix(plane,pixels)');


Let me know if this works,
Sebastien

Hello Sebastien,
Thank you for the help! I am sorry for the delay, my disk encryption at work had a problem and I had to reinstall my OS. I was able to open an image with your commented code. It is a lot more clear now, and now I have a more narrow set of methods I can look at in the API first. (So that I can switch planes, and find the image number, etc.. )

Thanks,
Damien

Hi,

I tried to enter the following code in my MATLAB installation (installed on RedHat Linux), but get some error message on the line

list = proxy.getImages('omero.model.Image', ids, omero.sys.ParametersI());

The error message is:

Java exception occurred:
java.lang.ClassCastException: java.lang.Double cannot be cast to java.lang.Long
at omero.sys.LongListHelper.write(LongListHelper.java:35)
...
at omero.api.IContainerPrxHelper.getImages(IContainerPrxHelper.java.1181)

Is there some change done in the meantime? Should I do it in some other manner?

By the way, the following calls from the documentation do not work:
projects = getProjects(session)
datasets = getDatasets(session)
images = getImages(session)

The error message is Ice.UnmarshalOutOfBoundsException.

Do you have any explanation why this does not work?

Thanks in advance,
Andreas

How is 'ids' being set? The error message seems to be saying that there's a double as opposed to a long in there. All image IDs should be java.lang.Long instances.

Cheers,
~Josh

Hi,

sorry, but I realized afterwards that we used version 4.4.10 on the server side and version 5 on the client side. After downloading the corrent version, everything worked as expected.

Thanks,
Andreas

Thanks for letting us know, Andreas.

Cheers,
~Josh