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Image analysis

General user discussion about using the OMERO platform to its fullest. Please ask new questions at https://forum.image.sc/tags/omero
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Historical discussions about OMERO. Please look for and ask new questions at https://forum.image.sc/tags/omero

There are workflow guides for various OMERO functions on our help site - http://help.openmicroscopy.org

You should find answers to any basic questions about using the clients there.

Image analysis

Postby ray » Fri Oct 09, 2009 8:43 am

Hi. We have got installed a Omero 3.0-Beta 3.0 platform. And I was wondering if there is already a possibility to run e.g. a matlab script on my image data.
Normally -without omero- I'm working on microscopy image data and I'm always making local copies, process the data with matlab and store the results local. Make the results visible and extracting excel-sheets. Then I copy everything back to a folder on a server.

I was wondering if we could use omero to get a little bit more structure to all this.

So far uploading works fine and the viewer is great! But we also need to process the data and store the results. Results could be an image or a data-sheet or even a file from a custom build software.

I read about the possibility to access the image data from matlab. But could it also work the other way around? I'm thinking about something like: After uploading my image data from the microscope I choose the data I want to process than I choose a already by myself developed algorithm I want to perform and then I just click on process and omero calls whatever is needed. This could be some ready matlab remote desktops, other computing power waiting to perform c++ code ... or even a grid computing network.
The results are written back to the database and I can browse to the result images with omero. And access Results-sheets in excel or any other format.

Is this already -somehow- possible with omero? Or are there plans for something comparable for the future?

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Joined: Fri Oct 09, 2009 7:56 am

Re: Image analysis

Postby cxallan » Fri Oct 09, 2009 9:49 am

This is not possible with Beta 3.0 but is possible with the released Beta 4.0 and the soon to be released Beta 4.1. You can see some examples of programming with Matlab in Beta 4.0 and later here:

http://trac.openmicroscopy.org.uk/omero ... meroMatlab
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Posts: 509
Joined: Fri May 01, 2009 8:07 am

Re: Image analysis

Postby sophie » Wed Jun 09, 2010 9:35 am

I'm attempting to get started with image analysis in Matlab. I would like to get access to the images and its metadata for reading and writing.
So far I'm getting the image information like name, description,date, x-,y,z,t-size(...) for a special image id.
But I', stuck with the overwriting of metadata.
My procedure is to start in Matlab an omero session, after that I create a omero.model.ImageI or omero.model.PixelsI object:
Code: Select all
image = getImage(gateway, ImageId) 
pixels = gateway.getPixels(ImageId)   

Now I look for useful commands with for example >>methods omero.modelImageI <<or I'm searching through the omero API documentation. But it isn't really clearly arranged and I don't get on very fast.
Is there a user guide which could help me? Or perhaps a better way to proceed in programming?
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Joined: Mon Apr 26, 2010 11:15 am

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