Open Microscopy Environment

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?


best
ray

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

Hello,
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?
regards,
Sophie