[ome-devel] omero & imagej

[Michael Porter (Staff)]

Hi Alessandro

A while ago I did a similar thing using the matlab toolkit. While verifying I was putting the pixel values in the right place I realised I had to transpose the plane I got from the server before creating the byteArray. This might be specific to the matlab row/col ordering, but worth keeping in mind for however you're doing it maybe.

-------------------------------------
imageStack = ij.ImageStack(sizeX,sizeY);
for thisPlane = 1:numPlanes
    byteArray = reshape(stackIn(:,:,thisPlane)', sizeX * sizeY, 1 );
    imageStack.addSlice('',byteArray);
end

imp = ij.ImagePlus();
imp.setStack(imageStack, numC, numZ, numT);
-------------------------------------

Michael.




-----Original Message-----
From: ome-devel [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of Alex Rigano
Sent: 17 April 2015 19:07
To: OME External Developer List
Subject: [ome-devel] omero & imagej

Hi there,

I'm trying to create an ImageStack object from raw image data retrieved from an OMERO server via the java API.
My current strategy is to get each frame of the image as a byte array and transform it in a int array.
Then create a FloatProcessor for each frame and add it to the ImageStack.

The problem I'm experiencing is that if I execute the same analysis procedure in imageJ and in my application I obtain different results.
So I'm trying to understand if the approach I use to create ImageStack is correct.

I realized that you probably already did that for the OMERO.insight plugin for ImageJ.
Would it be possible for you to let me know what is the strategy you used?

Thanks
Have a great day

--
Alessandro Rigano
Application and Database Developer II
Program in Molecular Medicine
University of Massachusetts Medical School
373 Plantation Street, Biotech II, Suite 114 Worcester, MA, 01605

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