[ome-devel] omero & imagej

[Jean-Marie Burel (Staff)]

Dear Alessandro

To import an image in omero using the Omero.insight plugin we follow two
paths:
If the image has not been modified, we import the image in its original
format.
If the image has been modified, we generate an OME-TIFF using the
Bio-Format Exporter.
Below is a link to the Exporter call so you can follow the steps required.
https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-fo
rmats-plugins/src/loci/plugins/out/Exporter.java


Cheers

jmarie

On 17/04/2015 19:50, "Michael Porter (Staff)" <m.porter at dundee.ac.uk>
wrote:

>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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