[ome-devel] Examples of using RawPixelsStore setPlane

[Sebastien Besson (Staff)]

Hi Curtis,

following-up on this thread and the 5.1.2 release announcement [1], the Java
training example has been modified as part of the 5.1.2 release [2] and should
now provide a concrete example of multi-C, multi-T, multi-Z image upload using
the RawPixelsStore service.
The corresponding code should be available under GitHub [3].

[1] http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2015-May/003315.html
[2] https://github.com/openmicroscopy/openmicroscopy/pull/3826
[3] https://github.com/openmicroscopy/openmicroscopy/blob/v5.1.2/examples/Training/java/src/training/CreateImage.java#L209

Thanks again for highlighting this,
Sebastien

On 15 May 2015, at 10:30, Ian Munro <i.munro at imperial.ac.uk<mailto:i.munro at imperial.ac.uk>> wrote:

Hi Curtis

I don’t know if Matlab code would help.
https://github.com/openmicroscopy/Imperial-FLIMfit/blob/master/FLIMfitFrontEnd/Classes/%40flim_omero_data_manager/fit_results2omeroImage_Channels.m

I would add tough that this is extremely old code that I’m just in the
process of replacing.

Ian



On 15 May 2015, at 21:20, Curtis Rueden <ctrueden at wisc.edu> wrote:

Hi everyone,

I am trying to fix a long-standing ImageJ-OMERO bug relating to the
upload of multichannel images [1].

I thought I had found the obvious problem, but the expected bug-fix
[2] does not actually fix it. Instead, it seems to make things worse
somehow [3] (upload barfs on the first plane, rather than the second).

I was wondering if there are any examples of using the RawPixelsStore
service to upload multichannel image data. I saw the
RawPixelsStoreTest integration test [4], but it only tests for
single-channel data.

Relatedly: I am still developing against a dev_5_0 omero_client
uber-JAR. I'd be happy to try again with 5.0.8, but only if there is a
solid reason to believe it might improve the situation?

Thanks,
Curtis

[1] https://github.com/imagej/imagej-omero/issues/55

[2] https://github.com/imagej/imagej-omero/compare/issue-55

[3] https://gist.github.com/ctrueden/f960d3d7e67b957d4d9e

[4] https://github.com/openmicroscopy/openmicroscopy/blob/v5.1.1/components/tools/OmeroJava/test/integration/RawPixelsStoreTest.java

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