[SOLVED] OMERO Reader

HI all,

Today I tried out the OMERO Reader. Sadly it is very outdated. It is working with OMERO version 4.4 but the newest version is 5.0.2.

And will there be a OMERO Writer soon?

 

Kind regards,

Flo

Hi Flo,

I managed to update OMERO to Version 5.0.2.

If you have a developer version of KNIME running you can checkout the branch 0.8.2 in the repository knip-omero. If not, unfortunately you have to wait until next week when we release ;-)


Cheers,

Christian

 

PS: We of course would like to have a OMERO Writer Node, but since now we didn't find the time to implement one. ;-)

 

Thank you, I'm looking forward to 2.10 :-)

Datahandling is a big issue in the Microscopy World and there is a rising demand for Datahandling tools like OMERO.

 

Best regards,

Flo

Hi Flo,

does it work with KNIME Image Processing 1.2.0 and the new OMERO 0.8.2?

Christian

 

Everything looks fine :)

 

Thanks a lot,

Flo

 

Update: But I can't get the VTK 3D Viewer to work :/

the VTK 3D Viewer is currently not maintained and therefore we moved it to the nightly-build update-site. Anyway, the current version should still work. Could you quickly tell me which OS, KNIME, KNIME Image Processing and KNIME VTK Version you are using?
 

The ImageJ3D Viewer works way faster with the latest release btw ;-)

Windows 7 64 bit

KNIME 2.10.0

KNIME Image Processing    1.2.0.201407091732

Nightly Builds 201407101815

The problem is that after installing the VTK Integration I get the follow error messages:

ERROR     NativeLibBundleActivator           no lwjgl in java.library.path
ERROR     NativeLibBundleActivator           Could not load org.knime.knip.vtk
ERROR     RepositoryManager                  Node org.knime.knip.base.nodes.proc.ProcNodeSetFactory' from plugin 'org.knime.knip.base' could not be created.
ERROR     RepositoryManager                  Node org.knime.knip.base.nodes.seg.LabNodeSetFactory' from plugin 'org.knime.knip.base' could not be created.
ERROR     RepositoryManager                  Node org.knime.knip.base.nodes.view.ViewsNodeSetFactory' from plugin 'org.knime.knip.base' could not be created.
ERROR     RepositoryManager                  Node org.knime.knip.base.nodes.features.FeatureNodeSetFactory' from plugin 'org.knime.knip.base' could not be created.
ERROR     RepositoryManager                  Node org.knime.knip.base.nodes.proc.binary.BinaryProcNodeSetFactory' from plugin 'org.knime.knip.base' could not be created.
ERROR     RepositoryManager                  Node org.knime.knip.base.nodes.filter.FilterNodeSetFactory' from plugin 'org.knime.knip.base' could not be created.
ERROR     RepositoryManager                  Node org.knime.knip.base.nodes.metadata.MetadataNodeSetFactory' from plugin 'org.knime.knip.base' could not be created.
ERROR     RepositoryManager                  Node org.knime.knip.base.nodes.knimeimagebridge.ConversionNodeSetFactory' from plugin 'org.knime.knip.base' could not be created.
ERROR     RepositoryManager                  Node org.knime.knip.base.nodes.misc.MiscNodeSetFactory' from plugin 'org.knime.knip.base' could not be created.
ERROR     RepositoryManager                  Node org.knime.knip.base.nodes.io.IONodeSetFactory' from plugin 'org.knime.knip.base' could not be created.
ERROR     RepositoryManager                  Node org.knime.knip.io.nodes.IONodeSetFactory' from plugin 'org.knime.knip.io' could not be created.
ERROR     RepositoryManager                  Node org.knime.knip.imagej1.ImageJ1NodeSetFactory' from plugin 'org.knime.knip.imagej2.core' could not be created.
ERROR     RepositoryManager                  Node org.knime.knip.imagej.core.node.IJNodeSetFactory' from plugin 'org.knime.knip.imagej2.core' could not be created.
ERROR     RepositoryManager                  Node org.knime.knip.tess4j.base.node.Tess4JNodeSetFactory' from plugin 'org.knime.knip.tess4j.base' could not be created.

Windows 7 64 bit

KNIME 2.10.0

KNIME Image Processing            1.2.0.201407091732       

KNIME Image Processing - VTK Integration        1.1.1.201406271441       

On startup I get the following error messages:

https://www.dropbox.com/s/jvawnqdmso5zx6r/error.PNG

Hi Flo! Thanks for the error plot. I find out whats wrong and it should be fixed by tomorrow in the nightly build!

Cheers,

Christian

 

faster than expected: found the error and fixed it. changes should be available on the nightly build update-site in about 30minutes.

cheers,

christian

I have installed the build from today.

Where exactly is the node? I can't find it :D

It's basically a "Tab" in the Table Cell Viewer (like the Histogram,ImageJ3D Viewer, etc). Either you connect a Table Cell Viewer Node to the output of a node which contains images or on the most of the image processing nodes there is this "Table Cell View" available on right-click.

Anyway, VTK is only available via the Nightly-Build and not really maintained at the moment ;-)

Do your errors still occur?

 

Hi,

thanks it works now. The great thing about the VTK Viewer ist the Sllice View which is not included in the ImageJ3D viewer.

 

Kind regards,

Flo

Hi,

I wrote a feature request. Maybe we can include this in one of our next releases.

Christian