OMERO connection unavailable

Hi,

I have freshly installed KNIME and wanted to try an upload from an OMERO database.
I first tried to use the OMERO reader node but the login failed. Apparently this might be due to the fact that we still have a 5.4 version of OMERO (Can't connect to OMERO server)
So then I tried to use an old workflow with the OMERO connection node but KNIME apparently can’t find the node in the library:

ERROR LoadWorkflowRunnable Status: Error: Node “OMERO Connection” not available from extension “KNIME Image Processing - OMERO Integration”
ERROR LoadWorkflowRunnable Status: Error: Node “OMERO Labeling Reader” not available from extension “KNIME Image Processing - OMERO Integration”

It recognizes it because it suggests to install the KNIME Image Processing - OMERO Integration extension but then ignores it when it gets at the installation step because it is already installed. I’ve tried uninstalling and reinstalling it but it didn’t change the result.

Could you let me know how I can connect an OMERO database 5.4?

Thanks,

Sebastien

Hi @sebherbert,

try to install the OMERO integration from the nightly community update site:
https://www.knime.com/wiki/knime-image-processing-nightly-build
That version is newer and should contain the nodes you are missing in your workflow.

best,
Gabriel

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Hi.

Thanks, it indeed installed the connection, labeling reader and table reader nodes as well as depretiated the OMERO reader node.
Surprisingly the connection test fails but the node can still execute without error.
However I have no clue how to use the connection node since there are no image reader anymore. I’ve tried to find documentation but couldn’t find anything. Is there guidelines somewhere?

Best,

Sebastien

Hi @sebherbert,
There is a special image reader node that will work with OMERO, the Image Reader (Table) Remote node. You can also get it from the nightly community update site, it is part of the KNIME Image Processing extension.
best,
Gabriel

Hi @gab1one ,

Thanks for the fast reply.
I’m still trying to get it to work but I’ve found it. Thanks.

Sebastien

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