Can't connect to OMERO server

KNIME Extensions Image Processing
#1

Hello,
I´m trying to connect the “OMERO Reader (5.2)” node to our OMERO server. I introduced the user credentials, but when I press the “start OMERO.insight” button it says "login failed.

I´m running KNIME v 3.7.0 on Windows 10, and OMERO server v5.4.5.

The output of the Knime.log is the following:

2019-01-16 10:32:38,385 : DEBUG : KNIME-Worker-8 : WorkflowManager : OMERO Reader (5.2) : 2:1 : OMERO Reader (5.2) 2:1 doBeforePostExecution
2019-01-16 10:32:38,385 : DEBUG : KNIME-Worker-8 : NodeContainer : OMERO Reader (5.2) : 2:1 : OMERO Reader (5.2) 2:1 has new state: POSTEXECUTE
2019-01-16 10:32:38,385 : DEBUG : KNIME-Worker-8 : WorkflowManager : OMERO Reader (5.2) : 2:1 : OMERO Reader (5.2) 2:1 doAfterExecute - failure
2019-01-16 10:32:38,386 : DEBUG : KNIME-Worker-8 : Node : OMERO Reader (5.2) : 2:1 : reset
2019-01-16 10:32:38,386 : DEBUG : KNIME-Worker-8 : Node : OMERO Reader (5.2) : 2:1 : clean output ports.
2019-01-16 10:32:38,386 : DEBUG : KNIME-Worker-8 : WorkflowDataRepository : OMERO Reader (5.2) : 2:1 : Removing handler 21e1728f-3e33-425f-ba22-9d793ec71888 (OMERO Reader (5.2) 2:1: <no directory>) - 0 remaining
2019-01-16 10:32:38,386 : DEBUG : KNIME-Worker-8 : NodeContainer : OMERO Reader (5.2) : 2:1 : OMERO Reader (5.2) 2:1 has new state: IDLE
2019-01-16 10:32:38,386 : WARN  : KNIME-Worker-8 : OmeroReaderNodeModel : OMERO Reader (5.2) : 2:1 : the connection settings are incomplete
2019-01-16 10:32:38,386 : WARN  : KNIME-Worker-8 : OmeroReaderNodeModel : OMERO Reader (5.2) : 2:1 : please select some image ids
2019-01-16 10:32:38,386 : DEBUG : KNIME-Worker-8 : Node : OMERO Reader (5.2) : 2:1 : Configure succeeded. (OMERO Reader (5.2))
2019-01-16 10:32:38,386 : DEBUG : KNIME-Worker-8 : NodeContainer : OMERO Reader (5.2) : 2:1 : OMERO Reader (5.2) 2:1 has new state: CONFIGURED
2019-01-16 10:32:38,386 : DEBUG : KNIME-Worker-8 : NodeContainer : OMERO Reader (5.2) : 2:1 : KNIME_project 2 has new state: CONFIGURED

Looking to the log it´s looks like the node is properly configured, but I´ve got an error, and the OMERO.insight doesn´t open.

What I´m doing wrong?

Thank you.

OMERO connection unavailable
#2

Hi @_Itu,

The node that you are trying to use does currently not support OMERO 5.4.x. We are working on an updated version that does support the OMERO 5.4 release line. You can try out the latest, non-stable version of the OMERO integration by adding the Nightly Update Site to your KNIME Analytics Platform and installing KNIME Image Processing - OMERO Integration (0.20.1.201901160633 as of today).

Be warned that those nodes do not support OMERO.insight anymore (since its future is somewhat unclear).

Best regards,
Stefan

#3

Thank you very much for your answer.
I´ve instaled the nightly build and now the “OMERO Conexion” node seems to conect correctly to the OMERO server, but i dont really understand how it works. I´ve also triedto the labeling and table reader nodes, but the intructions are not very clear.

Could you please tell me where I can find a description of how to use it?

Thank you,
Best regards

#4

Hi @_Itu,
You need to connect the OMERO Connection node to a List Remote Files node:


you can then select a project or folder and it will create a list of all contained images.
You can then feed this list to the Image Reader Table (Remote) node together with the OMERO connection. The labeling reader can read the labelings attached to an image, it also consumes the URIs produced by List Remote Files node.
The table reader can read table attachments from OMERO, it requires the object id of the table which you can get from the OMERO web interface.

best,
Gabriel

3 Likes
#5

Thank you very much @stelfrich and @gab1one for your explanations! Everything works know.

Best regards.

2 Likes
#6

This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.