Design of new OMERO Writer / Reader Nodes

[gab1one]

We are planing to create new OMERO reader and writer nodes. This issue gives an overview over the planed features and serves as a platform for discussion about them.

Planed features

General

• Omero connection node / port (like the database connections)
• Use workflow credentials instead of KNIME Masterkey

Reader

• Browse omero server without needing to open OMERO.insight

Writer

• Write to omero dataset
• Create new dataset

Reader / Writer

• JavaScript based view reflecting the same dialog as in the original nodes

Technical

• Based on ImageJ-Omero / SCIFIO

[stelfrich]

Use workflow credentials instead of KNIME Masterkey

What exactly do you mean by workflow credentials @gab1one? Letting the user specify the credentials in the node configuration?

[gab1one]

Workflow credentials is related to the encryption of the credentials / the ability to ship workflows without storing the passwords in the nodes.

• Omero connection node / port (like the database connections)

This will be a node where the user can enter connection details.

[dnmason]

Hello all,
I'd really like to get knime working with our OMERO server (running v 5.2.7-ice35-b40). I've the nightly build and the 5.2 node, I can access the omero server, open the insight client and "View in KNIME" to select imageIDs.

When I go to execute the node, I get "Execute Failed: IO object cannot be null." whether I have the insight client open or not.

Has there been any progress on an OMERO/ImageJ2/KNIME node?

Cheers,

Dave

[gab1one]

Hi @dnmason I will look into reproducing this bug tomorrow. In any case we are currently working on new image reader and writer nodes (first beta estimated end of the month), which will allow you to read from and write to many remote locations including OMERO.

[ctrueden]

Has there been any progress on an OMERO/ImageJ2/KNIME node?

@awalter17 is actively working on the ImageJ-OMERO integration layer. Expect progress before year's end. Current priorities are support for OMERO tables (complete pending review) and ROIs (actively developed in collaboration with ImgLib2 team). We hope/expect this functionality will Just Work (TM) from KNIME thanks to the SciJava integration. We will make an announcement when there is a stable release.

[dnmason]

Thanks both for the replies. I look forward to seeing what you come up with. Will be happy to test it out in our environment!

@gab1one let me know if you need any more info to replicate, but it's not urgent at this point if there's another solution in the pipe.