Point KNIME to local FIJI installations

Dear All

In a previous thread Gabriel mentioned that"

"you can point KNIME to your FIJI installation to make use of the
many plugins that are included in it (provided they are headless)."

In that thread he provided a screen shot with instructions, which essentially consisted in pointing the ImageJ1 Preferences>ImageJ1 plugin directory to a specific local Fiji installation.

We have followed those instructions and could not get any additional plugin or command nodes to populate  either the ImageJ2 or ImageJ1 node groups

I feel as if we are missing something obvious.

Could you please point us in the right direction?





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Hi Caterina,

I am sorry for your confusion, I did not explain the how the ImageJ integration setting work, there are two differnet integrations with different intentions.

The ImageJ1 integration via the ImageJ Macro node:

The goal of this intention is to allow users to run their ImageJ macros in KNIME. Setting the path in the KNIME settings to the FIJI plugin path, enables you to call headless Macros and Commands that are shipped with FIJI from your macro code in the IJ1 Macro Node.

The ImageJ2 integration

The ImageJ2 integration aims to make ImageJ2 Plugins available as KNIME nodes. You can use the ImageJ2 Plugin Installation (experimental) settings page to point the option selected knimedirectory to the FIJI plugin directory. After a restart of KNIME this will result in new nodes appearing in the ImageJ2 sub-tree of the Node Repository. Note that not all of the new nodes will work, as this is still an experimental feature.

The correct directory to set:

Something I did not point out in the other post, you need to select the plugins folder within the Fiji installation directory, not just to the FIJI installation directory itself.