KNIME Image Processing - OMERO Extension (trusted extension)

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OMERO is a client-server software for visualisation, management and analysis of biological microscope images. OMERO handles all your images in a secure central repository. You can view, organise, analyse and share your data from anywhere you have internet access.

We plan a tight, bidirectional integration of OMERO and KNIME. Hence, the current OMERO Reader Node in KNIME allows you to start the OMERO INSIGHT Client directly within KNIME to import images from an OMERO database.

After installing the KNIME Image Processing - OMERO Integration from the Community Contributions Update-Site the OMERO Reader node is available. The node stores the server path and credentials and allows to start the INSIGHT client to select the images, which will then be loaded in KNIME (In Insight: Rightclick -> View -> View in KNIME...). Once configured, the reader fetches the selected images automatically during execution. The images can then be processed within KNIME.

Unfortunately writing images back to OMERO is not yet possible but we hope to further improve the integration of OMERO and provide bidirectional access to OMERO databases in the future.