OMERO Image Import and Annotation Workflow

Version 1

General workflow to upload data into OMERO using KNIME

The workflow consists of two main branches: the Green Branch, which imports a folder containing images, and the Purple Branch, which enables the annotation of metadata as key-value pairs.

• Fetching Images: The first step involves fetching images from a locally accessible folder.
• User Authentication: Users are prompted to input their OMERO username and password through a Java snippet. This information is then converted into variables that can be used by the Python script node.
• Image Import: The Python script node utilizes ezomero to execute the image import process.
• Temporary Folder Deletion: After the import process is complete, the temporary folder is deleted.

A dataset for testing can be found at: https://zenodo.org/records/14205500

Important Security Note: It is crucial to be aware that storing credentials as variables can pose security risks, particularly if accessed by administrators. Therefore, it is essential to handle user credentials securely and in accordance with best practices.