OMERO: VAST Data Preparation, Metadata Creation, and ROI Upload with FishInspector Annotations

Version 1

This KNIME workflow is designed to facilitate the loading of image data from OMERO. It includes key preprocessing steps for VAST data, such as metadata creation and the linking of 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.
• Import Metadata: Purple and Green branch allows to upload metada as Key-Value Pairs and Tables
• Import ROIs: ROI created with Fish Inspector will be automatically uploaded into OMERO. (ROIs need to be reported in a json file)
• 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/14790777

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.