ImageJ is a public domain image analysis program written by Wayne Rasband of NIH. We have created ImageJ plugins for interacting with an OME database, including the ability to upload images to the database, as well as search, browse, and download images from it, using the OME-Java API for remote access to OME.

The OME plugins were written by Melissa Linkert based on code originally by Phil Huettl.

OME plugins for ImageJ

The OME plugins have been used to download and visualize several datasets from an OME database. The search results window shows details of all datasets matching the specified criteria.

The "Download from OME or OMERO" plugin is capable of accessing an OME Perl or OMERO database and searching it for images matching the specified criteria. It brings up a list of matches through which the user can browse, and select which to actually download. It is capable of downloading both pixels and some associated metadata.

The "Upload to OME" plugin uploads pixel data to an OME Perl database.

Unfortunately, we have not had the resources to robustly test the OME plugins with new versions of OME and OMERO as development continues, and the plugins are not under active development at the moment. We do plan to resume development once we have the resources, but until then we can provide only limited support.

You can download ome_tools.jar from the Bio-Formats downloads page. The license is GPL. You will also need to download loci_tools.jar.

Place both ome_tools.jar and loci_tools.jar in your ImageJ plugins folder. To access the plugins, choose "Download from OME" or "Upload to OME" from the OME submenu of ImageJ's Plugins menu.

The OME plugins will communicate with OME server 2.6.0 or newer. They will not work properly with OME 2.4.0.

The OME plugins can also download images from OMERO. It communicates with OMERO 3.0 beta 3, and will not work with other versions.