Examples of the OME Server in use
Some examples of OME Server being used as a foundation for research programs outside of the OME project.
Center for Bio-Image Informatics
BISQUE (Bio-Imaging Semantic Query User Environment) is being developed by the Center for Bio-Image Informatics at UCSB, an NSF-funded project aimed at developing techniques for using images to generate understanding of biological processes such as retinal detachment and microtubule dynamics. BISQUE uses OME Server as a base platform for providing novel analysis and visualisation functionality, including search and comparison of datasets by image metadata.
Columbia University
In support of the Molecular Libraries Screening Center Network, Bernd Jagla of Columbia University has developed an OME Server importer for the GE INCELL 3000. Bernd has implemented two importers for the INCELL 3000 confocal microscope. One reads in the acquisition parameters from the "Run"-file, converted into XML format, plus the images, converted into single colour TIFF files, that are residing in the directory structure underneath the run file. Still to come is the import of the flat field image that is used to normalise the images. The other importer reads in analysis results that are produced by the INCELL software.
Figure 1: Screenshot from Bernd Jagla showing INCELL 3000 data imported into an OME Server instance running at Molecular Libraries Screening Center Network at Columbia
Figure 2: Screenshot from Bernd Jagla showing INCELL 3000 data imported into an OME Server instance running at Molecular Libraries Screening Center Network at Columbia, with integration of Partek for data analysis and visualisation.
Escuela Superior Politécnica del Litoral
The Computer Vision and Robotics Center at the Escuela Superior Politécnica del Litoral in Ecuador promotes the use of OME to expedite communication between their technicians and pathologists at APROFE (Association to Promote the Health of Ecuadorian Families) an important non-profit health care provider in Ecuador. Daniel Ochoa, Javier Tibau and Jorge Faytong at CVR worked with Josiah Johnston at the NIH to establish an internationalisation layer in OME. Jorge then proceeded to translate OME's entire web interface as well as Semantic Types into Spanish. Thanks to these efforts by the CVR and the support from VLIR (Vlaamse Interuniversitaire Raad), OME now has an internationalisation layer as well as a full translation into Spanish. We look forward to future collaborations with this group in their efforts to integrate OME into health care applications and research.
Figure 1: OME Server running in Spanish
Figure 2: The new internationalisation layer supports a rich translation
Vanderbilt University School of Medicine
The Vanderbilt University School of Medicine is deploying a custom OME Server installation to manage images generated by the Cell Imaging Shared Resource, a multi-million dollar optical microscopy centre. Designed to accommodate millions of image files - as much as 256TB of data - including high-speed image acquisition systems, CISR's OME Server installation will greatly ease the storage, co-ordination, and management of image data used by hundreds of medical research professionals.
