The Open Microscopy Environment is a project started by Dr. Ilya Goldberg at MIT two years ago, in the group of Dr. Peter Sorger. The purpose is to develop an information framework for computational cell biology - a sub-specialty of bioinformatics called 'Image Informatics'. This open-source framework consists of a database, several analytic modules, and an application program interface (API) that ties the modules to the database. The database provides a semantic framework and a data model for biological information obtained by analyzing images. It also keeps track of the images themselves, and of all the analyses performed on them. The database is also the communication link between analysis modules permitting the multiplexing of analysis algorithms. Finally, the entire system provides a web-based user interface allowing for remote interaction. During the past 3 months, since Dr. Goldberg has established his new unit at the NIA, we have seen major developments in OME. 1) He has developed and published an XML Schema specifying an image file standard for biological light microscopy. 2) In collaboration with Dr. Jason Swedlow at the University of Dundee, we have demonstrated the functionality and flexibility of this system for performing 3-D particle identification and tracking in living cultured cells. 3) In collaboration with Drs. Brian DeDecker and Yan Fang of the Harvard Institute of Chemistry and Cell Biology, we have performed several automated cell-based imaging screens for small chemical compounds affecting neuronal outgrowth and nuclear import of transcription factors. Further information about OME is available at

National Institute of Health (NIH)
National Institute on Aging (NIA)
Intramural Research (Z01)
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Smith, Barry; Arabandi, Sivaram; Brochhausen, Mathias et al. (2015) Biomedical imaging ontologies: A survey and proposal for future work. J Pathol Inform 6:37
Schiffmann, David A; Dikovskaya, Dina; Appleton, Paul L et al. (2006) Open microscopy environment and findspots: integrating image informatics with quantitative multidimensional image analysis. Biotechniques 41:199-208
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Goldberg, Ilya G; Allan, Chris; Burel, Jean-Marie et al. (2005) The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging. Genome Biol 6:R47
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Platani, Melpomeni; Goldberg, Ilya; Lamond, Angus I et al. (2002) Cajal body dynamics and association with chromatin are ATP-dependent. Nat Cell Biol 4:502-8