Development/Applications Of Open Microscopy Environment

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The Open Microscopy Environment is a project started by Dr. Ilya Goldberg at MIT three 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. Since Dr. Goldberg has established his new unit at the NIA, we have seen major developments in OME. 1) He has finalized an XML schema and submited it for review by academic and industrial groups as a new standard for the exchange of image information for light microscopy. Together with Josiah Johnston, they have fully implemented this standard in OME software for both input and output of images and associated information. 2) Josiah Johnston has also been instrumental in developing a web-based 5-dimensional image viewer so that these multi-dimensional images can be recalled and viewed without additional software. 3) Goldberg and Johnston have migrated the entire specification of the database layout to XML. This allows the dynamic creation of database fields from new kinds of information stored in incomming OME XML files. 4) Drs. Goldberg and Orlov have embarked on a new application of OME - automated image classification. Using Bayesian networks, preliminary indications are that we can automatically classify images to a much higher precision than is possible with naive or expert human subjects. we are pursuing further refinements of this technique and investigating applications outside of the light-microscopy area including medical diagnostics. 6) Dr. Harry Hochheiser is pursuing novel ways of visualizing and interacting with the complex inter-related information made available by OME. 7) In collaboration with Dr. Wang at CIT, we are attempting a staged deployment of OME institute-wide, and are investigating the application of this technology for processing the tissue arrays collected through the BLSA.