The Open Microscopy Environment (OME):

Image Informatics for Functional Genomics

Ilya Goldberg

National Institute on Aging
National Institutes of Health

Date: Friday, January 28, 2005
Place: Engineering Sciences Building, Room 2001
Time: 2:00 pm — 3:00 pm (Refreshments served at 1:30 pm)

Abstract:
Imaging has played a key role in biology since Antoni Van Leeuwenhoek used his own microscope to observe cells for the first time over 300 years ago. Today, advances in technology allow us to use imaging in cell-based or high-content assays (HCA) that can generate tens of thousand of images, and allow us to examine the response of a cell or organism when we manipulate each gene in its entire genome one by one. We describe our design and implementation of a data model and software framework for biological imaging called the Open Microscopy Environment (OME, http://www.openmicroscopy.org).OME manages image data as well as descriptions of the imaging experiment including acquisition parameters, annotations and results of image analysis. The OME data model, expressed in XML and realized in a traditional database, is both extensible and self-describing, allowing it to meet emerging imaging needs. To address the challenges posed by HCS experiments specifically, we have developed a general automated image classifier in OME capable of assigning images to classes based on rules automatically inferred from a user-defined set of training images. The classifier uses naïve Bayes networks to recognize relevant image features out of a set of over 400. We demonstrate both the generality and effectiveness of this classifier when used with traditional image acquisition methods as well as with the automated microscopes used in HCS experiments.

ILYA GOLDBERG received his undergraduate education at University of Wisconsin-Madison, receiving a BS in Biochemistry in 1990. He went on to Johns Hopkins University Medical School, receiving a PhD in 1997 in Biochemistry and Cell Biology where he studied the structure of human and primate centromere DNA and the proteins that bind to it. His first post-doctoral position was in crystallography at Harvard studying the structure of human polyoma and papiloma viruses and their mechanisms of infection. In his second post-doc at MIT, he started the Open Microscopy Environment (OME) project. Since his high school years, Dr. Goldberg has been applying computing to study biological problems, but that was the first time he committed himself to this pursuit fully. After MIT, he returned to Baltimore and joined the Laboratory of Genetics at the National Institute on Aging, where he started a group dedicated to quantitative morphology and systematic functional genomics.


Host: B.S. Manjunath, Professor of ECE