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SUMMARY:The Open Microscopy Environment Analysis System: Workflow Composit
 ion and Enactment for Quantitative Pattern Analysis of Large Microscopy Da
 tasets - Tom Macura\, Computer Laboratory\, University of Cambridge
DTSTART:20080205T143000Z
DTEND:20080205T153000Z
UID:TALK9599@talks.cam.ac.uk
CONTACT:Minor Gordon
DESCRIPTION:\nThe Open Microscopy Environment (OME) Analysis System is sof
 tware that supports modelling and enacting workflows for the quantitative 
 analysis of microscopy images. This system is based on OME – an extensib
 le infrastructure with plug-in ontologies for managing large sets of biolo
 gical images and data. Integrated into the analysis system is a multi-purp
 ose image classifier for scoring high content screens (HCS) and other high
  throughput imaging applications. The image classification workflow is com
 posed of 53 nodes with 189 links that output 1025 numerical values modeled
  as 48 ontological terms.  Nodes are MATLAB scripts\, with unaltered sourc
 e code\, around which XML execution instructions wrappers have been writte
 n to incorporate the scripts into OME. Users can convert their legacy imag
 e analysis tools into OME workflows or customize the integrated image clas
 sification workflow to suit their task-specific needs.\n \nThe OME Analysi
 s System has been validated on an example high content\, high throughput e
 xperiment called the Atlas of Gene Expression in Mouse Aging Project (AGEM
 AP). The AGEMAP dataset is ~30\,000 microscope images of mouse livers\, sk
 eletal muscles\, and kidney tubules. Beginning with 18GB of raw pixels\, i
 t took the OME approximately 2000 processor hours (luckily\, OME supports 
 distributed computation) to generate 125GB of intermediary pixels and extr
 act 90 million image descriptor features used for classification.\n \nIn t
 his presentation I will briefly introduce high content\, high throughput b
 iological imaging\, describe the design and development of OME as well its
  validation (including performance) on AGEMAP\, and conclude by mentioning
  some of the biological insights we learned about aging from the AGEMAP an
 alysis.
LOCATION:Room FW11\, Computer Laboratory\, William Gates Building
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