Navigation Links
Carnegie Mellon technique accelerates biological image analysis
Date:5/1/2008

PITTSBURGHResearchers in Carnegie Mellon Universitys Lane Center for Computational Biology have discovered how to significantly speed up critical steps in an automated method for analyzing cell cultures and other biological specimens.

The new technique, published online in the Journal of Machine Learning Research, http://jmlr.csail.mit.edu/, promises to enable higher accuracy analysis of the microscopic images produced by todays high-throughput biological screening methods, such as the ones used in drug discovery, and to help decipher the complex structure of human tissues.

Improved accuracy could reduce the cost and the time necessary for these screening methods, make possible new types of experiments that previously would have required an infeasible amount of resources, and perhaps uncover interesting but subtle anomalies that otherwise would go undetected, the researchers said.

The technique also will be applicable in fields beyond biology because it improves the efficiency of the belief propagation algorithm, a widely used method for drawing conclusions about interconnected networks.

Current automated screening systems for examining cell cultures look at individual cells and do not fully consider the relationships between neighboring cells, said Geoffrey Gordon, associate research professor in the School of Computer Sciences Machine Learning Department. This is in large part because simultaneously examining many cells with existing methods requires impractical amounts of computational time.

In many cases, computer vision systems have been shown to distinguish patterns that are difficult for humans to detect, he added. However, even automated systems may confuse two similar patterns, and the confusion may be resolvable by considering neighboring cells.

Gordon and his fellow authors, biomedical engineering student Shann-Ching Sam Chen and computational biologist Robert F. Murphy, were able to expand their focus from single to multiple cells by increasing the efficiency of the belief propagation algorithm. The algorithm has become a workhorse for researchers because it enables a computer to make inferences about a set of data by drawing on multiple sources of information. In the case of biological specimens, for instance, it can be used to infer which parts of the image are individual cells or to determine whether the distributions of particular proteins within each cell are abnormal.

But as the number of variables increase, the belief propagation algorithm can grow unwieldy and require an impractical amount of computing time to solve these problems.

The belief propagation algorithm assumes that neighbors whether they are cells, or bits of text have effects on each other. So the algorithm represents each piece of evidence used to make inferences as a node in an interconnected network, and exchanges messages between nodes. The Carnegie Mellon researchers found shortcuts for generating these messages, which significantly improved the speed of the entire network.

Murphy, director of the Lane Center for Computational Biology, said this technique could improve the performance of belief propagation algorithms in many applications, including text analysis, Web analysis and medical diagnosis. For this paper, the researchers applied their techniques to analysis of protein patterns within HeLa cells. They found the technique speeded analysis by several orders of magnitude.

In high-throughput screening processes used for drug discovery and other research, tens of thousands of wells each containing tens or hundreds of cells need to be analyzed each day, Murphy said. Automated analysis of the cellular relationships within so many wells would be impossible without the sort of speedups achieved in the new study, he added.


'/>"/>

Contact: Byron Spice
bspice@cs.cmu.edu
412-268-9068
Carnegie Mellon University
Source:Eurekalert

Related medicine news :

1. Teams From Carnegie Mellon, Yale, Manitoba Win Tepper Schools 2008 McGinnis Venture Competition
2. Carnegie Mellons Tepper School of Business to Host 2008 Cornerstones Symposium on Building City of the Future, March 25
3. ANSYS Sponsors Dinosaurs Exhibit at Carnegie Museum of Natural History
4. Carnegie Mellon study shows just listening to cell phones significantly impairs drivers
5. NSF awards Carnegie Mellons Jacobo Bielak
6. Carnegie Mellon study identifies where thoughts of familiar objects occur inside the human brain
7. SuperArray Bioscience Corporation Licenses RNA Interference Patent From The Carnegie Institution
8. Carnegie Mellon algorithm identifies top 100 blogs for news
9. Carnegie Mellon neuroscientist proposes new theory of brain flexibility
10. Carnegie Mellon Establishes Ray and Stephanie Lane Center for Computational Biology
11. The Bank of New York Mellon Recognized as Change Agent Shaping the Direction of Healthcare Transaction Processing
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:6/25/2016)... ... June 25, 2016 , ... "With 30 hand-drawn hand gesture animations, FCPX ... Austin - CEO of Pixel Film Studios. , ProHand Cartoon’s package transforms over ... Cut Pro X . Simply select a ProHand generator and drag it above media ...
(Date:6/25/2016)... ... June 25, 2016 , ... Conventional wisdom preaches the benefits of moderation, ... the latter, setting the bar too high can result in disappointment, perhaps even self-loathing. ... toward their goal. , Research from PsychTests.com reveals that behind the ...
(Date:6/24/2016)... ... June 24, 2016 , ... The Pulmonary Hypertension Association ... it will receive two significant new grants to support its work to advance ... 25th anniversary by recognizing patients, medical professionals and scientists for their work in ...
(Date:6/24/2016)... ... June 24, 2016 , ... People across the U.S. are sharpening their pencils ... an essay contest in which patients and their families pay tribute to a genetic ... 2016 National Society of Genetic Counselors (NSGC) Annual Education Conference (AEC) this September. ...
(Date:6/24/2016)... , ... June 24, 2016 , ... National recruitment firm ... life sciences executive with extensive sequencing and genomics experience, as Vice President of North ... Ms. Hill will be responsible for leading the sales team in the commercialization of ...
Breaking Medicine News(10 mins):
(Date:6/24/2016)... , June 24, 2016 Dehaier Medical Systems ... "Company"), which develops, markets and sells medical devices and ... , signed a strategic cooperation agreement with Hongyuan Supply ... Supply Chain") on June 20, 2016, to develop Dehaier,s ... strategic cooperation agreement, Dehaier will leverage Hongyuan Supply Chain,s ...
(Date:6/24/2016)... , June 24, 2016   Pulmatrix, Inc ., ... developing innovative inhaled drugs, announced today that it was ... Investments reconstituted its comprehensive set of U.S. and ... "This is an important milestone for Pulmatrix," said Chief ... shareholder awareness of our progress in developing drugs for ...
(Date:6/23/2016)... Research and Markets has announced the addition of ... report to their offering. ... kidney failure, it replaces the function of kidneys by removing ... thus the treatment helps to keep the patient body,s electrolytes ... Increasing number of ESRD patients & substantial healthcare expenditure ...
Breaking Medicine Technology: