Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Carnegie Mellon technique accelerates biological image analysis

05.05.2008
Will improve automated high-throughput screening techniques

Researchers in Carnegie Mellon University’s 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, promises to enable higher accuracy analysis of the microscopic images produced by today’s 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.

... more about:
»Analysis »Screening »algorithm »propagation

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 Science’s 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.

Byron Spice | EurekAlert!
Further information:
http://jmlr.csail.mit.edu
http://lane.compbio.cmu.edu
http://www.cmu.edu

Further reports about: Analysis Screening algorithm propagation

More articles from Life Sciences:

nachricht Ambush in a petri dish
24.11.2017 | Friedrich-Schiller-Universität Jena

nachricht Meadows beat out shrubs when it comes to storing carbon
23.11.2017 | Norwegian University of Science and Technology

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: New proton record: Researchers measure magnetic moment with greatest possible precision

High-precision measurement of the g-factor eleven times more precise than before / Results indicate a strong similarity between protons and antiprotons

The magnetic moment of an individual proton is inconceivably small, but can still be quantified. The basis for undertaking this measurement was laid over ten...

Im Focus: Frictional Heat Powers Hydrothermal Activity on Enceladus

Computer simulation shows how the icy moon heats water in a porous rock core

Heat from the friction of rocks caused by tidal forces could be the “engine” for the hydrothermal activity on Saturn's moon Enceladus. This presupposes that...

Im Focus: Nanoparticles help with malaria diagnosis – new rapid test in development

The WHO reports an estimated 429,000 malaria deaths each year. The disease mostly affects tropical and subtropical regions and in particular the African continent. The Fraunhofer Institute for Silicate Research ISC teamed up with the Fraunhofer Institute for Molecular Biology and Applied Ecology IME and the Institute of Tropical Medicine at the University of Tübingen for a new test method to detect malaria parasites in blood. The idea of the research project “NanoFRET” is to develop a highly sensitive and reliable rapid diagnostic test so that patient treatment can begin as early as possible.

Malaria is caused by parasites transmitted by mosquito bite. The most dangerous form of malaria is malaria tropica. Left untreated, it is fatal in most cases....

Im Focus: A “cosmic snake” reveals the structure of remote galaxies

The formation of stars in distant galaxies is still largely unexplored. For the first time, astron-omers at the University of Geneva have now been able to closely observe a star system six billion light-years away. In doing so, they are confirming earlier simulations made by the University of Zurich. One special effect is made possible by the multiple reflections of images that run through the cosmos like a snake.

Today, astronomers have a pretty accurate idea of how stars were formed in the recent cosmic past. But do these laws also apply to older galaxies? For around a...

Im Focus: Visual intelligence is not the same as IQ

Just because someone is smart and well-motivated doesn't mean he or she can learn the visual skills needed to excel at tasks like matching fingerprints, interpreting medical X-rays, keeping track of aircraft on radar displays or forensic face matching.

That is the implication of a new study which shows for the first time that there is a broad range of differences in people's visual ability and that these...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Ecology Across Borders: International conference brings together 1,500 ecologists

15.11.2017 | Event News

Road into laboratory: Users discuss biaxial fatigue-testing for car and truck wheel

15.11.2017 | Event News

#Berlin5GWeek: The right network for Industry 4.0

30.10.2017 | Event News

 
Latest News

IceCube experiment finds Earth can block high-energy particles from nuclear reactions

24.11.2017 | Physics and Astronomy

A 'half-hearted' solution to one-sided heart failure

24.11.2017 | Health and Medicine

Heidelberg Researchers Study Unique Underwater Stalactites

24.11.2017 | Earth Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>