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Deep learning tool identifies bacteria in micrographs: Omnipose is trained to recognize bacteria of all shapes and sizes in mixed bacterial cultures

Omnipose, a deep learning software, is helping to solve the challenge of identifying varied and miniscule bacteria in microscopy images. It has gone beyond this initial goal to identify several other types of tiny objects in micrographs.

The UW Medicine microbiology lab of Joseph Mougous and the University of Washington physics and bioengineering lab of Paul A. Wiggins tested the tool. It was developed by University of Washington physics graduate student Kevin J. Cutler and his team.

Mougous said that Cutler, as a physics student, “demonstrated an unusual interest in immersing himself in a biology environment so that he could learn first-hand about problems in need of solution in this field. He came over to my lab and quickly found one that he solved in spectacular fashion.”

Their results are reported in the Oct. 17 edition of Nature Methods.

The scientists found that Omnipose, trained on a large database of bacterial images, performed well in characterizing and quantifying the myriad of bacteria in mixed microbial cultures and eliminated some of the errors that can occur in its predecessor, Cellpose.

Moreover, the software wasn’t easily fooled by extreme changes in a cell’s shape due to antibiotic treatment or antagonism by chemicals produced during interbacterial aggression. In fact, the program showed that it could even detect cell intoxication in a trial using E. coli.

In addition, Omnipose did well in overcoming recognition problems due to differences in the optical characteristics across diverse bacteria.

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