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An Artificial Intelligence Workflow for Defining Host-Pathogen Interactions

By Daniel H Fisch, Artur Yakimovich, Barbara Clough, Joseph Wright, Monique Bunyan, Michael Howell, Jason Mercer, Eva-Maria Frickel

Posted 05 Sep 2018
bioRxiv DOI: 10.1101/408450 (published DOI: 10.7554/eLife.40560)

For image-based infection biology, accurate unbiased quantification of host-pathogen interactions is essential, yet often performed manually or using limited enumeration employing simple image analysis algorithms based on image segmentation. Host protein recruitment to pathogens is often refractory to accurate automated assessment due to its heterogeneous nature. An intuitive intelligent image analysis program to assess host protein recruitment within general cellular pathogen defense is lacking. We present HRMAn (Host Response to Microbe Analysis), an open-source image analysis platform based on machine learning algorithms and deep learning. We show that HRMAn has the capability to learn phenotypes from the data, without relying on researcher-based assumptions. Using Toxoplasma gondii and Salmonella typhimurium we demonstrate HRMAn's capacity to recognize, classify and quantify pathogen killing, replication and cellular defense responses.

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