Defining host–pathogen interactions employing an artificial intelligence workflow

Research output: Contribution to journalArticlepeer-review


  • Daniel Fisch
  • Artur Yakimovich
  • Barbara Clough
  • Joseph Wright
  • Monique Bunyan
  • Michael Howell
  • Eva Frickel

Colleges, School and Institutes

External organisations

  • The Francis Crick Institute
  • UCL


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 capacity to learn phenotypes from the data, without relying on researcher-based assumptions. Using Toxoplasma gondii and Salmonella enterica Typhimurium we demonstrate HRMAn’s capacity to recognize, classify and quantify pathogen killing, replication and cellular defense responses. HRMAn thus presents the only intelligent solution operating at human capacity suitable for both single image and high content image analysis.


Original languageEnglish
Article numbere40560
Publication statusPublished - 12 Feb 2019