Interactive phenotyping of large-scale histology imaging data with HistomicsML

Michael Nalisnik, Mohamed Amgad, Sanghoon Lee*, Sameer H. Halani, Jose Velazquez Vega, Daniel J. Brat, David A. Gutman, Lee A.D. Cooper

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Whole-slide imaging of histologic sections captures tissue microenvironments and cytologic details in expansive high-resolution images. These images can be mined to extract quantitative features that describe histologic elements, yielding measurements for hundreds of millions of objects. A central challenge in utilizing this data is enabling investigators to train and evaluate classification rules for identifying objects related to processes like angiogenesis or immune response. Here we present HistomicsML, an interactive machine-learning framework for large whole-slide imaging data. HistomicsML uses active learning direct user feedback, making classifier training efficient and scalable in datasets containing 108+ histologic objects. We demonstrate how HistomicsML can be used to phenotype microvascular structures in gliomas to predict survival, and to explore the molecular pathways associated with these phenotypes. Our approach enables researchers to unlock phenotypic information from digital pathology datasets to investigate prognostic image biomarkers and genotype-phenotype associations.

Original languageEnglish (US)
JournalUnknown Journal
StatePublished - May 19 2017
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Immunology and Microbiology(all)
  • Neuroscience(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

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