Deepometry, a framework for applying supervised and weakly supervised deep learning to imaging cytometry

Minh Doan, Claire Barnes, Claire McQuin, Juan C. Caicedo, Allen Goodman, Anne E. Carpenter, Paul Rees

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


Deep learning offers the potential to extract more than meets the eye from images captured by imaging flow cytometry. This protocol describes the application of deep learning to single-cell images to perform supervised cell classification and weakly supervised learning, using example data from an experiment exploring red blood cell morphology. We describe how to acquire and transform suitable input data as well as the steps required for deep learning training and inference using an open-source web-based application. All steps of the protocol are provided as open-source Python as well as MATLAB runtime scripts, through both command-line and graphic user interfaces. The protocol enables a flexible and friendly environment for morphological phenotyping using supervised and weakly supervised learning and the subsequent exploration of the deep learning features using multi-dimensional visualization tools. The protocol requires 40 h when training from scratch and 1 h when using a pre-trained model.

Original languageEnglish (US)
Pages (from-to)3572-3595
Number of pages24
JournalNature Protocols
Issue number7
StatePublished - Jul 2021


  • Deep Learning
  • Image Cytometry/methods
  • Software
  • Supervised Machine Learning
  • User-Computer Interface

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)


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