Reconstructing cell cycle and disease progression using deep learning

Philipp Eulenberg, Niklas Köhler, Thomas Blasi, Andrew Filby, Anne E. Carpenter, Paul Rees, Fabian J. Theis, F. Alexander Wolf

Research output: Contribution to journalArticle

75 Scopus citations

Abstract

We show that deep convolutional neural networks combined with nonlinear dimension reduction enable reconstructing biological processes based on raw image data. We demonstrate this by reconstructing the cell cycle of Jurkat cells and disease progression in diabetic retinopathy. In further analysis of Jurkat cells, we detect and separate a subpopulation of dead cells in an unsupervised manner and, in classifying discrete cell cycle stages, we reach a sixfold reduction in error rate compared to a recent approach based on boosting on image features. In contrast to previous methods, deep learning based predictions are fast enough for on-the-fly analysis in an imaging flow cytometer.

Original languageEnglish (US)
Article number463
JournalNature Communications
Volume8
Issue number1
DOIs
StatePublished - Dec 1 2017

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

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