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Nat Commun DOI:10.1038/s41467-017-00623-3

Reconstructing cell cycle and disease progression using deep learning.

Publication TypeJournal Article
Year of Publication2017
AuthorsEulenberg, P, Köhler, N, Blasi, T, Filby, A, Carpenter, AE, Rees, P, Theis, FJ, F Wolf, A
JournalNat Commun
Volume8
Issue1
Pages463
Date Published2017 09 06
ISSN2041-1723
KeywordsCell Cycle, Cell Division, Computer Simulation, Diabetic Retinopathy, Disease Progression, DNA, Flow Cytometry, Humans, Jurkat Cells, Machine Learning, Mitosis, Neural Networks (Computer), Reproducibility of Results
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.The interpretation of information-rich, high-throughput single-cell data is a challenge requiring sophisticated computational tools. Here the authors demonstrate a deep convolutional neural network that can classify cell cycle status on-the-fly.

DOI10.1038/s41467-017-00623-3
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/28878212?dopt=Abstract

Alternate JournalNat Commun
PubMed ID28878212
PubMed Central IDPMC5587733