title: Prospective identification of hematopoietic lineage choice by deep learning.
abstract: Differentiation alters molecular properties of stem and progenitor cells, leading to changes in their shape and movement characteristics. We present a deep neural network that prospectively predicts lineage choice in differentiating primary hematopoietic progenitors using image patches from brightfield microscopy and cellular movement. Surprisingly, lineage choice can be detected up to three generations before conventional molecular markers are observable. Our approach allows identification of cells with differentially expressed lineage-specifying genes without molecular labeling.
authors.affiliation: Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
authors.forename: Felix
authors.initials: F
authors.lastname: Buggenthin
authors.affiliation: Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.|European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK.
authors.forename: Florian
authors.initials: F
authors.lastname: Buettner
authors.affiliation: Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, 4058 Basel, Switzerland.|Research Unit Stem Cell Dynamics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
authors.forename: Philipp S
authors.initials: PS
authors.lastname: Hoppe
authors.affiliation: Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, 4058 Basel, Switzerland.
authors.forename: Max
authors.initials: M
authors.lastname: Endele
authors.affiliation: Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.|Department of Mathematics, Technische Universität München, 85748 Garching, Germany.
authors.forename: Manuel
authors.initials: M
authors.lastname: Kroiss
authors.affiliation: Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Strasser
authors.affiliation: Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Schwarzfischer
authors.affiliation: Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, 4058 Basel, Switzerland.|Research Unit Stem Cell Dynamics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
authors.forename: Dirk
authors.initials: D
authors.lastname: Loeffler
authors.affiliation: Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, 4058 Basel, Switzerland.|Research Unit Stem Cell Dynamics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
authors.forename: Konstantinos D
authors.initials: KD
authors.lastname: Kokkaliaris
authors.affiliation: Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, 4058 Basel, Switzerland.|Research Unit Stem Cell Dynamics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Hilsenbeck
authors.affiliation: Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, 4058 Basel, Switzerland.|Research Unit Stem Cell Dynamics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
authors.forename: Timm
authors.initials: T
authors.lastname: Schroeder
authors.affiliation: Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.|Department of Mathematics, Technische Universität München, 85748 Garching, Germany.
authors.forename: Fabian J
authors.initials: FJ
authors.lastname: Theis
authors.affiliation: Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
authors.forename: Carsten
authors.initials: C
authors.lastname: Marr
mesh_terms: D000818:Animals; D019540:Area Under Curve; D015415:Biomarkers / Q000378:metabolism; D002454:Cell Differentiation; D019070:Cell Lineage; D055879:Gene Knock-In Techniques; D006412:Hematopoietic Stem Cells / Q000166:cytology* / Q000502:physiology*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D000069550:Machine Learning; D008297:Male; D008817:Mice, Mutant Strains; D016571:Neural Networks, Computer; D011518:Proto-Oncogene Proteins / Q000235:genetics / Q000378:metabolism; D059008:Time-Lapse Imaging / Q000379:methods*; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism; D000099232:Proto-Oncogene Protein Spi-1
chemical_list: D015415:Biomarkers; D011518:Proto-Oncogene Proteins; D015534:Trans-Activators; D000099232:Proto-Oncogene Protein Spi-1