title: Graphical model for joint segmentation and tracking of multiple dividing cells.
abstract: BACKGROUND
  To gain fundamental insight into the development of embryos, biologists seek to understand the fate of each and every embryonic cell. For the generation of cell tracks in embryogenesis, so-called tracking-by-assignment methods are flexible approaches. However, as every two-stage approach, they suffer from irrevocable errors propagated from the first stage to the second stage, here from segmentation to tracking. It is therefore desirable to model segmentation and tracking in a joint holistic assignment framework allowing the two stages to maximally benefit from each other.
  
  
  RESULTS
  We propose a probabilistic graphical model, which both automatically selects the best segments from a time series of oversegmented images/volumes and links them across time. This is realized by introducing intra-frame and inter-frame constraints between conflicting segmentation and tracking hypotheses while at the same time allowing for cell division. We show the efficiency of our algorithm on a challenging 3D+t cell tracking dataset from Drosophila embryogenesis and on a 2D+t dataset of proliferating cells in a dense population with frequent overlaps. On the latter, we achieve results significantly better than state-of-the-art tracking methods.
  
  
  METHODS
  Source code and the 3D+t Drosophila dataset along with our manual annotations will be freely available on http://hci.iwr.uni-heidelberg.de/MIP/Research/tracking/
authors.affiliation: University of Heidelberg, IWR/HCI, 69115 Heidelberg, Germany and European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Schiegg
authors.affiliation: University of Heidelberg, IWR/HCI, 69115 Heidelberg, Germany and European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany.
authors.forename: Philipp
authors.initials: P
authors.lastname: Hanslovsky
authors.affiliation: University of Heidelberg, IWR/HCI, 69115 Heidelberg, Germany and European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany.
authors.forename: Carsten
authors.initials: C
authors.lastname: Haubold
authors.affiliation: University of Heidelberg, IWR/HCI, 69115 Heidelberg, Germany and European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany.
authors.forename: Ullrich
authors.initials: U
authors.lastname: Koethe
authors.affiliation: University of Heidelberg, IWR/HCI, 69115 Heidelberg, Germany and European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany.
authors.forename: Lars
authors.initials: L
authors.lastname: Hufnagel
authors.affiliation: University of Heidelberg, IWR/HCI, 69115 Heidelberg, Germany and European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany.
authors.forename: Fred A
authors.initials: FA
authors.lastname: Hamprecht
mesh_terms: D000465:Algorithms; D000818:Animals; D002455:Cell Division; D002467:Cell Nucleus; D004330:Drosophila / Q000166:cytology* / Q000196:embryology; D004625:Embryo, Nonmammalian / Q000648:ultrastructure*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D015233:Models, Statistical