Segmenting and Tracking Multiple Dividing Targets Using ilastik

  • Carsten Haubold
  • Martin Schiegg
  • Anna Kreshuk
  • Stuart Berg
  • Ullrich Koethe
  • Fred A. Hamprecht
Part of the Advances in Anatomy, Embryology and Cell Biology book series (ADVSANAT, volume 219)


Tracking crowded cells or other targets in biology is often a challenging task due to poor signal-to-noise ratio, mutual occlusion, large displacements, little discernibility, and the ability of cells to divide. We here present an open source implementation of conservation tracking (Schiegg et al., IEEE international conference on computer vision (ICCV). IEEE, New York, pp 2928–2935, 2013) in the ilastik software framework. This robust tracking-by-assignment algorithm explicitly makes allowance for false positive detections, undersegmentation, and cell division. We give an overview over the underlying algorithm and parameters, and explain the use for a light sheet microscopy sequence of a Drosophila embryo. Equipped with this knowledge, users will be able to track targets of interest in their own data.


Tracking Algorithm Tracking Result Division Classifier Tracking Optimization Probable Configuration 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We thank all ilastik developers for providing this open source software: Bernhard Kausler, Thorben Kroeger, Christoph Sommer, Christoph Straehle, Markus Doering, Kemal Eren, Burcin Erocal, Luca Fiaschi, Ben Heuer, Philipp Hanslovsky, Kai Karius, Jens Kleesiek, Markus Nullmeier, Oliver Petra, Buote Xu, and Chong Zhang.

Partial financial support by the HGS MathComp Graduate School, the SFB 1129 for integrative analysis of pathogen replication and spread, the RTG 1653 for probabilistic graphical models, and the CellNetworks Excellence Cluster/EcTop is gratefully acknowledged.


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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Carsten Haubold
    • 1
  • Martin Schiegg
    • 1
  • Anna Kreshuk
    • 1
  • Stuart Berg
    • 2
  • Ullrich Koethe
    • 1
  • Fred A. Hamprecht
    • 1
  1. 1.University of Heidelberg, IWR/HCIHeidelbergGermany
  2. 2.Howard Hughes Medical InstituteAshburnUSA

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