, Volume 9, Issue 2–3, pp 279–302 | Cite as

Automated Reconstruction of Dendritic and Axonal Trees by Global Optimization with Geometric Priors

  • Engin Türetken
  • Germán González
  • Christian Blum
  • Pascal Fua
Original Article


We present a novel probabilistic approach to fully automated delineation of tree structures in noisy 2D images and 3D image stacks. Unlike earlier methods that rely mostly on local evidence, ours builds a set of candidate trees over many different subsets of points likely to belong to the optimal tree and then chooses the best one according to a global objective function that combines image evidence with geometric priors. Since the best tree does not necessarily span all the points, the algorithm is able to eliminate false detections while retaining the correct tree topology. Manually annotated brightfield micrographs, retinal scans and the DIADEM challenge datasets are used to evaluate the performance of our method. We used the DIADEM metric to quantitatively evaluate the topological accuracy of the reconstructions and showed that the use of the geometric regularization yields a substantial improvement.


DIADEM Tree reconstruction Global optimization Minimum arborescence k-MST Ant colony optimization 



This work was supported in part by the Swiss National Science Foundation and in part by the MicroNano ERC project. Christian Blum also acknowledges support from the Ramón y Cajal program of the Spanish Government.

We would like to thank Felix Schürmann for his advice and for giving us access to the brightfield dataset and corresponding ground-truth.


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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Engin Türetken
    • 1
  • Germán González
    • 1
  • Christian Blum
    • 2
  • Pascal Fua
    • 1
  1. 1.Computer Vision Laboratory, Faculté Informatique et CommunicationsÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
  2. 2.ALBCOM, Dept. Llenguatges i Sistemes InformàticsUniversitat Politècnica de CatalunyaBarcelonaSpain

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