Geometric Analysis of 3D Electron Microscopy Data

  • Ullrich Köthe
  • Björn Andres
  • Thorben Kröger
  • Fred Hamprecht
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7346)


We present a complete pipeline for the segmentation of 3-dimensional electron microscopy data. Efficient algorithms and parallelization have been developed to make the system applicable to data as large as eight gigavoxels. Discrete geometry plays a prominent role at several processing stages (initial watershed segmentation, cell complex representation, reduction of oversegmentation by a graphical model, topological and geometric feature computation). Many modules described here are available via our open-source software repository.


Random Forest Graphical Model Cell Complex Geometric Analysis Topological Grid 
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.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Ullrich Köthe
    • 1
  • Björn Andres
    • 1
  • Thorben Kröger
    • 1
  • Fred Hamprecht
    • 1
  1. 1.Multidimensional Image Processing GroupUniversity of HeidelbergGermany

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