Geometric analysis of 3D electron microscopy data

Abstract

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. © 2012 Springer-Verlag.