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- Björn Andres, Thorben Kröger, +5 authors Fred A. Hamprecht
- ECCV
- 2012

We address the problem of partitioning a volume image into a previously unknown number of segments, based on a likelihood of merging adjacent supervoxels. Towards this goal, we adapt a higher-order probabilistic graphical model that makes the duality between supervoxels and their joint faces explicit and ensures that merging decisions are consistent and… (More)

- Jörg H. Kappes, Björn Andres, +10 authors Carsten Rother
- International Journal of Computer Vision
- 2015

Szeliski et al. published an influential study in 2006 on energy minimization methods for Markov random fields. This study provided valuable insights in choosing the best optimization technique for certain classes of problems. While these insights remain generally useful today, the phenomenal success of random field models means that the kinds of inference… (More)

- Björn Andres, Ullrich Köthe, Thorben Kröger, Fred A. Hamprecht
- ArXiv
- 2010

Multi-dimensional arrays are among the most fundamental and most useful data structures of all. In C++, excellent template libraries exist for arrays whose dimension is fixed at runtime. Arrays whose dimension can change at runtime have been implemented in C. However, a generic object-oriented C++ implementation of runtime-flexible arrays has so far been… (More)

- Björn Andres, Ullrich Köthe, +4 authors Fred A. Hamprecht
- Medical Image Analysis
- 2012

The segmentation of large volume images of neuropil acquired by serial sectioning electron microscopy is an important step toward the 3D reconstruction of neural circuits. The only cue provided by the data at hand is boundaries between otherwise indistinguishable objects. This indistinguishability, combined with the boundaries becoming very thin or faint in… (More)

Recently, unsupervised image segmentation has become increasingly popular. Starting from a superpixel segmentation, an edge-weighted region adjacency graph is constructed. Amongst all segmentations of the graph, the one which best conforms to the given image evidence, as measured by the sum of cut edge weights, is chosen. Since this problem is NP-hard, we… (More)

- Thorben Kröger, Shawn Mikula, Winfried Denk, Ullrich Köthe, Fred A. Hamprecht
- MICCAI
- 2013

Segmentation schemes such as hierarchical region merging or correllation clustering rely on edge weights between adjacent (super-)voxels. The quality of these edge weights directly affects the quality of the resulting segmentations. Unstructured learning methods seek to minimize the classification error on individual edges. This ignores that a few local… (More)

- Thorsten Beier, Thorben Kroeger, Jorg H. Kappes, Ullrich Kothe, Fred A. Hamprecht
- 2014 IEEE Conference on Computer Vision and…
- 2014

Recently, unsupervised image segmentation has become increasingly popular. Starting from a superpixel segmentation, an edge-weighted region adjacency graph is constructed. Amongst all segmentations of the graph, the one which best conforms to the given image evidence, as measured by the sum of cut edge weights, is chosen. Since this problem is NP-hard, we… (More)

For image segmentation, recent advances in optimization make it possible to combine noisy region appearance terms with pairwise terms which can not only discourage, but also encourage label transitions, depending on boundary evidence. These models have the potential to overcome problems such as the shrinking bias. However, with the ability to encourage… (More)

- Björn Andres, Ullrich Köthe, Thorben Kröger, Fred A. Hamprecht
- ArXiv
- 2010

Segmentation is often an essential intermediate step in image analysis. A volume segmentation characterizes the underlying volume image in terms of geometric information–segments, faces between segments, curves in which several faces meet–as well as a topology on these objects. Existing algorithms encode this information in designated data structures, but… (More)

- F. Boray Tek, Thorben Kröger, Shawn Mikula, Fred A. Hamprecht
- ISBI
- 2014

Volumetric electron microscopy techniques, such as serial block-face electron microscopy (SBEM), generate massive amounts of image data that are used for reconstructing neural circuits. Typically, this requires time-intensive manual annotation of cells and their connections. To facilitate this analysis, we study the problem of automated detection of cell… (More)