Publications
2015
Kreshuk, A, Walecki, R, Köthe, U, Gierthmühlen, M, Plachta, D, Genoud, C, Haastert-Talini, K and Hamprecht, F A (2015).
Automated Tracing of Myelinated Axons and Detection of the Nodes of Ranvier in Serial Images of Peripheral Nerves.
Journal of Microscopy.
259 (2) 143-154
Krasowski, N, Beier, T, Knott, G W, Köthe, U, Hamprecht, F A and Kreshuk, A (2015).
Improving 3D EM Data Segmentation by Joint Optimization over Boundary Evidence and Biological Priors.
12th {IEEE} International Symposium on Biomedical Imaging, {ISBI} 2015, Brooklyn, NY, USA, April 16-19, 2015. 536-539
Technical Report (2.25 MB) 2014
Kröger, T, Kappes, J H, Beier, T, Köthe, U and Hamprecht, F A (2014).
Asymmetric Cuts: Joint Image Labeling and Partitioning.
Pattern Recognition - 36th German Conference, {GCPR} 2014, Münster, Germany, September 2-5, 2014, Proceedings.
http://dx.doi.org/10.1007/978-3-319-11752-2_16 Technical Report (3.46 MB) Beier, T, Kröger, T, Kappes, J H, Köthe, U and Hamprecht, F A (2014).
Cut, Glue and Cut: A Fast, Approximate Solver for Multicut Partitioning.
2014 {IEEE} Conference on Computer Vision and Pattern Recognition, {CVPR} 2014, Columbus, OH, USA, June 23-28, 2014.
http://dx.doi.org/10.1109/CVPR.2014.17 Technical Report (10.06 MB) Kleesiek, J, Biller, A, Urban, G, Köthe, U, Bendszus, M and Hamprecht, F A (2014).
ilastik for Multi-modal Brain Tumor Segmentation.
MICCAI BraTS (Brain Tumor Segmentation) Challenge. Proceedings, 3rdplace. 12-17
Technical Report (405.91 KB) Fiaschi, L, Diego, F, Grosser, K - H, Schiegg, M, Köthe, U, Zlatic, M and Hamprecht, F A (2014).
Tracking indistinguishable translucent objects over time using weakly supervised structured learning.
CVPR. Proceedings. 2736 - 2743
Technical Report (1.47 MB) 2012
Andres, B, Köthe, U, Kröger, T, Helmstaedter, M, Briggmann, K L, Denk, W and Hamprecht, F A (2012).
3D Segmentation of SBFSEM Images of Neuropil by a Graphical Model over Supervoxel Boundaries.
Medical Image Analysis.
16 (2012) 796-805
Technical Report (20.85 MB) Hanselmann, M, Röder, J, Köthe, U, Renard, B Y, Heeren, R M A and Hamprecht, F A (2012).
Active Learning for Convenient Annotation and Classification of Secondary Ion Mass Spectrometry Images.
Analytical Chemistry.
85 (1) 147-155
Technical Report (2.58 MB) Kausler, B X, Schiegg, M, Andres, B, Lindner, M, Köthe, U, Leitte, H, Wittbrodt, J, Hufnagel, L and Hamprecht, F A (2012).
A Discrete Chain Graph Model for 3d+t Cell Tracking with High Misdetection Robustness.
ECCV 2012. Proceedings.
7574 144-157
Technical Report (809.07 KB) Andres, B, Kröger, T, Briggmann, K L, Denk, W, Norogod, N, Knott, G W, Köthe, U and Hamprecht, F A (2012).
Globally Optimal Closed-Surface Segmentation for Connectomics.
ECCV 2012. Proceedings, Part 3. 778-791
Technical Report (2.72 MB) Andres, B, Kappes, J H, Beier, T, Köthe, U and Hamprecht, F A (2012).
The Lazy Flipper: Efficient Depth-Limited Exhaustive Search in Discrete Graphical Models.
Computer Vision - {ECCV} 2012 - 12th European Conference on Computer Vision, Florence, Italy, October 7-13, 2012, Proceedings, Part {VII}.
http://dx.doi.org/10.1007/978-3-642-33786-4_12 Technical Report (446.28 KB) 2011
Kreshuk, A, Straehle, C N, Sommer, C, Köthe, U, Cantoni, M, Knott, G W and Hamprecht, F A (2011).
Automated Detection and Segmentation of Synaptic Contacts in Nearly Isotropic Serial Electron Microscopy Images.
PLoS ONE.
6 (10) Technical Report (290.48 KB) Kreshuk, A, Straehle, C N, Sommer, C, Köthe, U, Knott, G W and Hamprecht, F A (2011).
Automated Segmentation of Synapses in 3D EM Data.
Eighth IEEE International Symposium on Biomedical Imaging (ISBI 2011).
Proceedings. 220-223
Hanselmann, M, Voss, B, Renard, B Y, Lindner, M, Köthe, U, Kirchner, M and Hamprecht, F A (2011).
SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists.
Bioinformatics.
27 (7) 987-993
Technical Report (2.2 MB) 2010
Kirchner, M, Renard, B Y, Köthe, U, Pappin, D J, Hamprecht, F A, Steen, J A J and Steen, H (2010).
Computational Protein Profile Similarity Screening for Quantitative Mass Spectrometry Experiments.
Bioinformatics.
26 (1) 77-83
Technical Report (380.19 KB) Köthe, U, Andres, B, Kröger, T and Hamprecht, F A (2010).
Geometric Analysis of 3D Electron Microscopy Data.
Proceedings of Workshop on Discrete Geometry and Mathematical Morphology (WADGMM). 22-26
Technical Report (1.43 MB) Köthe, U, Andres, B, Kröger, T and Hamprecht, F A (2010).
Geometric Analysis of 3D Electron Microscopy Data.
Proceedings of Workshop on Discrete Geometry and Mathematical Morphology (WADGMM). 22-26
Technical Report (1.43 MB) 2009
Hanselmann, M, Köthe, U, Renard, B Y, Kirchner, M, Heeren, R M A and Hamprecht, F A (2009).
Multivariate Watershed Segmentation of Compositional Data.
Proceedings of the 15th International Conference on Discrete Geometry for Computer Imagery (DGCI), in press. Springer.
5810 180-192
Technical Report (1.25 MB) Andres, B, Köthe, U, Bonea, A, Nadler, B and Hamprecht, F A (2009).
Quantitative Assessment of Image Segmentation Quality by Random Walk Relaxation Times.
Pattern Recognition. 31st DAGM Symposium, Jena, Germany, September 9-11, 2009. Proceedings. Springer.
5748 502-511
Technical Report (3.08 MB) Hanselmann, M, Köthe, U, Kirchner, M, Renard, B Y, Amstalden, E R, Glunde, K, Heeren, R M A and Hamprecht, F A (2009).
Towards Digital Staining using Imaging Mass Spectrometry and Random Forests.
Journal of Proteome Research.
8 3558-3567
Technical Report (1.47 MB) 2008
Andres, B, Kondermann, C, Kondermann, D, Köthe, U, Hamprecht, F A and Garbe, C S (2008).
On errors-in-variables regression with arbitrary covariance and its application to optical flow estimation.
Computer Vision and Pattern Recognition, 2008. CVPR 2008. IEEE Conference on. 1-6
Technical Report (1.58 MB) Andres, B, Köthe, U, Helmstaedter, M, Denk, W and Hamprecht, F A (2008).
Segmentation of SBFSEM Volume Data of Neural Tissue by Hierarchical Classification.
Pattern Recognition. 30th DAGM Symposium Munich, Germany, June 10-13, 2008. Proceedings. Springer.
5096 142-152
Technical Report (1.21 MB)
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