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2012
L. Fiaschi, Nair, R., Köthe, U., and Hamprecht, F. A., “Learning to Count with Regression Forest and Structured Labels”, ICPR 2012. Proceedings, pp. 2685-2688, 2012.PDF icon Technical Report (3.66 MB)
X. Lou, Fiaschi, L., Köthe, U., and Hamprecht, F. A., “Quality Classification of Microscopic Imagery with Weakly Supervised Learning”, MICCAI-MLMI. Proceedings, pp. 176-183, 2012.PDF icon Technical Report (4.15 MB)
C. N. Straehle, Köthe, U., Briggman, K., Denk, W., and Hamprecht, F. A., “Seeded watershed cut uncertainty estimators for guided interactive segmentation”, in CVPR 2012. Proceedings, 2012, pp. 765 - 772.PDF icon Technical Report (2.84 MB)
2011
A. Kreshuk, Straehle, C. N., Sommer, C., Köthe, U., Cantoni, M., Knott, G. W., and Hamprecht, F. A., “Automated Detection and Segmentation of Synaptic Contacts in Nearly Isotropic Serial Electron Microscopy Images”, PLoS ONE, vol. 6 (10), 2011.PDF icon Technical Report (290.48 KB)
A. Kreshuk, Straehle, C. N., Sommer, C., Köthe, U., Knott, G. W., and Hamprecht, F. A., “Automated Segmentation of Synapses in 3D EM Data”, in Eighth IEEE International Symposium on Biomedical Imaging (ISBI 2011). Proceedings, 2011, pp. 220-223.
C. N. Straehle, Köthe, U., Knott, G. W., and Hamprecht, F. A., “Carving: Scalable Interactive Segmentation of Neural Volume Electron Microscopy Images”, in MICCAI 2011, Proceedings., 2011, vol. 6891, pp. 653-660.PDF icon Technical Report (1.69 MB)
X. Lou, Kaster, F. O., Lindner, M., Kausler, B. X., Köthe, U., Höckendorf, B., Wittbrodt, J., Jänicke, H., and Hamprecht, F. A., “DELTR: Digital Embryo Lineage Tree Reconstructor”, in Eighth IEEE International Symposium on Biomedical Imaging (ISBI). Proceedings, 2011, pp. 1557-1560.PDF icon Technical Report (1.44 MB)
C. Sommer, Straehle, C. N., Köthe, U., and Hamprecht, F. A., “ilastik: Interactive Learning and Segmentation Toolkit”, in Eighth IEEE International Symposium on Biomedical Imaging (ISBI 2011).Proceedings, 2011, pp. 230-233.
B. H. Menze, Kelm, B. Michael, Splitthoff, N., Köthe, U., and Hamprecht, F. A., “On oblique random forests”, in European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases 2011. Proceedings., 2011, pp. 453-469.PDF icon Technical Report (665.33 KB)
B. Andres, Kappes, J. H., Beier, T., Köthe, U., and Hamprecht, F. A., “Probabilistic Image Segmentation with Closedness Constraints”, in Proceedings of ICCV, 2011.PDF icon Technical Report (2.95 MB)
B. Andres, Kappes, J. H., Beier, T., Köthe, U., and Hamprecht, F. A., “Probabilistic Image Segmentation with Closedness Constraints”, in Proceedings of ICCV, 2011.
B. Andres, Kappes, J. H., Beier, T., Köthe, U., and Hamprecht, F. A., “Probabilistic Image Segmentation with Closedness Constraints”, in ICCV, Proceedings, 2011, pp. 2611 - 2618.PDF icon Technical Report (8.18 MB)
M. Hanselmann, Voss, B., Renard, B. Y., Lindner, M., Köthe, U., Kirchner, M., and Hamprecht, F. A., “SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists”, Bioinformatics, vol. 27 (7), pp. 987-993, 2011.PDF icon Technical Report (2.2 MB)
2010
M. Kirchner, Renard, B. Y., Köthe, U., Pappin, D. J., Hamprecht, F. A., Steen, J. A. J., and Steen, H., “Computational Protein Profile Similarity Screening for Quantitative Mass Spectrometry Experiments”, Bioinformatics, vol. 26 (1), pp. 77-83, 2010.PDF icon Technical Report (380.19 KB)
X. Lou, Kirchner, M., Renard, B. Y., Köthe, U., Graf, C., Lee, C., Steen, J. A. J., Steen, H., Mayer, M. P., and Hamprecht, F. A., “Deuteration Distribution Estimation with Improved Sequence Coverage for HX/MS Experiments”, Bioinformatics, vol. 26(12), pp. 1535-1541, 2010.PDF icon Technical Report (518.01 KB)
B. Andres, Kappes, J. H., Köthe, U., Schnörr, C., and Hamprecht, F. A., “An Empirical Comparison of Inference Algorithms for Graphical Models with Higher Order Factors Using OpenGM”, in Pattern Recognition, Proc.~32th DAGM Symposium, 2010.PDF icon Technical Report (218.43 KB)
B. Andres, Kappes, J. H., Köthe, U., Schnörr, C., and Hamprecht, F. A., “An Empirical Comparison of Inference Algorithms for Graphical Models with Higher Order Factors Using OpenGM”, in Pattern Recognition, Proc.~32th DAGM Symposium, 2010, pp. 353-362.
U. Köthe, Andres, B., Kröger, T., and Hamprecht, F. A., “Geometric Analysis of 3D Electron Microscopy Data”, in Proceedings of Workshop on Discrete Geometry and Mathematical Morphology (WADGMM), 2010, pp. 22-26.PDF icon Technical Report (1.43 MB)
U. Köthe, Andres, B., Kröger, T., and Hamprecht, F. A., “Geometric Analysis of 3D Electron Microscopy Data”, in Proceedings of Workshop on Discrete Geometry and Mathematical Morphology (WADGMM), 2010, pp. 22-26.PDF icon Technical Report (1.43 MB)
B. Andres, Köthe, U., Kröger, T., and Hamprecht, F. A., “How to Extract the Geometry and Topology from Very Large 3D Segmentations”, ArXiv e-prints, 2010.PDF icon Technical Report (1.44 MB)
B. Andres, Kappes, J. H., Köthe, U., and Hamprecht, F. A., “The Lazy Flipper: MAP Inference in Higher-Order Graphical Models by Depth-limited Exhaustive Search”, ArXiv e-prints, 2010.PDF icon Technical Report (625.06 KB)
B. Andres, Köthe, U., Kröger, T., and Hamprecht, F. A., “Runtime-Flexible Multi-dimensional Views and Arrays for C++98 and C++0x”, ArXiv e-prints, 2010.PDF icon Technical Report (415.54 KB)
2009
C. Bähnisch, Stelldinger, P., and Köthe, U., “Fast and Accurate 3D Edge Detection for Surface Reconstruction”, in Pattern Recognition, 2009, vol. 5748, pp. 111-120.
M. Hanselmann, Köthe, U., Renard, B. Y., Kirchner, M., Heeren, R. M. A., and Hamprecht, F. A., “Multivariate Watershed Segmentation of Compositional Data”, in Proceedings of the 15th International Conference on Discrete Geometry for Computer Imagery (DGCI), in press, 2009, vol. 5810, pp. 180-192.PDF icon Technical Report (1.25 MB)
H. Meine, Köthe, U., and Stelldinger, P., “Pixel Approximation Errors in Common Watershed Algorithms”, in Discrete Geometry for Computer Imagery, 2009, vol. 5810, pp. 193-202.
H. Meine, Köthe, U., and Stelldinger, P., “Pixel Approximation Errors in Common Watershed Algorithms”, in Discrete Geometry for Computer Imagery, 2009, vol. 5810, pp. 193-202.PDF icon Technical Report (6.5 MB)
B. Andres, Köthe, U., Bonea, A., Nadler, B., and Hamprecht, F. A., “Quantitative Assessment of Image Segmentation Quality by Random Walk Relaxation Times”, in Pattern Recognition. 31st DAGM Symposium, Jena, Germany, September 9-11, 2009. Proceedings, 2009, vol. 5748, pp. 502-511.PDF icon Technical Report (3.08 MB)
M. Frank, Plaue, M., Rapp, H., Köthe, U., Jähne, B., and Hamprecht, F. A., “Theoretical and experimental error analysis of continuous-wave time-of-flight range cameras”, Opt. Eng., vol. 48, p. 013602, 2009.
M. Frank, Plaue, M., Rapp, H., Köthe, U., Jähne, B., and Hamprecht, F. A., “Theoretical and Experimental Error Analysis of Continuous-Wave Time-Of-Flight Range Cameras”, Optical Engineering, vol. 48, 013602, 2009.PDF icon Technical Report (2.03 MB)
M. Hanselmann, Köthe, U., Kirchner, M., Renard, B. Y., Amstalden, E. R., Glunde, K., Heeren, R. M. A., and Hamprecht, F. A., “Towards Digital Staining using Imaging Mass Spectrometry and Random Forests”, Journal of Proteome Research, vol. 8, pp. 3558-3567, 2009.PDF icon Technical Report (1.47 MB)
2008
B. Andres, Kondermann, C., Kondermann, D., Köthe, U., Hamprecht, F. A., and Garbe, C. S., “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, pp. 1-6, 2008.PDF icon Technical Report (1.58 MB)
U. Köthe, “Reliable Low-Level Image Analysis”, Habilitation thesis. Department Informatik, University of Hamburg, Hamburg, 2008.PDF icon Technical Report (12.44 MB)
B. Andres, Köthe, U., Helmstaedter, M., Denk, W., and Hamprecht, F. A., “Segmentation of SBFSEM Volume Data of Neural Tissue by Hierarchical Classification”, in Pattern Recognition. 30th DAGM Symposium Munich, Germany, June 10-13, 2008. Proceedings, 2008, vol. 5096, pp. 142-152.PDF icon Technical Report (1.21 MB)
H. Meine, Köthe, U., and Stelldinger, P., “A Topological Sampling Theorem for Robust Boundary Reconstruction and Image Segmentation”, Discrete Applied Mathematics, vol. 157, pp. 524-541, 2008.
U. Köthe, “What Can We Learn from Discrete Images about the Continuous World”, Discrete Geometry for Computer Imagery, vol. 4992. Springer, pp. 4-19, 2008.

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