L.  Ardizzone, Mackowiak, R., Rother, C., and Köthe, U., ?Exact Information Bottleneck with Invertible Neural Networks: Getting the Best of Discriminative and Generative Modeling?, 2020.

J.  Kruse, Ardizzone, L., Rother, C., and Köthe, U., ?Benchmarking Invertible Architectures on Inverse Problems?, i, 2019.

L.  Ardizzone, Lüth, C., Kruse, J., Rother, C., and Köthe, U., ?Guided Image Generation with Conditional Invertible Neural Networks?, 2019.

L.  Ardizzone, Lüth, C., Kruse, J., Rother, C., and Köthe, U., ?Guided Image Generation with Conditional Invertible Neural Networks?, 2019.

S.  Berg, Kutra, D., Kroeger, T., Straehle, C. N., Kausler, B. X., Haubold, C., Schiegg, M., Ales, J., Beier, T., Rudy, M., Eren, K., Cervantes, J. I., Xu, B., Beuttenmüller, F., Wolny, A., Zhang, C., Köthe, U., Hamprecht, F. A., and Kreshuk, A., ?ilastik: interactive machine learning for (bio)image analysis?, Nature Methods, vol. 16, pp. 1226-1232, 2019.

T. J.  Adler, Ayala, L., Ardizzone, L., Kenngott, H. G., Vemuri, A., Müller-Stich, B. P., Rother, C., Köthe, U., and Maier-Hein, L., ?Out of Distribution Detection for Intra-operative Functional Imaging?, in MICCAI UNSURE Workshop 2019, 2019, vol. 11840 LNCS, pp. 75?82.

S.  Wolf, Pape, C., Bailoni, A., Rahaman, N., Kreshuk, A., Köthe, U., and Hamprecht, F. A., ?The Mutex Watershed: Efficient, Parameter-Free Image   Partitioning?, ECCV. Proceedings. Springer, pp. 571-587, 2018.

S.  Wolf, Pape, C., Bailoni, A., Rahaman, N., Kreshuk, A., Köthe, U., and Hamprecht, F. A., ?The Mutex Watershed: Efficient, Parameter-Free Image Partitioning?, in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2018, vol. 11208 LNCS, pp. 571?587.

S.  Wolf, Schott, L., Köthe, U., and Hamprecht, F. A., ?Learned Watershed: End-to-End Learning of Seeded Segmentation?, ICCV. pp. 2030-2038, 2017.

T.  Beier, Pape, C., Rahaman, N., Prange, T., Berg, S., Bock, D., Cardona, A., Knott, G. W., Plaza, S. M., Scheffer, L. K., Köthe, U., Kreshuk, A., and Hamprecht, F. A., ?Multicut brings automated neurite segmentation closer to human performance?, Nature Methods, vol. 14, no. 2, pp. 101-102, 2017.

N.  Krasowki, Beier, T., Knott, G. W., Köthe, U., Hamprecht, F. A., and Kreshuk, A., ?Neuron Segmentation with High-Level Biological Priors?, IEEE Transactions on Medical Imaging, vol. 37, no. 4, 2017.

T.  Beier, Andres, B., Köthe, U., and Hamprecht, F. A., ?An Efficient Fusion Move Algorithm for the Minimum Cost Lifted Multicut Problem?, ECCV. Proceedings, vol. LNCS 9906. Springer, pp. 715-730, 2016.

C.  Haubold, Schiegg, M., Kreshuk, A., Berg, S., Köthe, U., and Hamprecht, F. A., ?Segmenting and Tracking Multiple Dividing Targets Using ilastik?, in Focus on Bio-Image Informatics, vol. 219, Springer, 2016, pp. 199-229.

J.  Kleesiek, Petersen, J., Döring, M., Maier-Hein, K., Köthe, U., Wick, W., Hamprecht, F. A., Bendszus, M., and Biller, A., ?Virtual Raters for Reproducible and Objective Assessments in Radiology?, Nature Scientific Reports, vol. 6, 2016.

A.  Kreshuk, Walecki, R., Köthe, U., Gierthmühlen, M., Plachta, D., Genoud, C., Haastert-Talini, K., and Hamprecht, F. A., ?Automated Tracing of Myelinated Axons and Detection of the Nodes of Ranvier in Serial Images of Peripheral Nerves?, Journal of Microscopy, vol. 259 (2), pp. 143-154, 2015.

M.  Schiegg, Hanslovsky, P., Haubold, C., Köthe, U., Hufnagel, L., and Hamprecht, F. A., ?Graphical Model for Joint Segmentation and Tracking of Multiple Dividing Cell?, Bioinformatics, vol. 31, no. 6, pp. 948-956, 2015.

N.  Krasowski, Beier, T., Knott, G. W., Köthe, U., Hamprecht, F. A., and Kreshuk, A., ?Improving 3D EM Data Segmentation by Joint Optimization over Boundary Evidence and Biological Priors?, in 12th {IEEE} International Symposium on Biomedical Imaging, {ISBI} 2015, Brooklyn, NY, USA, April 16-19, 2015, 2015, pp. 536-539.

M.  Schiegg, Heuer, B., Haubold, C., Wolf, S., Köthe, U., and Hamprecht, F. A., ?Proof-reading Guidance in Cell Tracking by Sampling from Tracking-by-assignment Models?, in ISBI. Proceedings, 2015, pp. 394-398.

T.  Kröger, Kappes, J. H., Beier, T., Köthe, U., and Hamprecht, F. A., ?Asymmetric Cuts: Joint Image Labeling and Partitioning?, in Pattern Recognition - 36th German Conference, {GCPR} 2014, Münster, Germany, September 2-5, 2014, Proceedings, 2014.

A.  Kreshuk, Köthe, U., Pax, E., Bock, D. D., and Hamprecht, F. A., ?Automated Detection of Synapses in Serial Section Transmission Electron Microscopy Image Stacks?, PLoS ONE, vol. 9, p. 2, 2014.

T.  Beier, Kröger, T., Kappes, J. H., Köthe, U., and Hamprecht, F. A., ?Cut, Glue and Cut: A Fast, Approximate Solver for Multicut Partitioning?, in 2014 {IEEE} Conference on Computer Vision and Pattern Recognition, {CVPR} 2014, Columbus, OH, USA, June 23-28, 2014, 2014.

J.  Kleesiek, Biller, A., Urban, G., Köthe, U., Bendszus, M., and Hamprecht, F. A., ?ilastik for Multi-modal Brain Tumor Segmentation?, in MICCAI BraTS (Brain Tumor Segmentation) Challenge. Proceedings, 3rdplace, 2014, pp. 12-17.

C. N.  Straehle, Kandemir, M., Köthe, U., and Hamprecht, F. A., ?Multiple instance learning with response-optimized random forests?, in ICPR. Proceedings, 2014, pp. 3768 - 3773.

U.  Köthe, Herrmannsdörfer, F., Kats, I., and Hamprecht, F. A., ?SimpleSTORM: a fast, self-calibrating reconstruction algorithm for localization microscopy?, Histochemistry and Cell Biology, vol. 141, pp. 613-627, 2014.

L.  Fiaschi, Diego, F., Grosser, K. - H., Schiegg, M., Köthe, U., Zlatic, M., and Hamprecht, F. A., ?Tracking indistinguishable translucent objects over time using weakly supervised structured learning?, in CVPR. Proceedings, 2014, pp. 2736 - 2743.

C. N.  Straehle, Peter, S., Köthe, U., and Hamprecht, F. A., ?K-smallest Spanning Tree Segmentations?, in German Conference on Pattern Recognition (DAGM/GCPR). Proceedings, 2013, pp. 375-384.

T.  Kröger, Mikula, S., Denk, W., Köthe, U., and Hamprecht, F. A., ?Learning to Segment Neurons with Non-local Quality Measures?, in MICCAI 2013. Proceedings, part II, 2013, vol. 8150, pp. 419-427.

C. N.  Straehle, Köthe, U., and Hamprecht, F. A., ?Weakly supervised learning of image partitioning using decision trees with structured split criteria?, in ICCV 2013. Proceedings, 2013, pp. 1849-1856.

B.  Andres, Köthe, U., Kröger, T., Helmstaedter, M., Briggmann, K. L., Denk, W., and Hamprecht, F. A., ?3D Segmentation of SBFSEM Images of Neuropil by a Graphical Model over Supervoxel Boundaries?, Medical Image Analysis, vol. 16 (2012), pp. 796-805, 2012.

M.  Hanselmann, Röder, J., Köthe, U., Renard, B. Y., Heeren, R. M. A., and Hamprecht, F. A., ?Active Learning for Convenient Annotation and Classification of Secondary Ion Mass Spectrometry Images?, Analytical Chemistry, vol. 85 (1), pp. 147-155, 2012.

B. X.  Kausler, Schiegg, M., Andres, B., Lindner, M., Köthe, U., Leitte, H., Wittbrodt, J., Hufnagel, L., and Hamprecht, F. A., ?A Discrete Chain Graph Model for 3d+t Cell Tracking with High Misdetection Robustness?, in ECCV 2012. Proceedings, 2012, vol. 7574, pp. 144-157.

B.  Andres, Kröger, T., Briggmann, K. L., Denk, W., Norogod, N., Knott, G. W., Köthe, U., and Hamprecht, F. A., ?Globally Optimal Closed-Surface Segmentation for Connectomics?, in ECCV 2012. Proceedings, Part 3, 2012, pp. 778-791.

B.  Andres, Kappes, J. Hendrik, Beier, T., Köthe, U., and Hamprecht, F. A., ?The Lazy Flipper: Efficient Depth-limited Exhaustive Search in Discrete Graphical Models?, in ECCV 2012, 2012.

B.  Andres, Kappes, J. H., Beier, T., Köthe, U., and Hamprecht, F. A., ?The Lazy Flipper: Efficient Depth-Limited Exhaustive Search in Discrete Graphical Models?, in Computer Vision - {ECCV} 2012 - 12th European Conference on Computer Vision, Florence, Italy, October 7-13, 2012, Proceedings, Part {VII}, 2012.

B.  Andres, Kappes, J. H., Beier, T., Köthe, U., and Hamprecht, F. A., ?The Lazy Flipper: Efficient Depth-limited Exhaustive Search in Discrete Graphical Models?, in ECCV 2012, 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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

B.  Andres, Kappes, J. H., Köthe, U., Schnörr, C., and Hamprecht, F. A., ?An Empirical Comparison of Inference Algorithms for Graphical Modelswith 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

U.  Köthe, ?Reliable Low-Level Image Analysis?, Habilitation thesis. Department Informatik, University of Hamburg, Hamburg, 2008.

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.

H.  Meine, Köthe, U., and Stelldinger, P., ?A Topological Sampling Theorem for Robust Boundary Reconstructionand 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.