Ullrich Köthe

Ullrich Koethe Picture

I moved to the Visual Learning Lab Heidelberg. Please refer to my new homepage.

Ullrich Köthe

apl. Prof., Dr. rer. nat., Dipl. phys.

Heidelberg Collaboratory for Image Processing (HCI)
Interdisciplinary Center for Scientific Computing (IWR)
University of Heidelberg
Im Neuenheimer Feld 205 (Mathematikon), Office 4.334
D-69120 Heidelberg

Tel: +49-6221-54 14834
Fax: +49-6221-54 5276
Email: ullrich.koethe AT iwr.uni-heidelberg.de
[ Scientific Interests | VIGRA | ilastik | Publications | Teaching | VLL Group ]

Scientific Interests

Welcome to my website! My research revolves around the connection between machine learning and multi-dimensional image analysis. In particular, I'm interested in
  • efficient computation of rich feature sets, reliable feature selection, optimal feature design vs. feature learning
  • fast and accurate prediction algorithms (most notably Random Forest variants) and their uncertainty
  • design and optimization of graphical models for image segmentation and object tracking
  • weak labelling strategies to reduce the human effort in training data and ground truth creation
  • generic software that brings state-of-the-art algorithms to the end user (in particular, I'm the maintainer of the VIGRA image analysis library and a core developer of ilastik, the interactive learning and segmentation toolkit)
Any image analysis chain is only as strong as its weakest link!


Summer Term 2017
Winter Term 2016/17
Summer Term 2016
Winter Term 2015/16
Summer Term 2015
Winter Term 2014/15
  • Lecture: Fundamentals of Machine Learning
  • Seminar: Algorithms to Analyse Big Data
  • C++ Programmierkurs, Blockkurs 9.3. bis 20.3.2015
Summer Term 2014

Curriculum Vitae

26. Nov. 2008 Habilitation for a thesis entitled "Reliable Low-Level Image Analysis", Department of Informatics, University of Hamburg
Since 01/2008 Senior scientist at Heidelberg Collaboratory for Image Processing (HCI)
Since 04/2007 Vice Group Leader of the Image Analysis ans Learning Group (formerly: Multidimensional Image Processing), University of Heidelberg
Spring semester 2004 Guest researcher at Computer Vision Laboratory, Linköping University, Sweden
1999-2007 Assistant professor (officially: "Hochschulassistent") in the Cognitive Systems Group, University of Hamburg
29. Feb. 2000 Dr. rer. nat. (PhD) for a thesis entitled "Generische Programmierung für die Bildverarbeitung", Department of Informatics, University of Hamburg
Spring semester 1993 Guest researcher at Sarnoff Corporation, Princeton, USA
1992-1999 Research assistant at the Fraunhofer Institute for Computer Graphics, Rostock
1986-1991 Study of physics at University of Rostock, Diploma thesis on "Mikroskopische Herleitung einer Ratengleichung am Beispiel der Nukleonen-Deuteron-Reaktion"

Important Publications

Please refer to our group publication list for the full list of papers since 2010. A complete list of my pre-2010 publications can be found here. You may also check out my profile at Google Scholar or the DBLP Citation Database.

  • U. Köthe: "Reliable Low-Level Image Analysis"
    Habilitation Thesis, Department Informatik, University of Hamburg, 318 pages, Hamburg 2008
    Abstract | PDF (10 MB)

  • U. Köthe: "Generische Programmierung für die Bildverarbeitung",
    PhD Thesis, Fachbereich Informatik, Universität Hamburg, 274 pages, Hamburg 2000, ISBN: 3-8311-0239-2. (in German)
    Abstract | PDF (12.5 MB)

  • C. Sommer, C. Straehle, U. Köthe, F.A. Hamprecht: "ilastik: Interactive learning and segmentation toolkit",
    In: IEEE International Symposium on Biomedical Imaging (ISBI), pp. 230-233, 2011.
    Abstract | PDF

  • U. Köthe: "Reusable Software in Computer Vision",
    in: B. Jähne, H. Haussecker, P. Geissler (Eds.): Hand-book of Computer Vision and Applications, Volume 3: Systems and Applications, pp. 103-132, San Diego: Academic Press, 1999.

  • U. Köthe: "Edge and Junction Detection with an Improved Structure Tensor",
    in: B. Michaelis, G. Krell (Eds.): Pattern Recognition, Proc. of 25th DAGM Symposium, Magdeburg 2003, Lecture Notes in Computer Science 2781, pp. 25-32, Berlin: Springer, 2003. (note: this article is © Springer-Verlag)
    Abstract | PDFAwarded the main prize of the German Pattern Recognition Society (DAGM) 2003

  • U. Köthe: "Integrated Edge and Junction Detection with the Boundary Tensor",
    in: ICCV ‘03, Proc. of 9th Intl. Conf. on Computer Vision, Nice 2003, vol. 1, pp. 424-431, 2003.
    Abstract | PDF

  • U. Köthe, M. Felsberg: "Riesz-Transforms Versus Derivatives: "On the Relationship Between the Boundary Tensor and the Energy Tensor",
    in: R. Kimmel, N. Sochen, J. Weickert (Eds.): Scale Space and PDE Methods in Computer Vision, Springer LNCS 3459, pp. 179-191, 2005.
    Abstract | PDF

  • B. Andres, T. Kröger, K. Briggmann, W. Denk, N. Norogod, G. Knott, U. Köthe, F.A. Hamprecht: "Globally Optimal Closed-Surface Segmentation for Connectomics",
    in: Fitzgibbon, A., Lazebnik, S., Perona, P., Sato, Y., Schmid, C. (Eds.) : 12th Eur. Conf. Computer Vision (ECCV 2012) part III, Springer LNCS 7574, pp. 778-791, 2012 (note: this article is © Springer-Verlag)
    Abstract | BibTeX | PDF

  • T. Beier, B. Andres, U. Köthe, F.A. Hamprecht: "An Efficient Fusion Move Algorithm for the Minimum Cost Lifted Multicut Problem",
    in: Leibe, B., Matas, J., Sebe, N., Welling, M. (Eds.) : 14th Eur. Conf. Computer Vision (ECCV 2016), in press, 2016 (note: this article is © Springer-Verlag)
    Abstract | PDF

  • B. Andres, U. Köthe, M. Helmstaedter, W. Denk, F.A. Hamprecht: "Segmentation of SBFSEM Volume Data of Neural Tissue by Hierarchical Classification",
    in: G. Rigoll (Ed.): Pattern Recognition, Proc. DAGM 2008, Lecture Notes in Computer Science 5096 , pp. 142-152, Berlin: Springer, 2008. (note: this article is © Springer-Verlag)
    Abstract | BibTeX | PDFReceived a Best Paper Award from the German Association for Pattern Recognition (DAGM)

  • A. Kreshuk, U. Köthe, E. Pax, D. Bock, F.A. Hamprecht: "Automated Detection of Synapses in Serial Section Transmission Electron Microscopy Image Stacks",
    PLoS ONE 9(2): e87351, 2014.
    Abstract | BibTeX | PDF

  • B. Kausler, M. Schiegg, B. Andres, M. Lindner, U. Köthe, H. Leitte, J. Wittbrodt, L. Hufnagel, F.A. Hamprecht: "A discrete chain graph model for 3d+ t cell tracking with high misdetection robustness",
    in: Fitzgibbon, A., Lazebnik, S., Perona, P., Sato, Y., Schmid, C. (Eds.) : 12th Eur. Conf. Computer Vision (ECCV 2012) part III, Springer LNCS 7574, pp. 144-157, 2012 (note: this article is © Springer-Verlag).
    Abstract | BibTeX | PDF

  • M. Hanselmann, U. Köthe, M. Kirchner, B.Y. Renard, E.R. Amstalden, K. Glunde, R.M.A. Heeren, F.A. Hamprecht: "Towards Digital Staining using Imaging Mass Spectrometry and Random Forests",
    Journal of Proteome Research, 8(7):3558-3567, 2009
    Abstract | BibTeX | PDF

  • B. Menze, B. Kelm, N. Splitthoff, U. Köthe, F.A. Hamprecht: "On oblique random forests",
    Mach. Learning and Knowledge Discovery in Databases, Springer LNCS 6912, pp. 453-469, 2011
    Abstract | PDF

  • U. Köthe, F. Herrmannsdörfer, I. Kats, F.A. Hamprecht: "SimpleSTORM: a fast, self-calibrating reconstruction algorithm for localization microscopy",
    Histochemistry and Cell Biology, 141(6):613–627, 2014.
    Abstract | PDF

  • H. Meine, U. Köthe, P. Stelldinger: "A Topological Sampling Theorem for Robust Boundary Reconstruction and Image Segmentation",
    Discrete Applied Mathematics (DGCI Special Issue), 157(3):524-541, 2009.
    Abstract | PDF

  • U. Köthe: "What Can We Learn from Discrete Images about the Continuous World?",
    in: D. Coeurjolly, I. Sivignon, L. Tougne, F. Dupont (Eds.): Discrete Geometry for Computer Imagery, Proc. DGCI 2008, Lecture Notes in Computer Science 4992, pp. 4-19, Berlin: Springer, 2008. (note: this article is © Springer-Verlag)
    Abstract | PDF

  • P. Stelldinger, U. Köthe: "Towards a general sampling theory for shape preservation",
    Image and Vision Computing, Special Issue Discrete Geometry for Computer Vision, 23(2): 237-248, 2005.
    Abstract | PDF