Ullrich Köthe


Ullrich Koethe Picture
    

Ullrich Köthe

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

Heidelberg Collaboratory for Image Processing (HCI)
Interdisciplinary Center for Scientific Computing (IWR)
University of Heidelberg
Mathematikon B (Berliner Str. 43), level 3, office A119
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 ]

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

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!

Teaching

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
Older

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.
    PDF

  • 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