![[-]](/navbar/open_category.gif){kind=small}
Professor:
Junior-Prof. Dr. Olaf Ronneber...Secretary:Research Ass.:Tech. Staff:Students:Visiting Scientists:Former members:![[+]](/navbar/closed_category.gif){kind=small}
)Former Visiting Scientists:
Printer optimized version of this page[keine Deutsche Seite verfügbar]
Homepage of Olaf Ronneberger
|
Junior-Prof. Dr. Olaf Ronneberger Albert-Ludwigs-Universität Freiburg Institut für Informatik Lehrstuhl für Mustererkennung und Bildverarbeitung Georges-Köhler-Allee 52 D-79110 Freiburg
|
Teaching
- WS 2009/2010: Lecture: 3D Image Analysis (2+2 SWS, 6 ECTS)
- WS 2009/2010: Proseminar: Image Processing Toolbox mit ImageJ (2 SWS, 3 ECTS)
Scientific Interests
- Biomedical image analysis in 3D / 4D (3D+t) data
- 3D invariants
- Computer enhanced microscopy (structured light techniques, deconvolution, etc.)
- Automated pollen recognition
Current Projects
- 3D and 4D Image Analysis for the 4D-Analyser
(Excellence Cluster Bioss, Area D) - 4D Genexpression Atlas of the Zebrafish and Quantitative Description of Axon/Dendrite patterns in zebrafish brain
(Cooperation with Prof. Dr. Wolfgang Driever, Institute of Biology 1, Universität Freiburg and Dr. Roland Nitschke, Life Imaging Center, Universität Freiburg) - 3D/4D Analysis of Protoplasts
(Cooperation with Prof. Dr. Klaus Palme, Institute of Biology 2, Universität Freiburg and Prof. Dr. Robert Murphy, Carnegie Mellon University, Pittsburgh) - Analysis of C. Elegans Fluorescence Profiles from High Throughput Sorter
(Cooperation with Prof. Dr. Ralf Baumeister, Institute of Biology 3, Universität Freiburg) - Spatio-temporal Analysis of Cellular and Subnuclear Protein Patterns
(Cooperation with Dr. Patrick Heun, Max-Planck-Institute of Immunobiology, Universität Freiburg) - Analysis of Pattern Formation of Leaf Trichomes in Arabidopsis
(Cooperation with Dr. Christian Fleck, Center for Biological Systems Analysis, Freiburg and Prof. Dr. Martin Hülskamp, Botanisches Institut III, Universität zu Köln) - Quantitative Description of Chromosome Territories
(Cooperation with Prof Dr. Thomas Cremer, Humangenetik, LMU München) - Analysis of 3D Tissue Samples of Colorectal Cancer
(Cooperation with Prof Dr. Martin Werner, Institut für Pathologie, Universitätsklinikum Freiburg)
Former Projects
- BMBF-Project OMNIBUSS (Online-Monitoring Nicht toxischer, Inhalativallergener Bioaerosole und Sonstiger Staubkomponenten)
- BMBF-Project OMIB (Online-Monitoring and Identification of Bioaerosols)
Software
- liblmbcam -- C++ library providing interfaces for digital cameras
- libsvmtl -- a Support Vector Machine Template Library
- XuvTools -- fast and reliable stitching for large 3D datasets
Supervised Master thesis ("Studien- und Diplomarbeiten")
| (May 2009) | Dominik Rueß "Markow-Random-Field-basierte Registrierungsverfahren für einen 4D Zebrafisch-Atlas" Diplomarbeit |
| Mar 2009 | Matthias Schlachter "Detektion und Klassifikation von Mitosen in 3D Gewebeproben von kolorektalen Karzinomen" Diplomarbeit |
| Okt 2008 | Matthias Demant "Analysis and Classification of Fluorescent Profiles of C. Elegans in High-Throughput Experiments" Diplomarbeit |
| Jul 2008 | Dominik Rueß "Robuste Korrespondenzsuche für Registrierungsprobleme" Studienarbeit |
| Jun 2008 | Robert Bensch "Quantitative Analyse der Musterbildungsprozesse von Trichomen in 4D Volumendaten" Masterarbeit |
| Apr 2007 | Mario Emmenlauer "Feature- und Deformationsmodell-basierte Registrierung von 3D Volumendaten von Zebrafischen" Diplomarbeit |
| Feb 2007 | Margret Keuper "Robuste invariante Merkmale zu Analyse und Vergleich von Chromosomenterritorien in Zellkernen" Diplomarbeit |
| Aug 2006 | Tonio Triebel "Automatische Wahl von hochspezifischen Kernfunktionen anhand von registrierten Trainingsdaten" Diplomarbeit |
Dez 2005 | Janina Schulz "Lokalisierung von Zellkernen und Bestimmung ihrer Mitosephase in konfokalen 3D-Aufnahmen von Arabidopsis thaliana" Diplomarbeit |
| Aug 2005 | Rafael Baumgartner "Erkennung von Pollen in Honig-Proben" Diplomarbeit |
| Nov 2004 | Janis Fehr "Lokalisierung und Erkennung von Zellkernen in Gewebeschnitten" Diplomarbeit |
| Mai 2004 | Christoph Keller "Klassifikation von Bewegungsmustern bei C. Elegans mit verschiedenen genetischen Defekten" Studienarbeit |
| Apr 2004 | Thorsten Schmidt "Automatische Selektion von optimalen Kernfunktionen für Grauwertbasierte Invarianten" Diplomarbeit |
| Jan 2004 | Anselm Vossen "Optische Schnitte mit Hilfe strukturierter Beleuchtung" Studienarbeit |
| Dez 2003 | Thorsten Schmidt "Entwicklung von Vorverarbeitungsverfahren für fluoreszenzmikroskopische 3D Volumendaten zur Verbesserung der nachfolgenden Erkennung mittels grauwertbasierter Invarianten" Studienarbeit |
| Okt 2003 | Rafael Baumgartner "Erkennung von verschiedenen Zellkernen in konfokalen Laser Scanning Aufnahmen mittels grauwertbasierter Invarianten" Studienarbeit |
Pollenmonitor on TV
17.3.2005: The first prototype of our Pollenmonitor, developed within the OMNIBUSS project was presented in a 6 minute long report in 3sat "nano". Thanks to the journalist Michael Ringesiep for this great work and for providing a digital version of this report:
- Pollenmonitor_3sat_nano_17.3.2005.mpg (154MB, DVD quality, MPEG2 720x576 25fps, 4400 kbps)
- Pollenmonitor_3sat_nano_17.3.2005_divx.avi (41MB lower quality, divx (MPEG 4) Codec,720x576 25fps, 800 kbps, variable bitrate)
- Pollenmonitor_3sat_nano_17.3.2005_xvid.avi (36MB better codec and smaller file size, 720x576 25fps, xvid (MPEG 4) Codec)
- Pollenmonitor_3sat_nano_17.3.2005_divx_small.avi (18MB half image size, divx (MPEG 4) Codec, 352x288 25fps, 320 kbps, variable bitrate)
Awards
| 2005 | DAGM Award for "Voxel-Wise Gray Scale Invariants for Simultaneous Segmentation and Classification" |
| 2006 | DAGM Award for "Fast scalar and vectorial grayscale based invariant features for 3d cell nuclei localization and classification" |
| 2006 | Competition winning program, MUSCLE CIS Coin Recognition Competition |
| 2008 | nominated for the GI-Dissertationspreis 2007 (best Dissertation in Computer Science in Germany, Austria and Switzerland, 2007) of the Gesellschaft für Informatik |
Publications
(last update: 8.4.2009)
| [29] | R. Bensch, O. Ronneberger,B. Greese, C. Fleck, K. Wester, M. Hülskamp, and H. Burkhardt "Image analysis of arabidopsis trichome patterning in 4D confocal datasets" accepted for publication in 6th IEEE International Symposium on Biomedical Imaging: From Nano to Macro. ISBI 2009. |
| [28] | Q. Wang, O. Ronneberger, and H. Burkhardt. "Rotational Invariance Based on Fourier Analysis in Polar and Spherical Coordinates" accepted for publication in IEEE Transactions on Pattern Analysis and Machine Intelligence (doi:10.1109/TPAMI.2009.29). |
| [27] | M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi,
R. Nitschke, W. Driever, and H. Burkhardt. "Xuvtools: Free, fast and reliable stitching of large 3d datasets" Journal of Microscopy (2009) Vol 233 Issue 1 pp. 42--60 (doi:10.1111/j.1365-2818.2008.03094.x) PDF on publisher site (free access)). |
| [26] | O. Ronneberger "3D-Invarianten zur automatischen Pollenerkennung. " In Dorothea Wagner, editor, Ausgezeichnete Informatikdissertationen 2007. Lecture Notes in Informatics (LNI) - Dissertations, Series of the Gesellschaft für Informatik e.V. (GI), Volume D-8. pages 239-248. ISBN 978-3-88579-412-7 (pdf) |
| [25] | O. Ronneberger, Q. Wang, and H. Burkhardt "Fast and robust segmentation of spherical particles in volumetric data sets from brightfield microscopy" Biomedical Imaging: From Nano to Macro. ISBI 2008. 5th IEEE International Symposium on, pages 372--375, 2008.(doi:10.1109/ISBI.2008.4541010) |
| [24] | O. Ronneberger, D. Baddeley, F. Scheipl, P. .J. Verveer, H. Burkhardt, C. Cremer, L. Fahrmeir, T.Cremer and B. Joffe "Spatial quantitative analysis of fluorescently labeled nuclear structures: problems, methods, pitfalls" Chromosome Research (2008) Vol16 pp. 523-562 (doi:10.1007/s10577-008-1236-4) |
| [23] | Fehr, J., Ronneberger, O., Schulz, J., Schmidt, T., Reisert, M. & Burkhardt, H. "Invariance via Group-Integration: A Feature Framework for 3D Biomedical Image Analysis" Computer Graphics and Imaging (CGIM), 2008 Innsbruck, Austria (URL) |
| [22] | O. Ronneberger "3D invariants for automated pollen recognition" PHD thesis, Albert-Ludwigs university of Freiburg, 2007 (URL, pdf) |
| [21] | M. Emmenlauer, O. Ronneberger, M. Temerinac, H. Burkhardt, A. Filippi, R. Nitschke and W. Driever "Fast Automatic Recombination of Multiple 3D Datasets for Large Volumes and High Dynamic Range (HDR)" 49th Symposium of the Society for Histochemistry 2007, Freiburg, Germany |
| [20] | O. Ronneberger, Q. Wang and H. Burkhardt "3D invariants with high robustness to local deformations for automated pollen recognition" Pattern Recognition -- Proceedings of the 29th DAGM Symposium 2007 Heidelberg, LNCS 4713/2007, Springer, pp. 425-435 doi:10.1007/978-3-540-74936-3_43 |
| [19] | M. Reisert, O. Ronneberger, and H. Burkhardt "Holomorphic filters for object detection" Pattern Recognition -- Proceedings of the 29th DAGM Symposium 2007 Heidelberg, LNCS 4713/2007, Springer, pp. 304-313 doi:10.1007/978-3-540-74936-3_31 |
| [18] | M. Reisert, O. Ronneberger, and H. Burkhardt "A fast and reliable coin recognition system" Pattern Recognition -- Proceedings of the 29th DAGM Symposium 2007 Heidelberg, LNCS 4713/2007, Springer, pp. 304-313 doi:10.1007/978-3-540-74936-3_42 |
| [17] | S. Scharring, A. Brandenburg, G. Breitfuss, H. Burkhardt,
W. Dunkhorst, M. v. Ehr, M. Fratz, D. Giel, U. Heimann, W. Koch, H. Lödding,
W. Müller, O. Ronneberger, E. Schultz, G. Sulz, and Q. Wang. "Online Monitoring of Airborne Allergenic Particles OMNIBUSS." In J. Popp, and M. Strehle. Biophotonics: Visions for Better Health Care., pages 31-88, 2006. |
| [16] | M. Reisert, O. Ronneberger and H. Burkhardt. "An Efficient Gradient Based Registration Technique for Coin Recognition." Proceedings of the Muscle CIS Coin Competition Workshop, Sep.11, 2006, Berlin, Germany, pages 19-31, Berlin, Germany, 2006. Competetion winning program! (pdf) |
| [15] | J. Schulz, T. Schmidt, O. Ronneberger, H. Burkhardt,
T. Pasternak A. Dovzhenko and K. Palme. "Fast Scalar and Vectorial Grayscale Based Invariant Features for 3D Cell Nuclei Localization and Classification." Proceedings of the 28th Pattern Recognition Symposium of the German Association for Pattern Recognition (DAGM06), Berlin, Germany, 2006 DAGM-Award! (pdf) |
| [14] | K.-D. Peschke, B. Haasdonk, O. Ronneberger, H. Burkhardt,
P. Rösch, M. Harz, J. Popp. "Using transformation knowledge for the classification of Raman spectra of biological samples." Proceedings of the fourth IASTED International Conference on biomedical engineering (BioMED 06) 2006. (pdf) |
| [13] | J. Popp, P. Rösch, R. Petry, S. Hofer, A. Schüle, G. Schmauz, M. Lankers, H. Burkhardt,
O. Ronneberger, K.-D. Peschke. "Verfahren und Vorrichtung zur Detektion und zum Identifizieren von Biopartikeln." Deutsches Patent Nr. 10 2004 008 762, 27.12.2005. |
| [12] | M. Harz, P. Rösch, K.-D. Peschke, O. Ronneberger, H. Burkhardt,
J. Popp. "Micro-Raman spectroscopical identification of bacterial cells of the genus Staphylococcus in dependence on their cultivation conditions." The Analyst, vol. 130(11), pages 1543-1550, 2005. |
| [11] | J. Fehr, O. Ronneberger, H. Kurz and H. Burkhardt. "Self-Learning Segmentation and Classification of Cell-Nuclei in 3D Volumetric Data using Voxel-Wise Gray Scale Invariants." In Proceedings of the 27th DAGM Symposium, in number 3663 LNCS, Springer, Vienna, Austria, 30.8 - 2.9. 2005. (pdf) |
| [10] | O. Ronneberger, J. Fehr and H. Burkhardt. "Voxel-Wise Gray Scale Invariants for Simultaneous Segmentation and Classification." In Proceedings of the 27th DAGM Symposium, in number 3663 LNCS, Springer, Vienna, Austria, 30.8 - 2.9. 2005., DAGM-Award! (pdf) |
| [9] | P. Rösch, M. Harz, K.-D. Peschke, O. Ronneberger, H.
Burkhardt, H.-W. Motzkus, M. Lankers, S. Hofer, H. Thiele, J. Popp. "Chemotaxonomic Identification of Single Bacteria by Micro-Raman Spectroscopy: Application to Clean-Room-Relevant Biological Contaminations." Applied and Environmental Microbiology, Vol. 71, Pages 1626-1637, 2005. (pdf) |
| [8] | O. Ronneberger and J. Fehr and H. Burkhardt. "Voxel-Wise Gray Scale Invariants for Simultaneous Segmentation and Classification -- Theory and Application to Cell-Nuclei in 3D Volumetric Data." Internal Report 2/05, IIF-LMB, University Freiburg, Germany, Apr. 2005. (pdf) |
| [7] | O. Ronneberger,
H. Burkhardt, and E. Schultz. "General-purpose Object Recognition in 3D Volume Data Sets using Gray-Scale Invariants - Classification of Airborne Pollen-Grains Recorded with a Confocal Laser Scanning Microscope." In Proceedings of the International Conference on Pattern Recognition, Quebec, Canada, September 2002. (pdf) |
| [6] | O. Ronneberger,
E. Schultz, and H. Burkhardt. "Automated Pollen Recognition using 3D Volume Images from Fluorescence Microscopy." Aerobiologia, 18 pages 107-115, 2002. (pdf) |
| [5] | J. Kompenhans, M. Raffel, L. Dieterle, T. Dewhirst, H. Vollmers, K. Ehrenfred, C. Willert, K. Pengel, C. Kähler, A. Schröder und O. Ronneberger "Particle image velocimetry in aerodynamics: technology and applications in wind tunnels." Journal of Visualization 2, Nos 3/4 229-244, 2000 |
| [4] | O. Ronneberger, M. Raffel und J. Kompenhans "Advanced evaluation algorithms for standard and dual plane particle image velocimetry." In: 9th international symposium on applications of laser techniques, Lissabon, 13. - 16. Juli, 1998. (pdf) |
| [3] | O. Ronneberger "Messung aller drei Geschwindigkeitskomponenten mit Hilfe der "Particle Image Velocimetry" mittels einer Kamera und zweier paralleler Lichtschnitte." Forschungsbericht DLR-FB 98-40, ISSN 1434-8454, Deutsches Zentrum für Luft- und Raumfahrt, 1998 |
| [2] | O. Ronneberger "Messung aller drei Geschwindigkeitskomponenten mit Hilfe der "Particle Image Velocimetry" mittels einer Kamera und zweier paralleler Lichtschnitte." Diplomarbeit am Institut für Nichtlineare Dynamik, Georg-August-Universität Göttingen. 1998 (pdf) |
| [1] | M. Raffel, M. Gharib, O. Ronneberger and J. Kompenhans "Feasibility study of three-dimensional PIV by correlating images of particles witthin parallel light sheets". Experiments in Fluids 19 69-77, 1995 (pdf) |