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 Tel: +49-(0)761-203-8285 Fax: +49-(0)761-203-8262 Email:

Scientific Interests

• Biomedical image analysis in 3D / 4D (3D+t) data
• 3D invariants
• Computer enhanced microscopy (structured light techniques, deconvolution, etc.)

Publications

2012

Journal

Influence of cell-to-cell variability on spatial pattern formation  

B. Greese, K. Wester, Robert Bensch, Olaf Ronneberger, J. Timmer, M. Hülskamp, C. Fleck

IET Systems Biology, 2012

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Multiview Deblurring for 3-D Images from Light Sheet based Fluorescence Microscopy   Publisher's Link Code

Maja Temerinac-Ott, Olaf Ronneberger, Peter Ochs, W. Driever, Thomas Brox, Hans Burkhardt

IEEE Transactions on Image Processing, 21(4): 1863-1873, 2012

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Fast Rotation Invariant 3D Feature Computation utilizing Efficient Local Neighborhood Operators   Publisher's Link Code

Henrik Skibbe, M. Reisert, Thorsten Schmidt, Thomas Brox, Olaf Ronneberger, Hans Burkhardt

IEEE Transactions on Pattern Analysis and Machine Intelligence, 2012

Conference

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Blind Deconvolution with PSF Regularization for Wide-field Microscopy  

Margret Keuper, Maja Temerinac-Ott, Jan. Padeken, Patrick. Heun, Thomas Brox, Hans Burkhardt, Olaf Ronneberger

IEEE International Symposium on Biomedical Imaging (ISBI), 2012

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2D/3D Rotation-Invariant Detection using Equivariant Filters and Kernel Weighted Mapping  

Kun Liu, Qing Wang, W. Driever, Olaf Ronneberger

IEEE International Conference on Computer Vision and Pattern Recognition (CVPR), 2012

 

2011

Journal

A comparison of different automated methods for the detection of white matter lesions in MRI data   Publisher's Link

S. Klöppel, A. Abdulkadir, S. Hadjidemetriou, S. Issleib, L. Frings, T.N. Thanh, I. Mader, S.J. Teipel, M. Hüll, Olaf Ronneberger

NeuroImage, 57(2): 416-422, 2011

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Comprehensive catecholaminergic projectome analysis reveals single-neuron integration of zebrafish ascending and descending dopaminergic systems   Publisher's Link

T.L. Tay, Olaf Ronneberger, S. Ryu, R. Nitschke, W. Driever

Nature Communications, 2: 171, Jan 2011

Conference

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spherical bessel filter for 3d object detection   Publisher's Link

H. Skibbe, M. Reisert, Olaf Ronneberger, Hans Burkhardt

IEEE International Symposium on Biomedical Imaging (ISBI): 728--733, 2011

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Spatially-Variant Lucy-Richardson Deconvolution for Multiview Fusion of Microscopical 3D Images   Publisher's Link

Maja Temerinac-Ott, Olaf Ronneberger, R. Nitschke, W. Driever, Hans Burkhardt

IEEE International Symposium on Biomedical Imaging (ISBI): 899 -- 904 , 2011

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3D Rotation-Invariant Description from Tensor Operation on Spherical HOG Field   Publisher's Link

Kun Liu, Henrik Skibbe, Thorsten Schmidt, T. Blein, K. Palme, Olaf Ronneberger

British Machine Vision Conference (BMVC), Aug 2011

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Hierarchical Markov Random Fields for Mast Cell Segmentation in Electron Microscopic Recordings  

Margret Keuper, Thorsten Schmidt, M. Rodriguez-Franco, W. Schamel, Thomas Brox, Hans Burkhardt, Olaf Ronneberger

IEEE International Symposium on Biomedical Imaging (ISBI), IEEE: 973 - 978, 2011

Others

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Multiview Deblurring for 3-D Images from Light Sheet based Fluorescence Microscopy - Supporting Online Material  

Maja Temerinac-Ott, Olaf Ronneberger, Peter Ochs, W. Driever, Thomas Brox, Hans Burkhardt

Technical Report 266, University of Freiburg(266), 2011

 

2010

Journal

Harmonic Filters for 3D Multi-Channel Data: Rotation Invariant Detection of Mitoses in Colorectal Cancer   Publisher's Link

M. Schlachter, M. Reisert, C. Herz, F. Schluermann, S. Lassmann, M. Werner, Hans Burkhardt, Olaf Ronneberger

IEEE Transactions on Medical Imaging, 29(8): 1485--1495, 2010

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Early functional magnetic resonance imaging activations predict language outcome after stroke   Publisher's Link

D. Saur, Olaf Ronneberger, D. Kummerer, I. Mader, C. Weiller, S. Klöppel

Brain, 133(4): 1252-1264, 2010

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Inversin relays Frizzled-8 signals to promote proximal pronephros development   Publisher's Link

S. Lienkamp, A. Ganner, C. Boehlke, Thorsten Schmidt, S.J. Arnold, T. Schäfer, D. Romaker, J. Schuler, S. Hoff, C. Powelske, A. Eifler, C. Krönig, A. Bullerkotte, R. Nitschke, E.W. Kuehn, E. Kim, Hans Burkhardt, Thomas Brox, Olaf Ronneberger, J. Gloy, G. Walz

Proceedings of the National Academy of Sciences, 207(47): 20388-20293, Nov 2010

Conference

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3D Deformable Surfaces with Locally Self-Adjusting Parameters - A Robust Method to Determine Cell Nucleus Shapes  

Margret Keuper, Thorsten Schmidt, J. Padeken, P. Heun, K. Palme, Hans Burkhardt, Olaf Ronneberger

IEEE International Conference on Pattern Recognition (ICPR): 2254-2257, 2010

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3D Object Detection Using a Fast Voxel-Wise Local Spherical Fourier Tensor Transformation   Publisher's Link

H. Skibbe, M. Reisert, Thorsten Schmidt, K. Palme, Olaf Ronneberger, Hans Burkhardt

Pattern Recognition (Proc. DAGM), Springer Berlin / Heidelberg, LNCS, Vol.6376: 412-421, 2010

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Mean Shift Gradient Vector Flow: A Robust External Force Field for 3D Active Surfaces  

Margret Keuper, J. Padeken, P. Heun, Hans Burkhardt, Olaf Ronneberger

IEEE International Conference on Pattern Recognition: 2784-2787, 2010

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Semi-Supervised Learning of Edge Filters for Volumetric Image Segmentation  

Margret Keuper, Robert Bensch, K. Voigt, A. Dovzhenko, K. Palme, Hans Burkhardt, Olaf Ronneberger

32nd DAGM Symposium, Springer, LNCS: 462--471, 2010

 

2009

Journal

XuvTools: free, fast and reliable stitching of large 3D datasets   Publisher's Link

M. Emmenlauer, Olaf Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, Hans Burkhardt

Journal of Microscopy, 233(1): 42--60, 2009

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Rotational Invariance Based on Fourier Analysis in Polar and Spherical Coordinates   Publisher's Link

Qing Wang, Olaf Ronneberger, Hans Burkhardt

IEEE Transactions on Pattern Analysis and Machine Intelligence, 31(9): 1715--1722, 2009

Conference

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Using Lateral Coupled Snakes for Modeling the Contours of Worms  

Qing Wang, Olaf Ronneberger, Hans Burkhardt

Pattern Recognition (Proc. DAGM), Springer, LNCS, Vol.10: 542--551, 2009

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Image Analysis of Arabidopsis Trichome Patterning in 4D Confocal Datasets   Publisher's Link

Robert Bensch, Olaf Ronneberger, B. Greese, C. Fleck, K. Wester, M. Hülskamp, Hans Burkhardt

IEEE International Symposium on Biomedical Imaging (ISBI): 742--745, 2009

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A 3D Active Surface Model for the accurate Segmentation of Drosophila Schneider Cell Nuclei and Nucleoli  

Margret Keuper, J. Padeken, P. Heun, Hans Burkhardt, Olaf Ronneberger

Advances in Visual Computing: 865-874, 2009

 

2008

Journal

Spatial quantitative analysis of fluorescently labeled nuclear structures: problems, methods, pitfalls   Publisher's Link

Olaf Ronneberger, D. Baddeley, F. Scheipl, P.J. Verveer, Hans Burkhardt, C. Cremer, L. Fahrmeir, T. Cremer, B. Joffe

Chromosome Research, 16(3): 523-562, May 2008

Conference

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Invariance via Group-Integration: A Feature Framework for 3D Biomedical Image Analysis  

J. Fehr, Olaf Ronneberger, J. Schulz, Thorsten Schmidt, M. Reisert, Hans Burkhardt

Proceedings of Computer Graphics and Imaging (CGIM): 276--285, Feb 2008

Others

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Fourier Analysis in Polar and Spherical Coordinates  

Qing Wang, Olaf Ronneberger, Hans Burkhardt

Technical Report 1, IIF-LMB, Computer Science Department, University of Freiburg (1), 2008

 

2006

Conference

Fast Scalar and Vectorial Grayscale Based Invariant Features for 3D Cell Nuclei Localization and Classification   Publisher's Link

J. Schulz, Thorsten Schmidt, Olaf Ronneberger, Hans Burkhardt, T. Pasternak, A. Dovzhenko, K. Palme

Pattern Recognition (Proc. DAGM), Springer, Vol.4174/2006: 182--191, 2006

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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

Awards

Supervised Master thesis ("Studien- und Diplomarbeiten")

(last update: march 2009)

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)