Robert Bensch
PhD Student 3D Image Analysis Lab / Computer Vision Lab Chair of Pattern Recognition and Image Processing Department of Computer Science University of Freiburg Office location: Georges-Köhler-Allee, building 052, 2nd floor, room 01-021 79110 Freiburg i.Br., Germany
Telefon:	+49-(0)761-203-8266
Fax:	+49-(0)761-203-8262
Email:

Research Interests

• Methods for the Analysis of Dynamic Biological Processes from 4D Biological Data

• Analysis of Motion Patterns from 4D Biomedical Data

• Image Analysis and Segmentation of 4D Biological Data

Publications

Conference Papers and Journal Articles

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

 

2010

Conference

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

Conference

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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Thesis

Current Projects

• 3D and 4D Image Analysis for the 4D-Analyser
  (Excellence Cluster Bioss, Area D)
• Cell Motion Analysis in Zebrafish
  (Cooperation with Prof. Dr. Wolfgang Driever, Institute of Biology 1, 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 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)

Awards

Teaching

Lecture assistance

Supervised Thesis

Master's thesis

Quantitative Analysis of Pattern Formation of Trichomes in 4D Volumetric Datasets
> original title: "Quantitative Analyse der Musterbildungsprozesse von Trichomen in 4D Volumendaten"
[pdf]



Abstract:
The leaf hairs of Arabidopsis thaliana (trichomes) are the most applicable cell types for the functional analysis of patterning processes. During cell growth different processes provide for a regular patterning of the trichomes. There is a need of quantitative data for the analysis of these processes and their simulation with mathematical models.
The purpose of this master thesis was to provide a feasibility study for the automatical measurement of the leaf surface and the positions of the trichomes. Furthermore the possibility of tracking the trichomes over time was investigated. The raw data were 4D volumetric data (3D + time) of Arabidopsis leaves and trichomes. For pattern recognition different methods were combined such that a low dependency on the acquisition parameters was achieved and the methods fit to a wide field of application.



Subtasks:

• Extraction of the leaf surface and the leaf edge
• Alignment of the leaves into a reference coordinate system
• Localization of the trichomes
• Find correspondences between two consecutive datasets