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LIFE - Transcriptomics Group

Bioinformatik Uni Leipzig

http://www.life.uni-leipzig.de

Outlook: A Concept for a Cooperative Imaging and Image Analysis Platform


Ulf-Dietrich Braumann, Jens-Peer Kuska, Markus Löffler
Interdisciplinary Centre for Bioinformatics
University of Leipzig

Cooperation:

Medical Faculty and life science related institutions within the University of Leipzig

Background: Today’s biomedical research heavily relies on digital imaging methods providing lots of excellent new possibilities for structural and functional analyses of cells and tissues. Many techniques have just recently experienced a significant technological breakthrough that offers new opportunities for cell and tissue imaging in situ but also raises new challenges to biologists, who must adapt to a rapidly evolving environment, and to computer scientists, who are required to develop new methods and tools of advanced multi-dimensional and cross-technology image analysis and management. These techniques include but are not restricted to confocal laser scanning microscopy, infrared and Raman imaging, multi-photon confocal microscopy, scanning acoustic microscopy, microscopic magnetic resonance imaging, positron emission tomography, as well as conventional transmitted light microscopy. While some methods are quite universal, others are very specific in their applications.
The understanding of cell biological processes needs a monitoring of the biochemical processes as well as a monitoring of the morphological changes in the cell and tissue. Image processing provides the only possibility to quantify e.g. morphological changes and certain functional effects. This regards, among others, the volume grow of tissues and organs as well as the analysis of cell collectives requiring different imaging techniques on various scales. In general, cross-technology analyses and assessments are indispensable. This demands a comprehensive set of image processing tools for registration, volume data processing, pattern and shape recognition, segmentation etc.

Own Technological Expertise: The image processing group at IZBI provides methods for the following areas:


  • 3D visualisation
  • Image compression and archiving
  • Image registration
  • Image restoration
  • Image segmentation
  • Colour correction
  • Image acquisition
  • and more


Own Related Work: The image processing group at IZBI is involved in research projects on the following areas:


  • Automatic 3-D reconstruction, segmentation and morphometry using histological serial sections
  • Automatic histometry in histological sections
  • Automatic reconstructions of tree-like structures (vessels, astrocytes) in volume data (confocal LASER-scanning microscopy)
  • Single-cell tracking in fluorescence microscopy
  • Automatic tissue differentiation using infrared-spectroscopic microscopy
  • Visualisation of anatomical volume data (visible woman, according to US planes)
  • Hardware-accelerated volume rendering
  • Lossless volume data compression using a context-sensitive arithmetic coder


Image Analysis Examples from Ongoing Work:



Graph-based analysis of malignant changes of prostate glandular structure.

Automatically tracked single HT1080 cells
3D-tumor invasion pattern analysis


Awarded Work:
Varian-Award 2005 of the Swiss Society of Radiobiology and Medical Physics (SGSMP):
Three-Dimensional Reconstruction and Quantification of Cervical Carcinoma Invasion Fronts from Histological Serial Sections.
(IEEE Transactions on Medical Imaging 24(10): 1286–1307, 2005, Braumann, U.-D., Kuska, J.-P., Einenkel, J., Horn, L.-C., Löffler, M., Höckel, M.)
1. Scientific Award 2005 of the German Society for Ultrasound in Medicine (DEGUM):
Topographical Anatomy of the Female Pelvis in Ultrasound.
(Ultraschall in der Medizin 26(5): 385–398, 2005, Einenkel, J., Braumann, U.-D., Baier, D., Kuska, J.-P., Horn, L.-C., Höckel, M.)

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