Bilge Karaçalı, PhD


Research Assistant Professor

Assistant Director of Bioimaging

Center for Integrated Bioinformatics

School of Biomedical Engineering, Science and Health Systems

Drexel University

3141 Chestnut Street
Philadelphia, PA 19104
tel: 215 - 895 2234
fax: 215 - 895 4983
e-mail: bilge@drexel.edu

CV


Research objectives:

My main interest lies in constructing quantitative measures for characterizing disease related tissue abnormality and damage using all available information sources including but not limited to bioimaging modalities, genomics, proteomics, as well as clinical history. In particular, I investigate the effects of tissue abnormality and damage associated with degenerative diseases like cancer on the appearance observed by radiological images as the macro scale and histology slides at the micro scale and to the molecular scale presentation as characterized by gene expression profiles and metabolite concentrations. The correlations between these appearances across macro, micro, and molecular scales reveal a much more complete picture of the cumulative degeneration and abnormality induced on the affected tissue by a disease process, allowing to predict one based on the others, and collectively depict the scope of the abnormality for diagnosis and staging, as well as prognosis and the most suitable therapeutic strategies.

 

Research interests:

  • Biomedical image analysis
  • Image registration and data fusion
  • Statistical learning theory
  • Machine vision
  • Signal and image processing
  • Multiscale analysis and wavelet theory
  • Target detection and classification
  • Pattern recognition
  • Artificial intelligence
     

    Software:

  • Simulation of tissue atrophy (distributed here/software)

     

    Educational History:

  • 1997 - 2002 North Carolina State University, Raleigh, North Carolina
    M.S., Ph. D. in Electrical Engineering
    Minor in Mathematics
    Dissertation "Vector Space Methods For Surface Reconstruction From One Or More Images Acquired From The Same View With Application To Scanning Electron Microscopy" web access
  • 1992 - 1997 Bilkent University, Ankara, Turkey
    B.S. in Electrical Engineering

    Recent publications: (see CV for a more complete list)
  • B. Karaçalı, C. Davatzikos, "Simulation of Tissue Atrophy Using a Topology Preserving Transformation Model," to appear in IEEE Trans. on Medical Imaging
  • B. Karaçalı, “Information theoretic deformable registration using local image information,” to appear International Journal of Computer Vision
  • B. Karaçalı, C. Davatzikos, "Estimating Topology Preserving and Smooth Displacement Fields," IEEE Transactions on Medical Imaging, vol. 23, no. 7, p. 868-880, 2004 web access
  • B. Karaçalı, "Fully elastic multi-modality image registration using mutual information," in Proceedings of the IEEE International Symposium on Biomedical Imaging, Arlington, p. 1455-1458, April 2004
  • C. Davatzikos, D. Shen, Z. Lao, Z. Xue, B. Karaçalı, "Morphological classification of medical images using nonlinear support vector machines", in Proceedings of the IEEE International Symposium on Biomedical Imaging (invited paper), Arlington, April 2004.
  • B. Karaçalı, W. Snyder, "Noise Reduction in Surface Reconstruction From a Given Gradient Field," International Journal of Computer Vision, vol. 60, no. 1, p. 25-44, 2004 web access
  • Z. Lao, D. Shen, Z. Xue, B. Karaçalı, S. M. Resnick and C. Davatzikos, "Morphological classification of brains via high-dimensional shape transformations and machine learning methods," NeuroImage, in press
  • B. Karaçalı, R. Ramanath, W. E. Snyder, "A comparative analysis of structural risk minimization by support vector machines and nearest neighbor rule," Pattern Recognition Letters, vol. 25, no. 1, p. 63-71, 2004 web access
  • B. Karaçalı, W. Snyder, “Reconstructing Discontinuous Surfaces from a Given Gradient Field Using Partial Integrability,” Computer Vision and Image Understanding, vol. 92, no. 1, p. 78-111, October, 2003 web access
  • B. Karaçalı, C. Davatzikos, “Topology Preservation and Regularity in Estimated Deformation Fields,” Information Processing in Medical Imaging, Lecture Notes in Computer Science, vol. 2732, 2003
  • B. Karaçalı, A. H. Krim, "Fast Minimization of Structural Risk by Nearest Neighbor Method," IEEE Trans. on Neural Networks, vol. 14, no. 1, p. 127-137, 2003 web access
  • B. Karaçalı, W. Snyder, "Automatic Target Detection Using Multispectral Imaging," Proceedings of AIPR, p. 55-59, 2002 web access
  • B. Karaçalı, W. Snyder, "Partial Integrability in Surface Reconstruction From a Given Gradient Field," Proceedings of ICIP, vol. 2, p. 525-528, 2002
  • B. Karaçalı, W. Snyder, “Hyperspectral versus multispectral:A comparative study in atr performance,” In ATRWG, October 2002.
  • B. Karaçalı, W. Snyder, “On-the-fly multispectral ATR,” In Combat Identi.cation Systems Conference, June 2002.

    Pictures:
  • Yetkin and I
  • Yetkin and toys
  • Yetkin after a meal
  • Yetkin and I