Tolga Tasdizen

Assistant Professor, Electrical and Computer Engineering Department
Assistant Professor, Scientific Computing and Imaging Institute
Adjunct Assistant Professor, School of Computing
Adjunct Assistant Professor, Department of Neurology

Curriculum Vitae
Publications Page

Research

I am an Assistant Professor in the Electrical and Computer Engineering Department at the University of Utah. I am also a USTAR faculty member at the Scientific Computing and Imaging Institute. My research interests are in the general areas of image processing and pattern recognition. More specifically we study geometry-based and statistics-based methods for image filtering, segmentation and feature extraction. Examples of our geometry-based methods include the use of high-order partial differential equations for image and surface reconstruction. Examples of our statistics-based methods include the use of patches for image denoising, texture segmentation and feature extraction. Papers on these subjects can be found here.

One important application of this research is biological image analysis. For instance, models of neural circuits are central to the study of the central nervous system. However, relatively little is known about the connectivities of neurons and state-of-the-art models are largely not based on anatomical ground truth. Neural circuit reconstruction, a.k.a connectome, research offers great promise for providing this anatomical ground truth. Serial-section electron microscopy images can provide the data necessary for reconstruction of large-scale neural circuits. However, the complexity and vast size of these images make human interpretation an extremely labor intensive task. The pipeline for reconstructing neural circuits from serial-section electron microscopy includes preprocessing the images, assembling 3D volumes, segmenting individual neurons and identifying synapses between the neurons. With this motivation, we have established a collaboration with researchers in ophthalmology and neurobiology  --funded by the National Institutes of Health--  aimed at building automate approaches for reconstructing the wiring diagram of neurons in the rabbit retina and the zebrafish optic tract from serial-section microscopy images. You can find out more about this line of research here and here. The neural circuit reconstruction toolset is a set of publicly available tools we have developed with funding from this project. The tool include image preprocessing, registration and mosaicking methods. We plan to add neuron segmentation and annottaion methods to the publicly available toolset in the near future. These tools were first used to buld a volume of the rabbit retina and details of the methods used can be found in our PLoS Biology Paper:

J.R. Anderson, B.W. Jones, J-H Yang, M.V. Shaw, C.B. Watt, P. Koshevoy, J. Spaltenstein, E. Jurrus, Kannan U V, R. Whitaker, D. Mastronarde , T. Tasdizen, R.E. Marc. "A Computational Framework for Ultrastructural Mapping of Neural Circuitry" in PLoS Biology, March, vol. 7, no. 3, pp. e74, 2009.
Teaching
Contact Information

Best way to get in touch with me is via email.
Office  WEB 3887
Phone  (801) 581-3539
Fax      (801) 585-6513
Mail     Scientific Computing and Imaging Institute
            University of Utah
            72 S. Central Campus Drive, 3750 WEB
            Salt Lake City, 84112, USA