Personal Details

Name:
Date of Birth:
e-mail:
Web:
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Nationality:
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Occupation:
Stefan Schenke
28th May 1978
stefan_schenke@yahoo.de
www.stefan-schenke.net/cv
+49 179 32 82 795

German
German, English
MSc. Student in Computer Science


Education

October 1998 to July 2005: Study of MSc. in Computer Science with minor subject Medical Science
at the Friedrich-Schiller-University in Jena, Germany

December 2004 to June 2005:

Preparation of MSc. Thesis "Analysis and Design of GPU-based Algorithms for Interactive Volume Segmentation" at the University of Auckland, New Zealand

Taken Computer Science courses including:
  • Object Oriented Analysis and Design, Software Development Techniques
  • Pattern Recognition, Digital Image Processing, 3D Computer Vision
  • Computational Geometry, Parallel Computing
Taken Medical courses:
  • Medical Imaging Techniques (X-Ray, MRT, CT, UltraSound, PET,...)
  • Image Processing Methods for Medical Diagnosis
  • Radiological Treatment
  • Basic courses in Pathophysiology, Physiology, Anatomy
February 2001: Associate Degree in Computer Science from the Friedrich-Schiller-University in Jena, Germany


Work Experience

November 2005 to April 2007: Research Associate at the Department for Experimental Ophthalmology at the Friedrich-Schiller-University, Jena, Germany.

In this project an industrial Laser Scanning Ophthalmoscope has been advanced to allow for 2-dimensional Fluorescence Lifetime Imaging (FLIM) at the human ocular fundus. The method of Time Correlated Single Photon Counting is used in conjunction with a sensitive detector to determine the decay-times of the natural fluorophores. The aim of this project is to measure certain parameters of metabolism in the retinal tissue and detect diseases like age-related macula degeneration (AMD), diabetic retinopathy or glaucoma before pathological changes are manifest.

Please see publications for further details.

Main achievements in this research group:
  • Design and implementation of a multithreaded, synchronized device-control, realtime data acquisition and alignment software; as plugin for vendor specific software-suite
  • Contribution to measurement system arrangement and improvement
  • Design of a Data Analysis and Visualization Tool for the spatial- and time-resolved multiexponential measurement data
  • Development of an Image Registration Tool using the ITK-Library

Head of Research Group: HDoz. Dr.-Ing. habil. Dietrich Schweitzer


TauMapper

FLIMVis

ImageRegistration


December 2004 to June 2005: Preparation of MSc. Thesis "Analysis and Design of GPU-based Algorithms for Interactive Volume Segmentation" at the University of Auckland, New Zealand

  • Design and implementation of GPU-based 3D image processing techniques, including:
    • Mean- and anisotropic diffusion filter for image enhancement
    • Threshold-based segmentation and seeding
    • 3D morphological seed manipulation
    • 3D theshold-based and anisotropic diffusion-based seeded region growing segmentation
  • Integration as a plugin into the Visualization Toolkit architecture
  • Development of an application providing
    • im/export of 3D datasets
    • GUI for interactive control of filter\segmentation process
    • basic volume rendering / slice viewing using VTK visualization functionality

Supervised by Prof. Denzler and Burkhard Wünsche, PhD


GPU-based Volume Segmentation

GPU-based Volume Segmentation

GPU-based Volume Segmentation


May 2004 to October 2004: Part-time based work in the Software Engineering Department of Carl Zeiss Meditec in Jena, Germany.
  • Design, implementation and test of a Windows Driver Model (WDM) device driver for an ophthalmic Fundus Camera under Windows XP
  • Contribution to technical project documentation

Carl Zeiss Meditec
March 2002 to July 2004: Collaboration in a research project at the Department for Experimental Ophthalmology at the Friedrich-Schiller-University, Jena, Germany.
In this project a Confocal Laser Scanning Ophthalmoscope has been advanced to measure the 2-dimensional time-resolved autofluorescence of the ocular fundus. The method of Time Correlated Single Photon Counting is used in conjunction with a sensitive detector to determine the decay-times of the natural fluorophores. The aim of this project is to measure certain parameters of metabolism in the retinal tissue and detect diseases like age-related macula degeneration (AMD), diabetic retinopathy or glaucoma before pathological changes are manifest. This research project is partially funded by the Federal Ministry for Education and Research.
I have contributed to the development of a measurement-technique which led to the application of a patent. Please see publication-section for further details and achievements.

My assignment was the development of the measurement software "EyeScan" with the following features:

  • control of the measurement sequence
  • streaming of continuous video images of reflected light from the Confocal Laser Scanning Ophthalmoscope in real-time
  • adjustment of the control-parameters of a special Time-Correlated-Single-Photon-Counting PCI device to detect fluorescence-photons
  • triggers synchronized measurements of a framegrabber and the TCSPC-device
  • visualization of the collected 2-dimensional autofluorescence distribution of the fundus in pseudo-color which can be interactively adjusted
  • automatical detection of eye-movements between different measurements by image-registration techniques
  • merge of several shift corrected measurements to increase the number of detected photons per pixel
  • visualization of the decay versus time curve for every pixel of the fluorescence image at the mouse-cursor
  • storage of the acquired reflection- and fluorescence-data in a specific fileformat
  • export of fluorescence-decay-data for further analysis
  • provides an easy to use graphical user interface
  • uses DirectDraw to increase performance

Supervised by HDoz. Dr.-Ing. habil. Dietrich Schweitzer


Screenshot of EyeScan
September 2003 to January 2004: Development of the software VesselO2 for a research project at the Department for Experimental Ophthalmology at the Friedrich-Schiller-University, Jena, Germany. It is used to compute the oxygen saturation in the retina from images taken by a fundus camera at different wavelengths of the reflected light.
  • reads a set of fundus camera images at different wavelengths
  • performs several image processing techniques to detect the location and expansion of retinal blood vessels
  • computes the 2-dimensional local distribution of the oxygen saturation in vessel areas as well as the ocular fundus itself
  • visualizes the oxygen saturation with a pseudocolor technique which the user can interactively adjust
  • allows export of computed saturation data to an ASCII-file format to easily enable further processing in other applications

Under direction by HDoz. Dr.-Ing. habil. Dietrich Schweitzer


Screenshot of VesselO2
March to June 2002: Development of the medical data-acquisition and -visualization software "Liquo" in conjunction with the MD thesis of a medical science student at the Department of Anesthesiology and Intensive Care Medicine of the Friedrich-Schiller-University, Jena, Germany.
  • receives real-time data from an arterial and central-venous-catheter based physiological monitor system
  • performs pulse-contour analysis on the blood-pressure curve to detect systoles and computes the systolic-pressure-variation, a new technique for clinical assessment of cardiac preload and volume responsiveness which was the subject of the PhD thesis
  • visualizes a detailed blood-pressure curve with a trend-curve as well as other physiological hemodynamic variables like current heart rate, systolic and diastolic arterial blood pressure
  • streams the received data to a file and offers export of relevant data to Excel compatible files
  • has successfully been used during major surgery and proved clinical relevance of the concept of systolic-pressure-variation

Supervised by Samir Sakka, MD, PhD


Screenshot of Liquo

www.pulsion.de
August to October 2001: Internship at Vulpine 3D Technologies GmbH which evolved to Trinigy GmbH, Reutlingen, Germany.
  • Conception, development and examination of automated test processes for the Vulpine Vision 3D Engine
  • Generation and tweaking of shaders within the Vulpine ShaderTool
  • Collaboration on the implementation of constructive solid geometry functions within Vulpine proprietary tools

References provided on request


www.trinigy.de
May 1998 to June 2001: Student Assistant at the Fraunhofer Institute for Applied Optics and Precision Engineering, Jena, Germany.
  • Development of a highspeed projection system for an optical 3D-Scanning-System using DirectDraw
  • Maintenance of the code of a configuration program of the optical 3D-Scanning-System
  • Programming a microcontroller for an underwater transmissiometer built for environmental investigations, which controls the electronic parts inside and communicates (receiving commands as well as transferring measured data) with an user above the water surface
  • Programming "VisualBasic for Applications"-macros for Excel to process the acquired data and storing it via ODBC in an Oracle database

References provided on request


www.iof.fhg.de


Referees

HDoz. Dr.-Ing. habil. Dietrich Schweitzer Research Department Experimental Ophthalmology at the
Friedrich-Schiller-University Hospital, Jena, Germany
Dietrich.Schweitzer@med.uni-jena.de
Phone: +49 3641 933027

Burkhard Wünsche, PhD Graphics Group / Biomedical Imaging & Visualization
Department of Computer Science
University of Auckland, Auckland, New Zealand
burkhard@cs.auckland.ac.nz
Phone: +64 9 3737 599 x83705

Samir Sakka, MD, PhD Department of Anesthesiology and Intensive Care Medicine of the
Friedrich-Schiller-University Hospital, Jena, Germany
Samir.Sakka@med.uni-jena.de
Phone: +49 3641 9 32 22 48


Publications

Publications

  • In vivo autofluorescence lifetime imaging at the fundus of the human eye
    Dietrich Schweitzer, Martin Hammer, Frank Schweitzer, Stefan Schenke, Eckhard Birckner, Wolfgang Becker, Axel Bergmann
    Proceedings of SPIE Vol. 6138 (2006) 613808-1 – 613808-10

  • GPU-Based Volume Segmentation
    Stefan Schenke and Burkhard C. Wünsche
    Image and Vision Computing New Zealand, Dunedin, 28.-29. November 2005

  • Comparison of time-resolved autofluorescence in the eye-ground of healthy subjects and patients suffering from age-related macula degeneration
    D. Schweitzer, F. Schweitzer, M. Hammer, S. Schenke, S. Richter
    Progress in Biomedical Optics and Imaging, Vol. 6, No. 31, SPIE 5862, 58620 R-1 – 58620 R-12, 2005

  • Time-Resolved Autofluorescence Yields More Information Than Intensity Measurements of Fundus Autofluorescence
    D. Schweitzer, F. Schweitzer, M. Hammer, S. Schenke, S. Richter
    Invest. Ophthalmol. Vis. Sci. 46: E-Abstract 227, 2005

  • In vivo measurement of time-resolved autofluorescence at the human ocular fundus
    D. Schweitzer, M. Hammer, F. Schweitzer, R. Anders, T. Doebbecke, S. Schenke, E. R. Gaillard
    Journal of Biomedical Optics, Vol. 9 No. 6 pp 1214-1222, 2004

  • Veränderungen der Autofluoreszenzlebensdauer am Fundus nach Sauerstoffprovokation
    (Alteration of autofluorescence decay time in the fundus after breathing 100% oxygen)

    Schweitzer D., Hammer M., Anders R., Doebbecke T., Schenke S.
    Ophthalmologe 2004, 101:66-72

  • Metabolic mapping by time-resolved autofluorescence
    Schweitzer D., Hammer M., Schenke S., Anders R.
    European Journal of Ophthalmology Vol. 13 No. 2, 2003, p 230

  • Evaluation of time-resolved autofluorescence images of the ocular fundus
    Schweitzer D., Hammer M., Schweitzer F., Schenke S., Gaillard E.R.
    Proceedings of SPIE 5141 "Diagnostic Optical Spectroscopy in Biomedicine II" ed. by G.A. Wagnieres, 2003 pp 8-17

Talks

  • Steuerung der intraoperativen Volumentherapie an Hand der systolischen Druckvariation: Gibt es Vorteile hinsichtlich der Organfunktionen?
    M. Büttner, S. Schenke, O. Thümer, W. Schummer, S. G. Sakka
    Deutscher Anästhesiecongress, München, 16.–19. April 2005

  • Systolic pressure variation guided volume therapy – are there any advantages in organ function?
    O. Thümer, M. Büttner, S. Schenke, W. Schummer, S. G. Sakka
    European Society of Intensive Care Medicine - 18th Annual Congress, Amsterdam, 25.–28. September 2005

  • Comparison of time-resolved autofluorescence in the eye-ground of healthy subjects and patients suffering from age-related macular degeneration
    D. Schweitzer, F. Schweitzer, M. Hammer, S. Schenke, S. Richter
    European Conference on Biomedical Optics, München, Mai 2005-10-04

  • Interpretation der dynamischen Autofluoreszenz am Augenhintergrund
    D. Schweitzer, F. Schweitzer, M. Hammer, S. Richter, S. Schenke
    XIV. Workshop „Okuläre Mikrozirkulation“, Weimar, 26.–27. Februar 2005

  • Diagnostische Möglichkeiten der zeitlich und spektral aufgelösten Autofluoreszenzbeobachtung bei alterbedingter Makuladegeneration
    M. Hammer, D. Schweitzer, S. Richter, S. Schenke
    13. Tagung der Gesellschaft der Augenärzte Sachsen-Anhalts und Thüringens, Jena, 12.–13. November 2004

  • Erste Studienergebnisse zur Messung der 2-dimensional zeitaufgelösten Autofluoreszenz am Augenhintergrund
    D. Schweitzer, F. Schweitzer, S. Schenke, M. Hammer, S. Richter
    XIII Workshop „Okuläre Mikrozirkulation“, München, 28.–29. Februar 2004

  • Evaluation of time-resolved autofluorescence images of the ocular fundus
    Schweitzer D., Hammer M., Schweitzer F., Schenke S., Gaillard E.R.
    European Conference on Biomedical Optics June, 22-25, 2003, Munich

  • Metabolic mapping by time-resolved autofluorescence
    Schweitzer D., Hammer M., Schenke S., Anders R.
    International Workshop NTG & PEX, April 3-5, 2003, Erlangen, Germany

  • Metabolic mapping by time-resolved autofluorescence
    Schweitzer D., Hammer M., Schenke S., Anders R.
    3. CAFIA meeting Computer Assisted Fundus Image Analysis, March 28-30, 2003, Torino, Italy

  • Änderung der zeitaufgelösten Autofluoreszenz nach Sauerstoffprovokation
    D. Schweitzer, M. Hammer, S. Schenke, P. Gänßler
    Workshop "Okuläre Mikro- und Makrozirkulation" Dresden, 28. Februar – 01. März 2003

Pending Patent

  • Verfahren und Anordnung zur Gewinnung und Auswertung kontrastreicher Bilder der zeitaufgelösten Fluoreszenz von bewegten Objekten, beispielsweise des Augenhintergrundes
    (Method and arrangement for acquisition and evaluation of contrast-rich images of time-resolved fluorescence of moving objects, e.g. the ocular fundus)

    Schweitzer D., Schweitzer F., Schenke S., Hammer M.
    10. February 2004, Aktenzeichen 102004006960.3

Skills

Programming:

  • Several years experience in Object Oriented Software Development in C/C++
    using Microsoft Visual Studio .NET
  • Developing Graphical / Image Processing Applications using
    • The Visualization Toolkit (VTK)
    • The Insight Toolkit (ITK)
    • OpenGL
    • High Level Shading Languages (GLSL, Cg)
    • DirectX, esp. Direct3D, DirectDraw
  • GPGPU-Development
    Implementing Image Processing Tasks on GPUs
  • Knowledge of Win32-API including
    GUI / Controls / Windowing / GDI / GDI+ / Multithreading
  • Basic knowledge in Matlab, JAVA, PASCAL, VisualBasic, HTML 4.0, CSS

General:

  • MS Windows XP, 2000, 98
  • MS Office including database design and VBA-macro-programming in MS Access
  • basic Unix/Linux

Personal:

  • ability to work in a team environment as well as self-dependent
  • research experience
  • working reliably and precisely
  • ability to learn quickly new methods and techniques
  • being versatile and flexible