RNDr. David Svoboda, Ph.D.

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Person Identification
  • David Svoboda
    year of birth: 1978, state: married, 3 children
    languages: Czech (native), English, elementary knowledge of German and Italian
Workplace
  • Centre for Biomedical Image Analysis
    Faculty of Informatics
    Masaryk University
    Botanická 68a
    602 00 BRNO, Czech Republic
Position
  • Assistant Professor
Education and Academic Qualifications
  • 2004: PhD Thesis: Cell boundary extraction from 3D histo-pathological images. Defended at FI MU Brno
  • 2001 - 2004: PhD studies under the supervision of Michal Kozubek. Laboratory of Optical Microscopy, Faculty of Informatics, Masaryk University, Brno.
  • 2003: RNDr. Thesis: Tissue image reconstruction. Defended at FI MU Brno
  • 2001: Obtained Mgr. (master's degree) in computer science, graduated with honours. Diploma thesis: Use of deformable models in biomedical image analysis (in czech). Faculty of Informatics, Masaryk University, Brno.
  • 1996 - 2001: student at the Faculty of informatics MU Brno
  • 1992 - 1996: Secondary grammar school with emphasis on math and physics in Brno, graduated with honours
Research Projects and Grants
  • Co-investigator:
    2006-2011: Ministry of Education, Czech Republic, 2B06052: "Determination of markers, screening and early diagnostics of cancer diseases using highly automated processing of multidimensional biomedical images"
    2005-2009: Ministry of Education, Czech Republic, LC535: "Dynamics and organization of chromosomes during cell cycle in norm and pathology"
    2005-2006: Ministry of Education, Czech Republic, 1K05021: "Reconstruction of objects from biomedical images using statistic methods and artificial intelligence"
    1999-2003: Ministry of Education, Czech Republic, MSM 143300002, "Application of computer image analysis in optical microscopy"
Pedagogical Activities
  • tutorials and lectures at FI MU (Brno, CZ):
    Digital Filtering - optional graduate course; spring 2007 - now
    Introduction to Programming - 1st year undergraduate course (tutoring); autumn 2001
    Design of Algorithms I - 1st year undergraduate course (tutoring); spring 2002, spring 2007 - now
    Digital Image Processing - optional undergraduate course (tutoring); autumn 2002 - now
  • tutorials and lectures at MMU (Manchester, UK):
    Mathematics I (tutoring) - autumn 2005, spring 2006
    Programming laboratory - autumn 2005, spring 2006
    Mathematics tutorial I - autumn 2005, spring 2006
Scientific and Research Activities
  • image processing; biomedical image segmentation; optimization; edge detection; simulation
Academical Stays
  • 2010: International School of Physics "Enrico Fermi"; topic: Advanced methods in optical fluorescence microscopy towards nanoscopy; location: Varenna (Italy)
  • 2009: 21st International School for Computer Science Researchers; topic: Molecular and Medical Image Analysis and BioInformatics; location: Lipari island (Italy)
  • 2007: ICVSS - International Computer Vision Summer School; topic: Detection, Recognition and Segmentation in Context; location: Sicily (Italy)
  • 2005 - 2006: Department of Engineering and Technology, Manchester Metropolitan Unversity, United Kingdom
Appreciation of Science Community
  • 2001 - Awarded the dean's prize for the educational results, Faculty of Informatics, Masaryk University, Brno.
Selected Publications
  • STOKLASA, Roman, Tomáš MAJTNER a David SVOBODA. Efficient k-NN based HEp-2 cells classifier. PATTERN RECOGNITION, OXFORD: PERGAMON-ELSEVIER SCIENCE LTD, 2014, roč. 47, č. 7, s. 2409-2418. ISSN 0031-3203. doi:10.1016/j.patcog.2013.09.021. URLinfo
  • WILLIAMS, Ian, Nicholas BOWRING a David SVOBODA. A performance evaluation of statistical tests for edge detection in textured images. Computer Vision and Image Understanding, Elsevier, 2014, roč. 122, May 2014, s. 115-130. ISSN 1077-3142. doi:10.1016/j.cviu.2014.02.009. info
  • SVOBODA, David, Luděk MATYSKA a Vladimír ULMAN. CytoPacq v2.0. 2013. URLinfo
  • SVOBODA, David a Vladimír ULMAN. Towards a Realistic Distribution of Cells in Synthetically Generated 3D Cell Populations. In Alfredo Petrosino. 17th International Conference on Image Analysys and Processing - ICIAP 2013. LNCS 8157, Part II. Berlin, Heidelberg: Springer-Verlag, 2013. s. 429-438, 10 s. ISBN 978-3-642-41183-0. doi:10.1007/978-3-642-41184-7_44. info
  • SVOBODA, David a Vladimír ULMAN. Generation of Synthetic Image Datasets for Time-Lapse Fluorescence Microscopy. In Campilho, Aurélio; Kamel, Mohamed. Proceedings of 9th International Conference on Image Analysis and Recognition. LNCS 7325, Part II. Heidelberg: Springer-Verlag, 2012. s. 473-482, 10 s. ISBN 978-3-642-31297-7. doi:10.1007/978-3-642-31298-4_56. info
  • MAJTNER, Tomáš a David SVOBODA. Extension of Tamura Texture Features for 3D Fluorescence Microscopy. In 2012 Second Joint 3DIM/3DPVT Conference: 3D Imaging, Modeling, Processing, Visualization & Transmission. Los Alamitos, CA, USA: IEEE Computer Society, 2012. s. 301-307, 7 s. ISBN 978-0-7695-4873-9. info
  • SVOBODA, David, Ondřej HOMOLA a Stanislav STEJSKAL. Generation of 3D Digital Phantoms of Colon Tissue. In M. Kamel and A. Campilho. Proceedings of 8th International Conference on Image Analysis and Recognition. LNCS 6754, Part II. Berlin, Heidelberg: Springer-Verlag, 2011. s. 31-39, 9 s. ISBN 978-3-642-21595-7. info
  • SVOBODA, David. Efficient Computation of Convolution of Huge Images. In Giuseppe Maino; Gian Luca Foresti. Image Analysys and Processing - ICIAP 2011. LNCS 6978, Part I. Berlin, Heidelberg: Springer-Verlag, 2011. s. 453-462, 10 s. ISBN 978-3-642-24084-3. info
  • WILLIAMS, Ian, David SVOBODA a Nicholas BOWRING. A Novel Performance Metric For Grey-Scale Edge Detection. In Proceedings of the International Conference on Computer Vision Theory and Applications. Vol. 1. Portugal: Institute for Systems and Technologies of Information, Control and Communication, 2010. s. 91-97, 7 s. ISBN 978-989-674-028-3. info
  • SVOBODA, David, Michal KOZUBEK a Stanislav STEJSKAL. Generation of Digital Phantoms of Cell Nuclei and Simulation of Image Formation in 3D Image Cytometry. Cytometry Part A, John Wiley & Sons, Inc., 2009, roč. 75A, č. 6, s. 494-509. ISSN 1552-4922. info
  • SVOBODA, David, Michal KOZUBEK a Stanislav STEJSKAL. Towards Proper Evaluation of Image Analysis Methods Used in Biomedical Research. In Analytical Cytometry V, International Conference. 2009. ISBN 978-80-254-2561-5. URLinfo
  • KOZUBEK, Michal, David SVOBODA, Marek KAŠÍK, Martin MAŠKA, Jan HUBENÝ, Stanislav STEJSKAL, Michal SEEMAN a Pavel ZEMČÍK. Simulation of fluorescence image formation in 3D image cytometry. In XXIV International Congress of International Society for Analytical Cytology. 2008. info
  • KOZUBEK, Michal, David SVOBODA, Marek KAŠÍK, Martin MAŠKA, Jan HUBENÝ, Stanislav STEJSKAL, Michal SEEMAN a Pavel ZEMČÍK. Simulation of fluorescence image formation in 3D light microscopy. In 8th Meeting of European Light Microscopy Initiative. 2008. info
  • WILLIAMS, Ian, David SVOBODA, Nicholas BOWRING a Elizabeth GUEST. Statistical Edge Detection of Concealed Weapons Using Artificial Neural Networks. In Proceedings of SPIE-IS&T Electronic Imaging. Vol. 6812. Bellingham, Washington: SPIE, 2008. s. 68121J-1-12, 12 s. ISBN 978-0-8194-6984-7. URLinfo
  • SVOBODA, David, Marek KAŠÍK, Martin MAŠKA, Jan HUBENÝ, Stanislav STEJSKAL a Michal ZIMMERMANN. On Simulating 3D Fluorescent Microscope Images. In Computer Analysis of Images and Patterns. Berlin, Heidelberg: Springer-Verlag, 2007. s. 309-316, 8 s. ISBN 978-3-540-74271-5. URLinfo
  • MAŠKA, Martin, Jan HUBENÝ, David SVOBODA a Michal KOZUBEK. A Comparison of Fast Level Set-Like Algorithms for Image Segmentation in Fluorescence Microscopy. In 3rd International Symposium on Visual Computing. Berlin, Heidelberg: Spinger-Verlag, 2007. s. 571-581, 11 s. ISBN 978-3-540-76855-5. URLinfo
  • SVOBODA, David, Ian WILLIAMS, Nicholas BOWRING a Elizabeth GUEST. Statistical techniques for edge detection in histological images. In First International Conference on Computer Vision Theory and Applications. Portugalsko: INSTICC Press, 2006. s. 457-462, 6 s. ISBN 972-8865-40-6. info
  • WILLIAMS, Ian, David SVOBODA, Nicholas BOWRING a Elizabeth GUEST. Improved statistical edge detection through neural networks. In 10th Conference on Medical Image Understanding and Analysis. Manchester: BMVA, 2006. s. 56-60, 5 s. ISBN 1-901727-31-9. URLinfo
  • KOZUBEK, Michal, Pavel MATULA, Petr MATULA a David SVOBODA. Analysis of biomedical image data acquired using optical microscopy. In Prague Post Genome Technology Workshop. Prague, Czech Republic: Czech Pattern Recognition Society, 2005. s. 24-27, 4 s. ISBN 80-01-03239-6. info
  • SVOBODA, David. Towards a Fully Automated Tissue Cell Segmentation Method. In Visualization, Imaging, and Image Processing. Anaheim, Calgary, Zurich: ACTA Press, 2004. s. 430-434, 5 s. ISBN 0-88986-454-3. URLinfo
  • SVOBODA, David a Pavel MATULA. Multilevel Adaptive Thresholding and Dual Simplex Mesh Deformation as a Tool for Tissue Reconstruction. In Visualization, Imaging, and Image Processing. Anaheim, Calgary, Zurich: ACTA Press, 2003. s. 499-503, 5 s. ISBN 0-88986-382-2. URLinfo
  • MATULA, Pavel a David SVOBODA. 3D Object reconstructions in image cytometry. In Biophysics of the Genome. Brno: Masaryk University, 2003. s. 49-50, 2 s. ISBN 80-210-3226-X. info
  • SVOBODA, David a Pavel MATULA. Tissue image reconstruction: Localization of nuclei markers and segmentation based on deformable models. In Biophysics of the Genome. Brno: Masaryk University, 2003. s. 67-70, 4 s. ISBN 80-210-3226-X. info
  • SVOBODA, David a Pavel MATULA. Tissue Reconstruction Based on Deformation of Dual Simplex Meshes. In Discrete Geometry for Computer Imagery. Berlin, Heidelberg, New York: Springer, 2003. s. 514-523, 10 s. ISBN 3-540-20499-7. URLinfo
  • MATULA, Pavel a David SVOBODA. Spherical Object Reconstruction Using Simplex Meshes from Sparse Data. In Discrete Geometry for Computer Imagery. Berlin Heidelberg New York: Springer-Verlag, 2003. s. 524-533, 10 s. ISBN 3-540-20499-7. URLinfo
  • MATULA, Pavel a David SVOBODA. Cell Nuclei Segmentation Using Star-Shaped Simplex Meshes. In Biophysics of the Genome and Its Interactions. Brno: Masaryk University, 2002. s. 74-76. ISBN 80-210-2853-X. info
  • MATULA, Pavel a David SVOBODA. Spherical Object Reconstruction Using Star-Shaped Simplex Meshes. In Energy Minimization Methods in Computer Vision and Pattern Recognition. Berlin, Heidelberg, New York: Springer-Verlag, 2001. s. 608-620. ISBN 3-540-42523-3. URLinfo

Last update: 2012/02/21