Curriculum vitae

Person Identification

• David Svoboda
  year of birth: 1978
  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

• Associate 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

• 2017-now: Czech Science Foundation, Czech Republic, GA17-05048S: "Multi-modal Live Cell Segmentation and Tracking", team member
• 2016-2017: Ministry of Education, Youth and Sports, Czech Republic, LM2015062: "National Infrastructure for Biological and Medical Imaging", team member
• 2014-2016: Czech Science Foundation, Czech Republic, GA14-22461S: "Development and Study of Methods for Live Cell Quantification", team member
• 2012-2018: Czech Science Foundation, Czech Republic, GBP302/12/G157: "Dynamics and Organization of Chromosomes in the Cell Cycle and during Differentiation under Normal and Pathological Conditions", team member
• 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", team member
• 2005-2011: Ministry of Education, Czech Republic, MSM-0021622419: "Highly parallel and distributed computing systems", team member
• 2005-2009: Ministry of Education, Czech Republic, LC535: "Dynamics and organization of chromosomes during cell cycle in norm and pathology", team member
• 2005-2006: Ministry of Education, Czech Republic, 1K05021: "Reconstruction of objects from biomedical images using statistic methods and artificial intelligence", key person
• 1999-2003: Ministry of Education, Czech Republic, MSM 143300002, "Application of computer image analysis in optical microscopy", team member

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 - spring 2014
  Digital Image Processing - optional undergraduate course (tutoring); autumn 2002 - now
  Introduction to Digital Image Processing - 1st year undergraduate course (tutoring); spring 2015 - now
  Mathematical Foundations of Computer Science - 1st year undergraduate course (tutoring); autumn 2016 - 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

• 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

• WIESNER, David, Julian SUK, Sven DUMMER, Tereza NEČASOVÁ, Ulman VLADIMÍR, David SVOBODA and Jelmer WOLTERINK. Generative modeling of living cells with SO(3)-equivariant implicit neural representations. Medical Image Analysis. Netherlands: Elsevier, 2024, vol. 2024, No 91, p. 102991-103008. ISSN 1361-8415. Available from: https://dx.doi.org/10.1016/j.media.2023.102991. URL info
• BURGOS, Ninon and David SVOBODA. Biomedical Image Synthesis and Simulation - Methods and Applications. 1st ed. Elsevier, 2022, 674 pp. ISBN 978-0-12-824349-7. URL info
• NEČASOVÁ, Tereza, Ninon BURGOS and David SVOBODA. Validation and evaluation metrics for medical and biomedical image synthesis. In Ninon Burgos, David Svoboda. Biomedical Image Synthesis and Simulation - Methods and Applications. 1st ed. Neuveden: Elsevier, 2022, p. 573-600. The MICCAI Society book Series. ISBN 978-0-12-824349-7. Available from: https://dx.doi.org/10.1016/B978-0-12-824349-7.00032-3. URL info
• ČAPEK, Martin, Michaela BLAŽÍKOVÁ, Ivan NOVOTNÝ, Helena CHMELOVÁ, David SVOBODA, Barbora RADOCHOVÁ, Jiří JANÁČEK and Ondrej HORVÁTH. The Wavelet-Based Denoising Of Images in Fiji, With Example Applications in Structured Illumination Microscopy. Image Analysis & Stereology. International Society for Stereology & Image Analysis, 2021, vol. 40, No 1, p. 3-16. ISSN 1580-3139. Available from: https://dx.doi.org/10.5566/ias.2432. URL info
• KOZLOVSKÝ, Martin, David WIESNER and David SVOBODA. Transfer Learning in Optical Microscopy. Online. In Svoboda D., Burgos N., Wolterink J., Zhao C. Simulation and Synthesis in Medical Imaging. LNCS 12965. Neuveden: Springer, 2021, p. 77-86. ISBN 978-3-030-87591-6. Available from: https://dx.doi.org/10.1007/978-3-030-87592-3_8. URL info
• SVOBODA, David, Ninon BURGOS, Jelmer M. WOLTERINK and Can ZHAO. Simulation and Synthesis in Medical Imaging. 1st ed. Cham: Springer, 2021, 154 pp. ISBN 978-3-030-87591-6. Available from: https://dx.doi.org/10.1007/978-3-030-87592-3. URL info
• SVOBODA, David and Tereza NEČASOVÁ. Image-based Simulations of Tubular Network Formation. Online. In 17th IEEE International Symposium on Biomedical Imaging. Neuveden: IEEE, 2020, p. 1608-1612. ISBN 978-1-5386-9330-8. Available from: https://dx.doi.org/10.1109/ISBI45749.2020.9098736. URL info
• NEČASOVÁ, Tereza and David SVOBODA. Visual and Quantitative Comparison of Real and Simulated Biomedical Image Data. In Laura Leal-Taixé, Stefan Roth. Computer Vision – ECCV 2018 Workshops. LNCS 11134. Munich, Germany: Springer, 2019, p. 385-394. ISBN 978-3-030-11023-9. Available from: https://dx.doi.org/10.1007/978-3-030-11024-6_28. URL info
• WIESNER, David, David SVOBODA, Martin MAŠKA and Michal KOZUBEK. CytoPacq: A web-interface for simulating multi-dimensional cell imaging. Bioinformatics. Oxford University Press, 2019, vol. 35, No 21, p. 4531-4533. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btz417. URL info
• WIESNER, David, Tereza NEČASOVÁ and David SVOBODA. On Generative Modeling of Cell Shape Using 3D GANs. Online. In Ricci Elisa, Rota Buló Samuel, Snoek Cees, Lanz Oswald, Messelodi Stefano, Sebe Nicu. Image Analysis and Processing – ICIAP 2019. LNCS 11752. Trento: Springer, 2019, p. 672-682. ISBN 978-3-030-30644-1. Available from: https://dx.doi.org/10.1007/978-3-030-30645-8_61. URL info
• SVOBODA, David, Tereza NEČASOVÁ, Lenka TESAŘOVÁ and Pavel ŠIMARA. Tubular Network Formation Process Using 3D Cellular Potts Model. In Gooya A., Goksel O., Oguz I., Burgos N. Simulation and Synthesis in Medical Imaging. LNCS 11037. Neuveden: Springer, 2018, p. 90-99. ISBN 978-3-030-00535-1. Available from: https://dx.doi.org/10.1007/978-3-030-00536-8_10. URL info
• SVOBODA, David and Vladimír ULMAN. MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy. IEEE Transactions on Medical Imaging. IEEE Engineering in Medicine and Biology Society, 2017, vol. 36, No 1, p. 310-321. ISSN 0278-0062. Available from: https://dx.doi.org/10.1109/TMI.2016.2606545. URL info
• SEČKÁŘ, Petr and David SVOBODA. FTutor: An Interactive Guide to the Fundamentals of Frequency Analysis. Computer Applications in Engineering Education. Wiley, 2017, vol. 25, No 3, p. 508-520. ISSN 1061-3773. Available from: https://dx.doi.org/10.1002/cae.21817. URL info
• SVOBODA, David and Michal KOZUBEK. Multimodal Simulations in Live Cell Imaging. In Tsaftaris S., Gooya A., Frangi A., Prince J. Simulation and Synthesis in Medical Imaging. LNCS 10557. Neuveden: Springer, 2017, p. 89-98. ISBN 978-3-319-68126-9. Available from: https://dx.doi.org/10.1007/978-3-319-68127-6_10. URL info
• SVOBODA, David, Vladimír ULMAN, Peter KOVÁČ, Barbara ŠALINGOVÁ, Lenka TESAŘOVÁ, Irena KRONTORÁD KOUTNÁ and Petr MATULA. Vascular Network Formation in Silico Using the Extended Cellular Potts Model. In 2016 IEEE International Conference on Image Processing. Piscataway, NJ, USA: IEEE Signal Processing Society, 2016, p. 3180-3183. ISBN 978-1-4673-9961-6. Available from: https://dx.doi.org/10.1109/ICIP.2016.7532946. URL info
• ULMAN, Vladimír, David SVOBODA, Matti NYKTER, Michal KOZUBEK and Pekka RUUSUVUORI. Virtual cell imaging: A review on simulation methods employed in image cytometry. Cytometry Part A. John Wiley & Sons, 2016, 89A, No 12, p. 1057-1072. ISSN 1552-4922. Available from: https://dx.doi.org/10.1002/cyto.a.23031. URL info
• SVOBODA, David, Vladimír ULMAN and Igor PETERLÍK. On Proper Simulation of Chromatin Structure in Static Images As Well As in Time-Lapse Sequences in Fluorescence Microscopy. In Proceedings of 2015 IEEE International Symposium on Biomedical Imaging. Stoughton (WI, USA): Engineering in Medicine and Biology Society, 2015, p. 712-716. ISBN 978-1-4799-2374-8. Available from: https://dx.doi.org/10.1109/ISBI.2015.7163972. info
• SVOBODA, David. Next Step Toward the Automation of Screening for Cervical Cancer. Cytometry Part A. John Wiley & Sons, 2015, 87a, No 3, p. 195-196. ISSN 1552-4922. Available from: https://dx.doi.org/10.1002/cyto.a.22564. URL info
• ULMAN, Vladimír, Zoltán ORÉMUŠ and David SVOBODA. TRAgen: A Tool for Generation of Synthetic Time-Lapse Image Sequences of Living Cells. In Vittorio Murino, Enrico Puppo, Gianni Vernazza. Proceedings of 18th International Conference on Image Analysis and Processing. Heidelberg, Německo: Springer International Publishing, 2015, p. 623-634. ISBN 978-3-319-23230-0. Available from: https://dx.doi.org/10.1007/978-3-319-23231-7_56. info
• STOKLASA, Roman, Tomáš MAJTNER and David SVOBODA. Efficient k-NN based HEp-2 cells classifier. PATTERN RECOGNITION. OXFORD: PERGAMON-ELSEVIER SCIENCE LTD, 2014, vol. 47, No 7, p. 2409-2418. ISSN 0031-3203. Available from: https://dx.doi.org/10.1016/j.patcog.2013.09.021. URL info
• WILLIAMS, Ian, Nicholas BOWRING and David SVOBODA. A performance evaluation of statistical tests for edge detection in textured images. Computer Vision and Image Understanding. Elsevier, 2014, vol. 122, May 2014, p. 115-130. ISSN 1077-3142. Available from: https://dx.doi.org/10.1016/j.cviu.2014.02.009. info
• SVOBODA, David, Vladimír ULMAN, Luděk MATYSKA, Martin MAŠKA, Ján BELLA and Stanislav STEJSKAL. On Proper Simulation of Phenomena Influencing Image Formation in Fluorescence Microscopy. In 2014 IEEE International Conference on Image Processing. Neuveden: IEEE Signal Processing Society, 2014, p. 3944-3948. ISBN 978-1-4799-5750-7. Available from: https://dx.doi.org/10.1109/ICIP.2014.7025801. URL info
• SVOBODA, David. The Importance of Computer Generated Data in Fluorescence Microscopy. In Advances in Molecular and Cancer Biology. 2014. info
• SVOBODA, David, Luděk MATYSKA and Vladimír ULMAN. CytoPacq v2.0. 2013. URL info
• SVOBODA, David and Vladimír ULMAN. Towards a Realistic Distribution of Cells in Synthetically Generated 3D Cell Populations. In Alfredo Petrosino. 17th International Conference on Image Analysis and Processing - ICIAP 2013. LNCS 8157, Part II. Berlin, Heidelberg: Springer-Verlag, 2013, p. 429-438. ISBN 978-3-642-41183-0. Available from: https://dx.doi.org/10.1007/978-3-642-41184-7_44. info
• SVOBODA, David and 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, p. 473-482. ISBN 978-3-642-31297-7. Available from: https://dx.doi.org/10.1007/978-3-642-31298-4_56. info
• MAJTNER, Tomáš and 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, p. 301-307. ISBN 978-0-7695-4873-9. info
• SVOBODA, David, Ondřej HOMOLA and 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, p. 31-39. ISBN 978-3-642-21595-7. Available from: https://dx.doi.org/10.1007/978-3-642-21596-4_4. info
• SVOBODA, David. Efficient Computation of Convolution of Huge Images. In Giuseppe Maino; Gian Luca Foresti. Image Analysis and Processing - ICIAP 2011. LNCS 6978, Part I. Berlin, Heidelberg: Springer-Verlag, 2011, p. 453-462. ISBN 978-3-642-24084-3. info
• WILLIAMS, Ian, David SVOBODA and 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, p. 91-97. ISBN 978-989-674-028-3. info
• SVOBODA, David, Michal KOZUBEK and 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, 75A, No 6, p. 494-509. ISSN 1552-4922. Available from: https://dx.doi.org/10.1002/cyto.a.20714. info
• SVOBODA, David, Michal KOZUBEK and 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. URL info
• SVOBODA, David and Michal KOZUBEK. CytoPacq – On-line Framework for Simulating Fluorescence Microscopy Images. In Hands-on Image Processing, Robotiker-Tecnalia, Bilbao, Spain. 2009. info
• KOZUBEK, Michal, David SVOBODA, Marek KAŠÍK, Martin MAŠKA, Jan HUBENÝ, Stanislav STEJSKAL, Michal SEEMAN and 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 and 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 and 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, p. 68121J-1-12, 12 pp. ISBN 978-0-8194-6984-7. URL info
• SVOBODA, David, Marek KAŠÍK, Martin MAŠKA, Jan HUBENÝ, Stanislav STEJSKAL and Michal ZIMMERMANN. On Simulating 3D Fluorescent Microscope Images. In Computer Analysis of Images and Patterns. Berlin, Heidelberg: Springer-Verlag, 2007, p. 309-316. ISBN 978-3-540-74271-5. URL info
• MAŠKA, Martin, Jan HUBENÝ, David SVOBODA and Michal KOZUBEK. A Comparison of Fast Level Set-Like Algorithms for Image Segmentation in Fluorescence Microscopy. Online. In 3rd International Symposium on Visual Computing. Berlin, Heidelberg: Spinger-Verlag, 2007, p. 571-581. ISBN 978-3-540-76855-5. URL info
• SVOBODA, David, Ian WILLIAMS, Nicholas BOWRING and Elizabeth GUEST. Statistical techniques for edge detection in histological images. In First International Conference on Computer Vision Theory and Applications. Portugalsko: INSTICC Press, 2006, p. 457-462. ISBN 972-8865-40-6. info
• WILLIAMS, Ian, David SVOBODA, Nicholas BOWRING and Elizabeth GUEST. Improved statistical edge detection through neural networks. In 10th Conference on Medical Image Understanding and Analysis. Manchester: BMVA, 2006, p. 56-60. ISBN 1-901727-31-9. URL info
• KOZUBEK, Michal, Pavel MATULA, Petr MATULA and 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, p. 24-27. 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, p. 430-434. ISBN 0-88986-454-3. URL info
• SVOBODA, David and 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, p. 499-503. ISBN 0-88986-382-2. URL info
• MATULA, Pavel and David SVOBODA. 3D Object reconstructions in image cytometry. In Biophysics of the Genome. Brno: Masaryk University, 2003, p. 49-50. ISBN 80-210-3226-X. info
• SVOBODA, David and Pavel MATULA. Tissue image reconstruction: Localization of nuclei markers and segmentation based on deformable models. In Biophysics of the Genome. Brno: Masaryk University, 2003, p. 67-70. ISBN 80-210-3226-X. info
• SVOBODA, David and Pavel MATULA. Tissue Reconstruction Based on Deformation of Dual Simplex Meshes. In Discrete Geometry for Computer Imagery. Berlin, Heidelberg, New York: Springer, 2003, p. 514-523. ISBN 3-540-20499-7. URL info
• MATULA, Pavel and David SVOBODA. Spherical Object Reconstruction Using Simplex Meshes from Sparse Data. In Discrete Geometry for Computer Imagery. Berlin Heidelberg New York: Springer-Verlag, 2003, p. 524-533. ISBN 3-540-20499-7. URL info
• MATULA, Pavel and David SVOBODA. Cell Nuclei Segmentation Using Star-Shaped Simplex Meshes. In Biophysics of the Genome and Its Interactions. Brno: Masaryk University, 2002, p. 74-76. ISBN 80-210-2853-X. info
• MATULA, Pavel and 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, p. 608-620. ISBN 3-540-42523-3. URL info

2018/02/01