Assoc. Prof. RNDr. Pavel Matula, Ph.D.

Vice-dean for bachelor and master studies – Faculty of Informatics


Office: A308
Botanická 554/68a
602 00 Brno

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Phone: +420 549 49 4752
E‑mail:
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Curriculum vitae

Person Identification
  • doc. RNDr. Pavel Matula, Ph.D., born January 26, 1975 in Ivančice, Czechoslovakia, 2 children
Workplace
  • Centre for Biomedical Image Analysis (cbia.fi.muni.cz)
    Faculty of Informatics
    Masaryk University
    Botanicka 68a
    602 00 Brno
    Czech Republic
Employment Position
  • Associate Professor, Vice-dean for Batchelor and Master Studies
Education and Academic Qualifications
  • 2013: Associate Professor of Computer Science, Faculty of Informatics, Masaryk University, Brno.
  • 2004: RNDr. in Computer Science, Faculty of Informatics, Masaryk University, RNDr Thesis: "Spherical Object Reconstruction Using Simplex Meshes and its Application in Cytometry" (in Czech)
  • 2003: Ph.D. in Computer Science, Faculty of Informatics, Masaryk University, PhD Thesis: "Three-dimensional Object Reconstruction and its Application in Cytometry" (in Czech)
  • 1998: MSc in Computer Science, Faculty of Informatics, Master Thesis: "Recognition of Basic Window Composition Diagrams" (in Czech)
Overview of Employment
  • 2013-present: Faculty of informatics, Masaryk University, Brno, Czech Republic, associate professor
  • 2009-2015: Institute of Biophysics, Academy of Sciences, Brno, Czech Republic, research and development
  • 2006-2013: Faculty of informatics, Masaryk University, Brno, Czech Republic, assistant professor
  • 2004-2006: Institute of Biophysics, Academy of Sciences, Brno, Czech Republic, research and development
  • 2003-2006: Faculty of informatics, Masaryk University, Brno, Czech Republic, research and development
Pedagogical Activities
  • 2001-present: Advisor of numerous bachelor and master thesis (more than 40)
  • 2005-present: Advisor of 3 Ph.D. students (3 already successfully finished)
  • 2005-present: Advanced Methods of Digital Image Processing
  • 2002-present: Labs on Digital Image Processing
  • 2006-present: Digital Geometry
  • 2013-present: Mathematics for Computer Graphics
  • 2007: Design of Algorithms
  • 2005,2011: Mathematical Morphology
Scientific and Research Activities
  • Image analysis using mathematically well founded methods
  • Cytogenetic applications
    Research projects:
  • 2014-2016: MUNI/M/1050/2013, "Automatizovaná analýza elektronmikroskopických snímků pro použití v biologii a medicíně" (main investigator)
  • 2003-2006: GACR 204/03/D034, "Three-dimensional analysis of cell nuclei using image cytometry" (main investigator)
  • 2014-2016: GA14-22461S, Development and Study of Methods for Live Cell Quantification (team member)
  • 2012-2018: Ministry of Education, Czech Republic, GAP302/12/G157: Dynamika a organizace chromosomů během buněčného cyklu a při diferenciaci v normě a patologii (team member)
  • 2006-2011: Ministry of Education, Czech Republic, MSM 2B06052: Vytipování markerů, screening a časná diagnostika nádorových onemocnění pomocí vysoce automatizovaného zpracování multidimenzionálních biomedicínských obrazů (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)
  • 2004-2006: EU FP6, "3d Genome structure and function" (team member) 2002-2006: Academy of Sciences, Czech Republic, A1065203, "The use of combination of laser microbeam and cytometric techniques in the study of the structure and dynamics of human genome" (team member)
  • 2000-2002: Volkswagen Stiftung, Germany, I/75 946, "Automated micro-axial tomography of tumor-correlated FISH pattern" (team member)
  • 2000-2004: Academy of Sciences, Czech Republic, S5004010, "Development of new diagnostic techniques for oncology" (team member)
  • 1999-2003: Ministry of Education, Czech Republic, MSM 143300002, "Application of computer image analysis in optical microscopy" (team member)
  • 1999-2003: MSMT CR MSM 143300002, "Application of computer image analysis in optical microscopy" (team member)
Academical Stays
  • 2008, one month: Center for Applied Medical Research, University of Navarra, Pamplona, Spain
  • 2005, one month: Mathematical Image Analysis Group, Saarland University, Germany
University Activities
  • 2015-present: Vice-dean for Batchelor and Master Studies
  • 2012-2015: Member, Academic senate MU
  • 2011-2015: Member, Academic senate FI MU
  • 2012-2015: Chair, Academic senate FI MU
  • 2011-2016: Member, Disciplinary committee FI MU
Membership in Scientific Societes
  • 2002-present: Member, Czechoslovak Microscopy Society (CSMS)
  • 2002-present: Member, European Microscopy Society (EMS)
  • 2004-present: Member, Czech Society for Analytical Cytology (CSAC)
  • 2008-present: Member, IEEE Engineering in Medicine and Biology Society (IEEE EMBS)
Selected Publications
  • MATULA, Pavel, Martin MAŠKA, Dmitry SOROKIN, Petr MATULA, Carlos ORTIZ-DE-SOLÓRZANO a Michal KOZUBEK. Cell tracking accuracy measurement based on comparison of acyclic oriented graphs. PLoS ONE, 2015, roč. 10, č. 12, s. "e0144959". ISSN 1932-6203. doi:10.1371/journal.pone.0144959. URL info
  • MAŠKA, Martin, Vladimír ULMAN, David SVOBODA, Pavel MATULA, Petr MATULA, Cristina EDERRA, Ainhoa URBIOLA, Tomás ESPAÑA, Subramanian VENKATESAN, Deepak M W BALAK, Pavel KARAS, Tereza BOLCKOVÁ, Markéta ŠTREITOVÁ, Craig CARTHEL, Stefano CORALUPPI, Nathalie HARDER, Karl ROHR, Klas E G MAGNUSSON, Joakim JALDÉN, Helen M BLAU, Oleh DZYUBACHYK, Pavel KŘÍŽEK, Guy M HAGEN, David PASTOR-ESCUREDO, Daniel JIMENEZ-CARRETERO, Maria J LEDESMA-CARBAYO, Arrate MUÑOZ-BARRUTIA, Erik MEIJERING, Michal KOZUBEK a Carlos ORTIZ-DE-SOLORZANO. A Benchmark for Comparison of Cell Tracking Algorithms. Bioinformatics, 2014, roč. 30, č. 11, s. 1609-1617. ISSN 1367-4803. doi:10.1093/bioinformatics/btu080. URL info
  • FOLTÁNKOVÁ, Veronika, Pavel MATULA, Dmitry SOROKIN, Stanislav KOZUBEK a Eva BÁRTOVÁ. Hybrid detectors improved time-lapse confocal microscopy of PML and 53BP1 nuclear body co-localization in DNA lesions. Microscopy and Microanalysis, Saarbrücken: Cambridge University Press, 2013, Volume 19, Issue 2, s. 360-369. ISSN 1431-9276. doi:10.1017/S1431927612014353. URL info
  • DANĚK, Ondřej, Pavel MATULA, Martin MAŠKA a Michal KOZUBEK. Smooth Chan-Vese Segmentation via Graph Cuts. Pattern recognition letters : an official publication of the International Association for Pattern Recognition., Amsterdam: Elsevier, 2012, roč. 33, č. 10, s. 1405-1410. ISSN 0167-8655. doi:10.1016/j.patrec.2012.03.013. URL info
  • ŠUSTÁČKOVÁ, Gabriela, Stanislav KOZUBEK, Lenka STIXOVÁ, Soňa LEGARTOVÁ, Pavel MATULA, Darya Yurevna ORLOVA a Eva BÁRTOVÁ. Acetylation-dependent nuclear arrangement and recruitment of BMI1 protein to UV-damaged chromatin. Journal of cellular physiology, United States: Wiley-Liss, 2012, roč. 227, č. 5, s. 1838-1850. ISSN 0021-9541. doi:10.1002/jcp.22912. URL info
  • STIXOVÁ, Lenka, Pavel MATULA, Stanislav KOZUBEK, Dušan CMARKO, Adriana GOMBITOVÁ, Ivan RAŠKA a Eva BÁRTOVÁ. Trajectories and nuclear arrangement of PML bodies are influenced by A-type lamin deficiency. Biology of the Cell, 2012, roč. 104, č. 7, s. 418-432. ISSN 0248-4900. doi:10.1111/boc.201100053. URL info
  • ORLOVA, Darya Yurevna, Lenka STIXOVÁ, Stanislav KOZUBEK, Hinco GIERMAN, Gabriela ŠUSTÁČKOVÁ, Andrei CHERNYSHEV, Ruslan MEDVEDEV, Soňa LEGARTOVÁ, Rogier VERSTEEG, Pavel MATULA, Roman STOKLASA a Eva BÁRTOVÁ. Arrangement of nuclear structures is not transmitted through mitosis but is identical in sister cells. Journal of Cellular Biochemistry, 2012, roč. 113, č. 11, s. 3313-3329. ISSN 0730-2312. doi:10.1002/jcb.24208. URL info
  • STIXOVÁ, Lenka, Eva BÁRTOVÁ, Pavel MATULA, Ondřej DANĚK, Soňa LEGARTOVÁ a Stanislav KOZUBEK. Heterogeneity in the kinetics of nuclear proteins and trajectories of substructures associated with heterochromatin. Epigenetics & Chromatin, 2011, roč. 4, č. 5, s. 1-17. ISSN 1756-8935. doi:10.1186/1756-8935-4-5. URL info
  • HARNIČAROVÁ, Andrea, Eva BÁRTOVÁ, Gabriela GALIOVÁ, Radka UHLÍŘOVÁ, Pavel MATULA a Stanislav KOZUBEK. SUV39h-independent association of HP1b with fibrillarin-positive nucleolar regions. Chromosoma, Springer, 2010, roč. 119, č. 3, s. 227-241. ISSN 0009-5915. doi:10.1007/s00412-009-0252-2. URL info
  • UHLÍŘOVÁ, Radka, Andrea HARNIČAROVÁ, Gabriela GALIOVÁ, Soňa LEGARTOVÁ, Pavel MATULA, Miloslava FOJTOVÁ, Miroslav VAŘECHA, Jana AMRICHOVÁ, Jan VONDRÁČEK, Stanislav KOZUBEK a Eva BÁRTOVÁ. SUV39h- and A-type Lamin-Dependent Telomere Nuclear Rearrangement. Journal of Cellular Biochemistry, 2010, roč. 109, č. 5, s. 915-926. ISSN 0730-2312. doi:10.1002/jcb.22466. URL info
  • MATULA, Pavel, Martin MAŠKA, Ondřej DANĚK, Petr MATULA a Michal KOZUBEK. Acquiarium: Free Software for the Acquisition and Analysis of 3D Images of Cells in Fluorescence Microscopy. In IEEE International Symposium on Biomedical Imaging. Boston: IEEE, 2009. s. 1138-1141, 4 s. ISBN 978-1-4244-3932-4. URL info
  • MATULA, Pavel, Ondřej DANĚK, Martin MAŠKA a Marek VINKLER. Acquiarium version 1.6. 2008. URL info
  • HUBENÝ, Jan, Vladimír ULMAN a Pavel MATULA. Estimating Large Local Motion in Live-Cell Imaging Using Variational Optical Flow. In VISAPP 2007 Second International Conference On Computer Vision Theory And Applications, Proceedings. Portugal: INSTICC PRESS, 2007. s. 542-548, 7 s. ISBN 978-972-8865-74-0. info
  • MATULA, Pavel, Martin MAŠKA, Ondřej DANĚK, Petr MATULA, Michal KOZUBEK a Petr KRONTORÁD. Acquiarium 1.0. 2007. URL info
  • MATULA, Petr, Pavel MATULA, Michal KOZUBEK a Vladimír DVOŘÁK. Fast Point-Based 3D Alignment of Live Cells. IEEE Transactions on Image Processing, 2006, roč. 15, č. 8, s. 2388-2396. ISSN 1057-7149. info
  • HUBENÝ, Jan, Pavel MATULA, Petr MATULA a Michal KOZUBEK. Improved 3D Reconstruction of Interphase Chromosomes Based on Nonlinear Diffusion Filtering. In Proceedings of PDE-Based Image Processing and Related Inverse Problems. Berlin: Springer-Verlag, 2006. s. 163-173, 10 s. ISBN 3-540-33266-9. info
  • HUBENÝ, Jan a Pavel MATULA. Fast and Robust Segmentation of Low Contrast Biomedical Images. In Visualization Imaging and Image Processing. Anaheim, Calgary, Zurich: ACTA Press, 2006. s. 189-196, 8 s. ISBN 0-88986-598-1. info
  • MATULA, Petr, Michal KOZUBEK a Pavel MATULA. Applications of Image Registration in Human Genome Research. In Computer Vision and Mathematical Methods in Medical and Biomedical Image Analysis. Berlin: Springer-Verlag, 2004. s. 376-384, 9 s. ISBN 3-540-22675-3. info
  • MATULA, Pavel, Jan HUBENÝ a Michal KOZUBEK. Fast Marching 3D Reconstruction of Interphase Chromosomes. In Computer Vision and Mathematical Methods in Medical and Biomedical Image Analysis. Berlin: Springer-Verlag, 2004. s. 385-394, 10 s. ISBN 3-540-22675-3. info
  • MATULA, Pavel, Petr MATULA, Michal KOZUBEK a Petr MEJZLÍK. High-Resolution Cytometry Network Project: Client/Server System for 3D Optical Microscope Data Storage and Analysis. In 2nd International Symposium on 3D Data Processing, Visualization, and Transmission. Los Alamitos: IEEE Computer Society, 2004. s. 580-583, 4 s. ISBN 0-7695-2223-8. info
  • KOZUBEK, Michal, Petr MATULA, Pavel MATULA a Stanislav KOZUBEK. Automated acquisition and processing of multidimensional image data in confocal in vivo microscopy. Microscopy research and technique, USA: Wiley-Liss, 2004, roč. 64, č. 2, s. 164-175. ISSN 1059-910X. info
  • KOZUBEK, Michal, Petr MATULA a Pavel MATULA. Automated confocal microscopy: The way of achieving both quality and quantity in 3D image cytometry. In International Symposium on Biomedical Imaging. Arlington, USA: IEEE, 2004. s. 69-72, 4 s. ISBN 0-7803-8389-3. info
  • 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. URL 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. URL info
  • 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. URL info
  • MATULA, Pavel. Effectivity of Spherical Object Reconstruction Using Star-Shaped Simplex Meshes. In 1st International Symposium on 3D Data Processing Visualization and Transmission. Los Alamitos: IEEE Computer Society, 2002. s. 794-799. ISBN 0-7695-7521-5. info
  • KOZUBEK, Michal, Petr MATULA a Pavel MATULA. The power of computerized light microscopy. Imaging & Microscopy, Darmstadt: GIT Verlag, 2002, roč. 4, č. 2, s. 25-28. ISSN 1439-4243. info
  • KOZUBEK, Michal, Petr MATULA, Pavel MATULA a Petr MEJZLÍK. High-resolution cytometry network project: Towards remote and distributed acquisition, processing and visualisation of 3D image data in human genome research. In 3D data processing, visualization and transmission. Los Alamitos: IEEE Computer Society, 2002. s. 99-106. ISBN 0-7695-1521-5. 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. URL info

2017/10/29

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