doc. RNDr. Pavel Matula, Ph.D.

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

• KOTRBOVÁ, Anna, Karel ŠTĚPKA, Martin MAŠKA, Juraj PÁLENIK, Ladislav ILKOVICS, Dobromila KLEMOVÁ, Marek KRAVEC, František HUBATKA, Zankruti DAVE, Aleš HAMPL, Vítězslav BRYJA, Pavel MATULA a Vendula POSPÍCHALOVÁ. TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images. Journal of Extracellular Vesicles. Taylor and Francis Ltd., 2019, roč. 8, č. 1, s. 1-13. ISSN 2001-3078. Dostupné z: https://dx.doi.org/10.1080/20013078.2018.1560808. Full Text info
• GÓMEZ-DE-MARISCAL, Estibaliz, Martin MAŠKA, Anna KOTRBOVÁ, Vendula POSPÍCHALOVÁ, Pavel MATULA a Arrate MUÑOZ-BARRUTIA. Deep-Learning-Based Segmentation of Small Extracellular Vesicles in Transmission Electron Microscopy Images. Scientific Reports. 2019, roč. 9, č. 13211, s. 1-10. ISSN 2045-2322. Dostupné z: https://dx.doi.org/10.1038/s41598-019-49431-3. URL info
• SOROKIN, Dmitry, Igor PETERLÍK, Marco TEKTONIDIS, Karl ROHR a Pavel MATULA. Non-rigid Contour-Based Registration of Cell Nuclei in 2-D Live Cell Microscopy Images Using a Dynamic Elasticity Model. IEEE Transactions on Medical Imaging. IEEE, 2018, roč. 37, č. 1, s. 173-184. ISSN 0278-0062. Dostupné z: https://dx.doi.org/10.1109/TMI.2017.2734169. URL info
• ŠIMARA, Pavel, Lenka TESAŘOVÁ, Daniela ŘEHÁKOVÁ, Pavel MATULA, Stanislav STEJSKAL, Aleš HAMPL a Irena KRONTORÁD KOUTNÁ. DNA double-strand breaks in human induced pluripotent stem cell reprogramming and long-term in vitro culturing. Stem Cell Research & Therapy. Springer Nature, 2017, roč. 8, č. 73, s. 1-13. ISSN 1757-6512. Dostupné z: https://dx.doi.org/10.1186/s13287-017-0522-5. URL info
• MAŠKA, Martin a Pavel MATULA. Particle Tracking Accuracy Measurement Based on Comparison of Linear Oriented Forests. Online. In 16th IEEE International Conference on Computer Vision Workshops. Venice: IEEE, 2017, s. 11-17. ISBN 978-1-5386-1034-3. Dostupné z: https://dx.doi.org/10.1109/ICCVW.2017.8. URL info
• ULMAN, Vladimír, Martin MAŠKA, Klas E G MAGNUSSON, Olaf RONNEBERGER, Carsten HAUBOLD, Nathalie HARDER, Pavel MATULA, Petr MATULA, David SVOBODA, Miroslav RADOJEVIC, Ihor SMAL, Karl ROHR, Joakim JALDÉN, Helen M BLAU, Oleh DZYUBACHYK, Boudewijn LELIEVELDT, Pengdong XIAO, Yuexiang LI, Siu-Yeung CHO, Alexandre C DUFOUR, Jean-Christophe OLIVO-MARIN, Constantino C REYES-ALDASORO, Jose A SOLIS-LEMUS, Robert BENSCH, Thomas BROX, Johannes STEGMAIER, Ralf MIKUT, Steffen WOLF, Fred A HAMPRECHT, Tiago ESTEVES, Pedro QUELHAS, Ömer DEMIREL, Lars MALMSTRÖM, Florian JUG, Pavel TOMANCAK, Erik MEIJERING, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK a Carlos ORTIZ-DE-SOLORZANO. An objective comparison of cell-tracking algorithms. Nature Methods. Macmillan Publishers Limited, part of Springer Nature, 2017, roč. 14, č. 12, s. 1141-1152. ISSN 1548-7091. Dostupné z: https://dx.doi.org/10.1038/nmeth.4473. URL info
• 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", 19 s. ISSN 1932-6203. Dostupné z: https://dx.doi.org/10.1371/journal.pone.0144959. URL info
• ŠTĚPKA, Karel, Pavel MATULA, Petr MATULA, Stefan WOERZ, Karl ROHR a Michal KOZUBEK. Performance and Sensitivity Evaluation of 3-D Spot Detection Methods in Confocal Microscopy. Cytometry Part A. John Wiley & Sons, 2015, roč. 87A, č. 8, s. 759-772. ISSN 1552-4922. Dostupné z: https://dx.doi.org/10.1002/cyto.a.22692. 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. Dostupné z: https://dx.doi.org/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. Dostupné z: https://dx.doi.org/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. Dostupné z: https://dx.doi.org/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. Dostupné z: https://dx.doi.org/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. Dostupné z: https://dx.doi.org/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. Dostupné z: https://dx.doi.org/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. Dostupné z: https://dx.doi.org/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. Dostupné z: https://dx.doi.org/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. Dostupné z: https://dx.doi.org/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. Online. In IEEE International Symposium on Biomedical Imaging. Boston: IEEE, 2009, s. 1138-1141. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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