Curriculum Vitae

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 and 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, vol. 8, No 1, p. 1-13. ISSN 2001-3078. Available from: https://dx.doi.org/10.1080/20013078.2018.1560808. Full Text info
• GÓMEZ-DE-MARISCAL, Estibaliz, Martin MAŠKA, Anna KOTRBOVÁ, Vendula POSPÍCHALOVÁ, Pavel MATULA and Arrate MUÑOZ-BARRUTIA. Deep-Learning-Based Segmentation of Small Extracellular Vesicles in Transmission Electron Microscopy Images. Scientific Reports. 2019, vol. 9, No 13211, p. 1-10. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-019-49431-3. URL info
• SOROKIN, Dmitry, Igor PETERLÍK, Marco TEKTONIDIS, Karl ROHR and 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, vol. 37, No 1, p. 173-184. ISSN 0278-0062. Available from: https://dx.doi.org/10.1109/TMI.2017.2734169. URL info
• ŠIMARA, Pavel, Lenka TESAŘOVÁ, Daniela ŘEHÁKOVÁ, Pavel MATULA, Stanislav STEJSKAL, Aleš HAMPL and 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, vol. 8, No 73, p. 1-13. ISSN 1757-6512. Available from: https://dx.doi.org/10.1186/s13287-017-0522-5. URL info
• MAŠKA, Martin and 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, p. 11-17. ISBN 978-1-5386-1034-3. Available from: 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 and Carlos ORTIZ-DE-SOLORZANO. An objective comparison of cell-tracking algorithms. Nature Methods. Macmillan Publishers Limited, part of Springer Nature, 2017, vol. 14, No 12, p. 1141-1152. ISSN 1548-7091. Available from: https://dx.doi.org/10.1038/nmeth.4473. URL info
• MATULA, Pavel, Martin MAŠKA, Dmitry SOROKIN, Petr MATULA, Carlos ORTIZ-DE-SOLÓRZANO and Michal KOZUBEK. Cell tracking accuracy measurement based on comparison of acyclic oriented graphs. PLoS ONE. 2015, vol. 10, No 12, p. "e0144959", 19 pp. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0144959. URL info
• ŠTĚPKA, Karel, Pavel MATULA, Petr MATULA, Stefan WOERZ, Karl ROHR and Michal KOZUBEK. Performance and Sensitivity Evaluation of 3-D Spot Detection Methods in Confocal Microscopy. Cytometry Part A. John Wiley & Sons, 2015, 87A, No 8, p. 759-772. ISSN 1552-4922. Available from: 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 and Carlos ORTIZ-DE-SOLORZANO. A Benchmark for Comparison of Cell Tracking Algorithms. Bioinformatics. 2014, vol. 30, No 11, p. 1609-1617. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btu080. URL info
• FOLTÁNKOVÁ, Veronika, Pavel MATULA, Dmitry SOROKIN, Stanislav KOZUBEK and 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, p. 360-369. ISSN 1431-9276. Available from: https://dx.doi.org/10.1017/S1431927612014353. URL info
• DANĚK, Ondřej, Pavel MATULA, Martin MAŠKA and 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, vol. 33, No 10, p. 1405-1410. ISSN 0167-8655. Available from: 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 and Eva BÁRTOVÁ. Acetylation-dependent nuclear arrangement and recruitment of BMI1 protein to UV-damaged chromatin. Journal of cellular physiology. United States: Wiley-Liss, 2012, vol. 227, No 5, p. 1838-1850. ISSN 0021-9541. Available from: https://dx.doi.org/10.1002/jcp.22912. URL info
• STIXOVÁ, Lenka, Pavel MATULA, Stanislav KOZUBEK, Dušan CMARKO, Adriana GOMBITOVÁ, Ivan RAŠKA and Eva BÁRTOVÁ. Trajectories and nuclear arrangement of PML bodies are influenced by A-type lamin deficiency. Biology of the Cell. 2012, vol. 104, No 7, p. 418-432. ISSN 0248-4900. Available from: 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 and Eva BÁRTOVÁ. Arrangement of nuclear structures is not transmitted through mitosis but is identical in sister cells. Journal of Cellular Biochemistry. 2012, vol. 113, No 11, p. 3313-3329. ISSN 0730-2312. Available from: https://dx.doi.org/10.1002/jcb.24208. URL info
• STIXOVÁ, Lenka, Eva BÁRTOVÁ, Pavel MATULA, Ondřej DANĚK, Soňa LEGARTOVÁ and Stanislav KOZUBEK. Heterogeneity in the kinetics of nuclear proteins and trajectories of substructures associated with heterochromatin. Epigenetics & Chromatin. 2011, vol. 4, No 5, p. 1-17. ISSN 1756-8935. Available from: https://dx.doi.org/10.1186/1756-8935-4-5. URL info
• HARNIČAROVÁ, Andrea, Eva BÁRTOVÁ, Gabriela GALIOVÁ, Radka UHLÍŘOVÁ, Pavel MATULA and Stanislav KOZUBEK. SUV39h-independent association of HP1b with fibrillarin-positive nucleolar regions. Chromosoma. Springer, 2010, vol. 119, No 3, p. 227-241. ISSN 0009-5915. Available from: 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 and Eva BÁRTOVÁ. SUV39h- and A-type Lamin-Dependent Telomere Nuclear Rearrangement. Journal of Cellular Biochemistry. 2010, vol. 109, No 5, p. 915-926. ISSN 0730-2312. Available from: https://dx.doi.org/10.1002/jcb.22466. URL info
• MATULA, Pavel, Martin MAŠKA, Ondřej DANĚK, Petr MATULA and 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, p. 1138-1141. ISBN 978-1-4244-3932-4. URL info
• MATULA, Pavel, Ondřej DANĚK, Martin MAŠKA and Marek VINKLER. Acquiarium version 1.6. 2008. URL info
• HUBENÝ, Jan, Vladimír ULMAN and 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, p. 542-548. ISBN 978-972-8865-74-0. info
• MATULA, Pavel, Martin MAŠKA, Ondřej DANĚK, Petr MATULA, Michal KOZUBEK and Petr KRONTORÁD. Acquiarium 1.0. 2007. URL info
• MATULA, Petr, Pavel MATULA, Michal KOZUBEK and Vladimír DVOŘÁK. Fast Point-Based 3D Alignment of Live Cells. IEEE Transactions on Image Processing. 2006, vol. 15, No 8, p. 2388-2396. ISSN 1057-7149. info
• HUBENÝ, Jan, Pavel MATULA, Petr MATULA and 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, p. 163-173, 10 pp. ISBN 3-540-33266-9. info
• HUBENÝ, Jan and Pavel MATULA. Fast and Robust Segmentation of Low Contrast Biomedical Images. In Visualization Imaging and Image Processing. Anaheim, Calgary, Zurich: ACTA Press, 2006, p. 189-196. ISBN 0-88986-598-1. info
• MATULA, Petr, Michal KOZUBEK and 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, p. 376-384. ISBN 3-540-22675-3. info
• MATULA, Pavel, Jan HUBENÝ and 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, p. 385-394. ISBN 3-540-22675-3. info
• MATULA, Pavel, Petr MATULA, Michal KOZUBEK and 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, p. 580-583. ISBN 0-7695-2223-8. info
• KOZUBEK, Michal, Petr MATULA, Pavel MATULA and Stanislav KOZUBEK. Automated acquisition and processing of multidimensional image data in confocal in vivo microscopy. Microscopy research and technique. USA: Wiley-Liss, 2004, vol. 64, No 2, p. 164-175. ISSN 1059-910X. info
• KOZUBEK, Michal, Petr MATULA and 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, p. 69-72. ISBN 0-7803-8389-3. 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
• 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. 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, p. 794-799. ISBN 0-7695-7521-5. info
• KOZUBEK, Michal, Petr MATULA and Pavel MATULA. The power of computerized light microscopy. Imaging & Microscopy. Darmstadt: GIT Verlag, 2002, vol. 4, No 2, p. 25-28. ISSN 1439-4243. info
• KOZUBEK, Michal, Petr MATULA, Pavel MATULA and 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, p. 99-106. ISBN 0-7695-1521-5. 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

2017/10/29

Another Variant: Czech(1)