doc. RNDr. Petr Matula, Ph.D.

Curriculum vitae

Person Identification

• Petr Matula, Ph.D., married, 1 child

Workplace

• Faculty of Informatics
  Masaryk University
  Botanicka 68a
  602 00 Brno
  Czech Republic
  

Employment Position

• Researcher and lecturer

Education and Academic Qualifications

• 2013: Associate Professor of Computer Science, Faculty of Informatics, Masaryk University, Brno. Habilitation thesis: "Automated Image Analysis in Fluorescence Microscopy"
• 2003: PhD in Computer Science, Faculty of Informatics, Masaryk University (FI MU), PhD Thesis: "Image registration and its applications in fluorescence microsopy"
• 1998: MSc in Computer Science, FI MU, Master Thesis: "Recognition of Czech hand-written text" (in Czech)

Employment overview

• 2005 - present: researcher and lecturer at FI MU
• 2011-2012: 1.5 year, researcher, Center for Mathematical Morphology, MINES ParisTECH, Fontainebleau, France
• 2007-2008: 1.5 year, postdoc, Biomedical Computer Vision Group, German Cancer Research Center (DKFZ) Heidelberg and University of Heidelberg
• 2008-2017: guest researcher, Biomedical Computer Vision Group, German Cancer Research Center (DKFZ) Heidelberg and University of Heidelberg
• 2003 - 2005: researcher at FI MU

Pedagogical Activities

• 2022-present: Machine Learning in Image Processing
• 2014-present: Introduction to Digital Image Processing
• 2008-present: Mathematical Morphology
• 2004-present: Biomedical Image Processing Project
• 2001-present: Advisor of numerous bachelor and master theses
• 2017-2020: Labs on Foundations of Programming
• 2016: Labs on Mathematical Foundations of Computer Science
• 2007-2015: Seminar on Digital Image Processing
• 2002-2012: Labs on Digital Image Processing
• 2005-2007: Advanced Methods of Digital Image Processing
• 1996-1997: Seminar on Design of Algorithms

Scientific and Research Activities

• 2021-2023: Segmentation and tracking of cells with complex shapes, GA21-20374S, principal investigator
• 2017-2020: Multi-modal live cell image segmentation and tracking, Czech grant agency, GA17-05048S, principal investigator
• 2015-2017: Development of new MUS81 nuclease inhibitors as chemical biology probe with clinical progression, Grant Agency of Masaryk University, MUNI/M/1894/2014, co-investigator
• 2014-2016: Development and Study of Methods for Live Cell Quantification, Czech grant agency, GA14-22461S, principal investigator 2013-2015: High-throughput screening of compound libraries aimed on discovery of novel inhibitors of the FGFR/ERK MAP kinase signaling, Grant Agency of Masaryk University, MUNI/M/0071/2013, co-investigator
• 2012-2018: Dynamics and Organization of Chromosomes in the Cell Cycle and during Differentiation under Normal and Pathological Conditions, team member
• 2012-2015: Development of human resources in the field of cell biology, CELLBIOL, OPVK, scientific manager
• 2011-2012 Image analysis of multi-photon microscopy images of human skin, L'Oreal Research, France, team member
• 2011-2012 Image analysis of reflectance confocal microscopy images of human skin, L'Oreal Research, France, team member
• 2007-2011 VIROQUANT: Systems biology of virus-cell interactions, German FORSYS initiative, Bundesministerium fuer Bildung und Forschung (BMBF), Germany, team member
• 2006-2011 Marker selection, screening and early diagnostics of cancer diseases using highly automated multidimensional biomedical image processing. Ministry of Education, Czech Republic, Project No. 2B06052, team member
• 2005-2011 Highly parallel and distributed computing systems, Ministry of Education, Czech Republic, Project No. MSM-0021622419, team member

Academical Stays

• 2010: one month, Center for Mathematical Morphology, Fontainebleau, France
• 2005: one month, Quantitative Imaging Group, Technical University of Delft, the Netherlands

University Activities

• 2013-present Head of Department of Visual Computing

Membership in Scientific Societes

• 2016-2020: Member of Panel P202-Computer Science, Czech Science Foundation
• 2019-present: Member of IEEE Society and Signal Processing Society (SPS)
• 2002-present: Member of Czechoslovak Microscopy Society (CSMS)
• 2002-present: Member of European Microscopy Society (EMS)
• 2004-present: Member of Czech Society for Analytical Cytology (CSAC)
• 2004-2007: Member of IEEE Society

Prizes and Awards

• 2003: The Masaryk University Rector's Prize (awarded anually to the best PhD students)

Selected Publications

• MELNIKOVA, Aleksandra a Petr MATULA. Topology Preserving Segmentation Fusion for Cells with Complex Shapes. Online. In The IEEE International Symposium on Biomedical Imaging. Nice: IEEE, 2021, s. 204-207. ISBN 978-1-6654-1246-9. Dostupné z: https://dx.doi.org/10.1109/ISBI48211.2021.9433867. info
• LUX, Filip a Petr MATULA. DIC Image Segmentation of Dense Cell Populations by Combining Deep Learning and Watershed. Online. In IEEE 16th International Symposium on Biomedical Imaging. Venice, Italy, Italy: IEEE 16th International Symposium on Biomedical Imaging, 2019, s. 236-239. ISBN 978-1-5386-3641-1. Dostupné z: https://dx.doi.org/10.1109/ISBI.2019.8759594. URL info
• CORTESE, Mirko, Anil KUMAR, Petr MATULA, Lars KADERALI, Pietro SCATURRO, Holger ERFLE, Eliana Gisela ACOSTA, Sandra BUEHLER, Alessia RUGGIERI, Laurent CHATEL-CHAIX, Karl ROHR a Ralf BARTENSCHLAGER. Reciprocal Effects of Fibroblast Growth Factor Receptor Signaling on Dengue Virus Replication and Virion Production. Cell Reports. CAMBRIDGE, Spojené státy americké: Cell Press, 2019, roč. 27, č. 9, s. 2579-2592,"e1"-"e6", 20 s. ISSN 2211-1247. Dostupné z: https://dx.doi.org/10.1016/j.celrep.2019.04.105. URL info
• DVOŘÁČKOVÁ, Martina, B. RAPOSO, Petr MATULA, J. FUCHS, V. SCHUBERT, Vratislav PEŠKA, B. DESVOYES, C. GUTIERREZ a Jiří FAJKUS. Replication of ribosomal DNA in Arabidopsis occurs both inside and outside the nucleolus during S phase progression. Journal of Cell Science. Cambridge: Company of Biologists Ltd., 2018, roč. 131, č. 2, s. nestránkováno, 12 s. ISSN 0021-9533. Dostupné z: https://dx.doi.org/10.1242/jcs.202416. 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
• WILLEMSEN, Joschka, Oliver WICHT, Julia WOLANSKI, Nina BAUR, Sandra BASTIAN, Darya HAAS, Petr MATULA, Bettina KNAPP, Laurene MEYNIEL-SCHICKLIN, Chen WANG, Ralf BARTENSCHLAGER, Volker LOHMANN, Karl ROHR, Holger ERFLE, Lars KADERALI, Joseph MARCOTRIGIANO, Andreas PICHLMAIR a Marco BINDER. Phosphorylation-Dependent Feedback Inhibition of RIG-I by DAPK1 Identified by Kinome-wide siRNA Screening. Molecular Cell. CAMBRIDGE: CELL PRESS, 2017, roč. 65, č. 3, s. "403"-"415.e8", 21 s. ISSN 1097-2765. Dostupné z: https://dx.doi.org/10.1016/j.molcel.2016.12.021. URL info
• SVOBODA, David, Vladimír ULMAN, Peter KOVÁČ, Barbara ŠALINGOVÁ, Lenka TESAŘOVÁ, Irena KRONTORÁD KOUTNÁ a 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, s. 3180-3183. ISBN 978-1-4673-9961-6. Dostupné z: https://dx.doi.org/10.1109/ICIP.2016.7532946. 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
• LISAUSKAS, Tautvydas, Petr MATULA, Christoph CLAAS, Susanne REUSING, Stefan WIEMANN, Holger ERFLE, Lars LEHMANN, Peter FISCHER, Roland EILS, Karl ROHR, Brian STORRIE a Vytaute STARKUVIENE. Live cell assays to identify regulators of ER to Golgi trafficking. Traffic. John Wiley & Sons, 2012, roč. 13, č. 3, s. 416–432. ISSN 1398-9219. Dostupné z: https://dx.doi.org/10.1111/j.1600-0854.2011.01318.x. info
• REISS, S., Ilka REBHAN, P. BACKES, I. ROMERO-BREY, Holger ERFLE, Petr MATULA, Lars KADERALI, Marion POENISCH, H. BLANKENBURG, M.S. HIET, T. LONGERICH, S. DIEHL, F. RAMIREZ, T. BALLA, Karl ROHR, A. KAUL, S. BÜHLER, Rainer PEPPERKOK, T. LENGAUER, M. ALBRECHT, Roland EILS, P. SCHIRMACHER, V. LOHMANN a Ralf BARTENSCHLAGER. Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment. Cell Host & Microbe. 2011, roč. 9, č. 1, s. 32-45. ISSN 1931-3128. Dostupné z: https://dx.doi.org/10.1016/j.chom.2010.12.002. info
• MATULA, Petr, Tautvydas LISAUSKAS, Vytaute STARKUVIENE a Karl ROHR. Quantification of Golgi Complex Assembly and Disassembly in LiveCell Fluorescence Microscopy Images. In Proceedings of Workshop on Microscopic Image Analysis with Applications in Biology. Neuveden: Neuveden, 2011, 4 s. URL info
• KNAPP, Bettina, Ilka REBHAN, Anil KUMAR, Petr MATULA, Narsis A KIANI, Marco BINDER, Hoger ERFLE, Karl ROHR, Roland EILS, Ralf BARTENSCHLAGER a Lars KADERALI. Normalizing for Individual Cell Population Context in the Analysis of High-Content Cellular Screens. BMC Bioinformatics. BioMed Central, 2011, roč. 12, č. 485, s. 1-14. ISSN 1471-2105. URL info
• MATULA, Petr, Fatima VERISSIMO, Stefan WÖRZ, Roland EILS, Rainer PEPPERKOK a Karl ROHR. Quantification of Fluorescent Spots in Time Series of 3D Confocal Microscopy Images of Endoplasmic Reticulum Exit Sites Based on the HMAX Transform. In Proceedings of SPIE Medical Imaging. Neuveden: Neuveden, 2010, 7 s. ISBN 978-0-8194-8027-9. URL info
• MATULA, Petr, Anil KUMAR, Ilka WÖRZ, Holger ERFLE, Ralf BARTENSCHLAGER, Roland EILS a Karl ROHR. Single-cell-based image analysis of high-throughput cell array screens for quantification of viral infection. Cytometry Part A. UNITED STATES: John Wiley & Sons, Inc., 2009, roč. 75A, č. 4, s. 309-318. ISSN 1552-4922. 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, 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
• 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
• MATULA, Petr, Michal KOZUBEK, Florian STAIER a Michael HAUSMANN. Precise 3D image alignment in micro-axial tomography. Journal of Microscopy. Oxford: Blackwell Science, 2003, roč. 209, č. 2, s. 126-142. ISSN 0022-2720. info
• KOZUBEK, Michal, Magdalena SKALNÍKOVÁ, Petr MATULA, Eva BÁRTOVÁ, Joachim RAUCH, Friedrich NEUHAUS, Heinz EIPEL a Michael HAUSMANN. Automated micro axial tomography of cell nuclei after specific labelling by fluorescence in situ hybridisation. Micron. Amsterdam: Elsevier, 2002, roč. 33, č. 7, s. 655-665. ISSN 0968-4328. info
• KOZUBEK, Michal a Petr MATULA. An efficient algorithm for measurement and correction of chromatic aberrations in fluorescence microscopy. Journal of Microscopy. Oxford: Blackwell Science, 2000, roč. 200, č. 3, s. 206-217. ISSN 0022-2720. URL info

2022/09/14