Prof. RNDr. Michal Kozubek, Ph.D.

Department head – Centre for Biomedical Image Analysis


Office: A311
Botanická 554/68a
602 00 Brno

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Phone: +420 549 49 4023
E‑mail:
CV

Curriculum Vitae

Basic Personal Data
  • Prof. Dr. Michal Kozubek, Ph.D.
    born February 15, 1974 in Havirov, Czech Republic, married, 2 children
Affiliation and Address
  • Centre for Biomedical Image Analysis
    Faculty of Informatics, Masaryk University
    Botanicka 68a, 602 00 Brno, Czech Republic
Current Position
  • Professor of Computer Science
    Head of Centre for Biomedical Image Analysis
Education and Academic Qualifications
  • 2012: Professor of Computer Science, Faculty of Informatics, Masaryk University, Brno, Czech Republic.
  • 2002: Associate Professor of Computer Science, Faculty of Informatics, Masaryk University, Brno, Czech Republic. Thesis: "Modern tools for automated high-resolution image acquisition and processing in the research of the spatial organization of the cell nucleus".
  • 1998: PhD in Computer Science, Faculty of Informatics, Masaryk University, Brno, Czech Republic. Thesis: "High-resolution cytometry: hardware approaches, image analysis techniques and applications".
  • 1995: MSc in Computer Science, Faculty of Informatics, Masaryk University, Brno, Czech Republic. Thesis: "Analysis of images obtained using fluorescence in situ hybridization".
Employment Summary
  • 2011 - 2015: Dean, Faculty of Informatics, Masaryk University, Brno, Czech Republic.
  • 1998 - present: Group Leader, Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic.
  • 1996 - 1998: Assistant, Dept. of Information Technologies, Faculty of Informatics, Masaryk University, Brno, Czech Republic.
Teaching Activities
  • 2006 - present: Responsibility for the new field of study "Image Processing"
  • 2000 - present: Digital Image Processing and related courses
  • 1993 - 1998: Design of Algorithms, Object-Oriented Programming
Scientific and Research Activities
  • Optical Microscopy
    - Image formation in wide-field, confocal and fluorescence microscopes
    - New techniques being introduced into optical microscopy
    - Automation in optical microscopy
  • Image Acquisition and Analysis
    - Image acquisition and its automation
    - Image enhancement, segmentation and object tracking
    - Benchmarking of image analysis algorithms
  • Biomedical Applications
    - Computer analysis of cells and tissues
    - Modeling of spatiotemporal behavior of cells
    - Clinical applications, comparing behavior of healthy and cancer cells
Academic Stays
  • 2008: A two-month stay at University of Navarra, Pamplona and San Sebastián, Spain
  • 2007: A one-month stay at Centre for Image Analysis, Uppsala University, Sweden
  • 2006: A six-week stay at Centre for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
  • 2004: A three-month stay at Dept. of Information Technology, Lappeenranta University of Technology, Finland (CIMO Fellowship)
  • 2001: A two-week stay at Kirchhoff Institute of Physics, University of Heidelberg, Germany (Volkswagen Stiftung Grant)
  • 1995 - 1996: A nine-month stay at Dept. of Engineering Science, University of Oxford, United Kingdom (Soros/FCO Scholarship)
  • 1994: A four-month stay at Technical University Darmstadt, Germany (TEMPUS Scholarship)
Major Research Projects
  • Principal investigator:
    2017 - 2020: "Benchmarking of algorithms for cell segmentation and tracking", Czech Ministry of Education, project INTER-COST LTC17016.
    2006 - 2011: "Determination of markers, screening and early diagnostics of cancer diseases using highly automated processing of multidimensional biomedical images", Czech Ministry of Education, Grant No. 2B06052
    2000 - 2002: "Automated micro-axial tomography of tumor-correlated FISH pattern", Volkswagen Stiftung (Germany), Grant No. I/75946
    1999 - 2004: "Application of computer image analysis in optical microscopy", Czech Ministry of Education, Grant No. MSM-143300002
    1999 - 2001: "Image analysis in the study of interphase nucleus structure", Grant Agency of the Czech Republic, Grant No. 202/99/P008
  • Co-investigator:
    2017 - 2019: "Optimazation of targeted therapy of colorectal carcinoma by influencing the efficiency of penetration and cytotoxicity of cell signaling regulators", Grant agency of MU, project MUNI/G/0974/2016.
    2016 - 2019: "National Infrastructure for Biological and Medical Imaging", Czech Ministry of Education, Large Infrastructure Projects No. LM2015062 and CZ.02.1.01/0.0/0.0/16_013/0001775
    2016 - 2020: "A new Network of European BioImage Analysts to advance life science imaging (NEUBIAS)", EU COST Action CA15124
    2012 - 2018: "Chromosome dynamics and structure during the cell cycle and during differentiation under normal and pathological conditions", Grant Agency of the Czech Republic, Centre of Excellence No. 302/12/G157
    2005 - 2011: "Chromosome dynamics and structure during the cell cycle under normal and pathological conditions", Czech Ministry of Education, Centre of Basic Research No. LC535
    2004 - 2006: "High-resolution cytometry of living cells", Grant Agency of the Czech Republic, Grant No. 202/04/0907
    2003 - 2007: "Human genome structure", Czech Academy of Sciences, Grant No. A5004306
    2002 - 2006: "The use of combination of laser microbeam and cytometric techniques in the study of the structure and dynamics of human genome", Czech Academy of Sciences, Grant No. A1065203
    2000 - 2004: "Development of new diagnostic techniques for oncology", Czech Academy of Sciences, Grant No. S5004010
    1997 - 2000: "Image analysis in the study of mechanisms of induction, in diagnosis and for prevention of deleterious human diseases", Czech Ministry of Education, Grant No. VS-97031
Membership in Academic Societies
  • International:
    2016 - present: Member, IEEE Signal Processing Society (IEEE SPS)
    2002 - present: Member, European Microscopy Society (EMS)
    2000 - present: Member, International Society for Analytical Cytology (ISAC)
  • National:
    2017 - present: Member, Scientific Council of Faculty of Mathematics and Physics of Charles University
    2012 - 2016: Member, Panel 202 Informatics, Czech Science Foundation
    2003 - 2014: Member, Czech Society for Analytical Cytology (CSAC)
    2002 - present: Member, Czechoslovak Microscopy Society (CSMS)
  • University:
    2013 - 2017: Member, Scientific Council of Institute of Computer Science of Masaryk University
    2011 - 2015: Member, Scientific Council of Masaryk University
    2009 - 2011: Member, 2018 - present: Member, Academic Senate of Masaryk University
    2006 - 2008: Member, 2009 - 2011: Chair, 2015 - 2017: Member, 2018 - present: Chair, Academic Senate of Faculty of Informatics of Masaryk University
    2004 - 2007: Member, 2011 - 2015: Chair, 2015 - present: Member, Scientific Council of Faculty of Informatics of Masaryk University
    2003 - 2006: Member, Scientific Council of Faculty of Science of Masaryk University
Prizes and Awards
  • 2005: Member of team winning the 1st Prize in national competition Best of Biotech (for the best project in biotechnologies entitled High-resolution image cytometer)
  • 2003 - 2016: Annual Rector's Prize, Masaryk University, awarded to four PhD graduates supervised by Michal Kozubek (2003: Petr Matula, 2011: Silvie Luisa Brázdilová, 2012: Ondřej Daněk, 2016: Martin Maška)
  • 1999: TALENT'98 Award, Czech Ministry of Education (for promoting inter-disciplinary research)
  • 1998: Annual Rector's Prize, Masaryk University (for excellent results during postgraduate studies)
  • 1995: Annual Rector's Prize, Masaryk University (for excellent results during undergraduate studies)
  • 1995: Annual Dean's Prize, Faculty of Informatics, Masaryk University (for excellent results during undergraduate studies)
  • 1993: Annual Dean's Prize, Faculty of Science, Masaryk University (for excellent results during undergraduate studies)
Major Publications
  • 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. doi:10.1038/nmeth.4473. webová stránka publikace výsledku info
  • KOZUBEK, Michal. Challenges and Benchmarks in Bioimage Analysis. In DeVos WH, Munck S, Timmermans JP. Focus on Bio-Image Informatics. Berlin: Springer, 2016. s. 231-262, 32 s. Advances in Anatomy, Embryology and Cell Biology 219. ISBN 978-3-319-28547-4. doi:10.1007/978-3-319-28549-8_9. URL info
  • ULMAN, Vladimír, David SVOBODA, Matti NYKTER, Michal KOZUBEK a Pekka RUUSUVUORI. Virtual cell imaging: A review on simulation methods employed in image cytometry. Cytometry Part A, John Wiley & Sons, 2016, roč. 89A, č. 12, s. 1057-1072. ISSN 1552-4922. doi:10.1002/cyto.a.23031. 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". ISSN 1932-6203. doi: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. doi:10.1002/cyto.a.22692. info
  • ORTIZ-DE-SOLÓRZANO, Carlos, Arrate MUÑOZ-BARRUTIA, Erik MEIJERING a Michal KOZUBEK. Toward a Morphodynamic Model of the Cell. IEEE Signal Processing Magazine, New York: IEEE, 2015, roč. 32, č. 1, s. 20-29. ISSN 1053-5888. doi:10.1109/MSP.2014.2358263. 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
  • 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
  • BRÁZDILOVÁ, Silvie Luisa a Michal KOZUBEK. Image Division Technique in Pre-acquisition Analysis of Information Content for Automated Microscopy. Journal of Microscopy, Oxford: Blackwell Science, 2011, roč. 242, č. 3, s. 279-289. ISSN 0022-2720. doi:10.1111/j.1365-2818.2010.03465.x. info
  • STAIER, Florian, Heinz EIPEL, Petr MATULA, Alexei V EVSIKOV, Michal KOZUBEK, Christoph CREMER a Michael HAUSMANN. Micro axial tomography: A miniaturized, versatile stage device to overcome resolution anisotropy in fluorescence light microscopy. Rev. Sci. Instrum., USA: American Institute of Physica, 2011, roč. 82, č. 9, s. "093701-1"-"093701-8". ISSN 0034-6748. info
  • SVOBODA, David, Michal KOZUBEK a 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, roč. 75A, č. 6, s. 494-509. ISSN 1552-4922. doi:10.1002/cyto.a.20714. info
  • BRÁZDILOVÁ, Silvie Luisa a Michal KOZUBEK. Information Content Analysis in Automated Microscopy Imaging using an Adaptive Autofocus Algorithm for Multimodal Functions. Journal of Microscopy, Oxford: Blackwell Science, 2009, roč. 236, č. 3, s. 194-202. ISSN 0022-2720. doi:10.1111/j.1365-2818.2009.03280.x. 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, 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. Image acquisition and its automation in fluorescence microscopy. In From cells to proteins: Imaging nature across dimensions. Dordrecht: Springer, 2005. s. 227-270, 44 s. NATO Science Series. ISBN 1-4020-3615-9. 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
  • 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. Theoretical versus experimental resolution in optical microscopy. Microscopy research and technique, USA: Wiley-Liss, 2001, roč. 53, č. 2, s. 157-166. ISSN 1059-910X. abstract info
  • KOZUBEK, Michal, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Eva BÁRTOVÁ, Magdalena SKALNÍKOVÁ, Pavel MATULA, Petr MATULA, Pavla JIRSOVÁ, Alena GAŇOVÁ a Irena KOUTNÁ. Combined confocal and wide-field high-resolution cytometry of FISH-stained cells. Cytometry, New York: International Society for Analytical Cyt, 2001, roč. 45, č. 1, s. 1-12. ISSN 0196-4763. abstract info
  • KOZUBEK, Michal. FISH Imaging. In Confocal and two-photon microscopy: Foundations, applications, and advances. New York: Wiley-Liss, 2001. s. 389-429. ISBN 0-471-40920-0. abstract 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. abstract info
  • KOZUBEK, Michal, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Andrea MAREČKOVÁ, Eva BÁRTOVÁ, Magdalena SKALNÍKOVÁ a Adriana JERGOVÁ. High-resolution cytometry of FISH dots in interphase cell nuclei. Cytometry, New York: International Society for Analytical Cyt, 1999, roč. 36, č. 4, s. 279-293. ISSN 0196-4763. info
  • SCHRADER, Martin, Michal KOZUBEK, Stefan HELL a Tony WILSON. Optical transfer functions of 4Pi confocal microscopes : theory and experiment. Optics Letters, 1997, roč. 22, č. 7, s. 436-438. ISSN 0146-9592. info
  • JUŠKAITIS, Rimas, Tony WILSON, Mark NEIL a Michal KOZUBEK. Efficient real-time confocal microscopy with white light sources. Nature, 1996, roč. 383, č. 6603, s. 804-806. ISSN 0028-0836. info
  • WILSON, Tony, Rimas JUŠKAITIS, Mark NEIL a Michal KOZUBEK. Confocal microscopy by aperture correlation. Optics Letters, 1996, roč. 21, č. 23, s. 1879-1881. ISSN 0146-9592. info

2018/03/23

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