Prof. RNDr. Michal Kozubek, Ph.D.

Department head – Centre for Biomedical Image Analysis


Office: A311
Botanická 554/68a
602 00 Brno

Show on the map

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)
Research Projects and Grants
  • Principal investigator:
    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:
    2016 - 2019: "National Infrastructure for Biological and Medical Imaging", Czech Ministry of Education, Large Infrastructure Project No. LM2015062
    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
    2002 - 2004: "Epigenetic control of gene expression in malignant diseases", Grant Agency of the Ministry of Health, Grant No. NC/6987-3
    2002 - 2004: "Chronic myeloid leukemia radiation risk estimation based on BCR-ABL distances in hematopoietic cells", Grant Agency of the Czech Republic, Grant No. 202/02/0804
    2001 - 2003: "Investigation of the local control of gene expression using spectral microscopy and image analysis techniques", Grant Agency of the Czech Republic, Grant No. 301/01/0186
    2001 - 2003: "Nuclear topology of some protooncogenes in human neutrophilic granulocytes and leukemic cells", Czech Academy of Sciences, Grant No. B5004102
    2000 - 2004: "Development of new diagnostic techniques for oncology", Czech Academy of Sciences, Grant No. S5004010
    2000 - 2002: "How the study of spatial order of specific genetic loci in nuclei of healthy and malignant tissue can contribute to the diagnostics and treatment of solid tumors", Grant Agency of the Ministry of Health, Grant No. NC/5955-3
    1998 - 2000: "The use of interphase FISH for the determination of individuals with elevated risk of the induction of hemoblastoses", Grant Agency of the Ministry of Health, Grant No. NM/15-3
    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
    1997 - 1999: "Interphase nucleus structure and its changes after irradiation", Grant Agency of the Czech Republic, Grant No. 202/97/0874
    1996 - 1998: "Detection of stable chromosomal aberrations induced by dense ionizing radiation in human blood cells", Grant Agency of the Czech Republic, Grant No. 202/96/1718
    1995 - 1996: "Utilization of interphase cytogenetic analysis by fluorescence in situ hybridization method for the monitoring of malignant cells clone by hemoblastic diseases", Grant Agency of the Ministry of Health, Grant No. IZ/2636-2
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 - present: Member, Czech Society for Analytical Cytology (CSAC)
    2002 - present: Member, Czechoslovak Microscopy Society (CSMS)
  • University:
    2011 - 2015: Member, Scientific Council of Masaryk University
    2009 - 2011: Member, Academic Senate of Masaryk University
    2006 - 2008: Member, 2009 - 2011: Chair, 2015 - present: Member, 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
  • 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. 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. 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

2017/02/24

You are running an old browser version. We recommend updating your browser to its latest version.

More info