prof. RNDr. Michal Kozubek, Ph.D.

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
  Botanická 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.

Educational Activities

• Regular teaching activities:
  2006 - present: Introduction and responsibility for the new Master study field "Image Processing"
  2000 - present: Digital Image Processing and related courses (created and presently teaches a basic course on Digital Image Processing, a course on Image Acquisition, Seminar on Image Processing and Project in Image Processing)
  1993 - 1998: Teaching Assistant during Master/Ph.D. studies (teaching computer labs Design of Algorithms, Object-Oriented Programming)
• Further activities:
  - Occasional teaching of selected courses at other universities (University of Navarra, Spain; Brno University of Technology, Czech Republic)
  - Membership in doctoral boards of selected Ph.D. study programs (Masaryk University and Brno University of Technology)
  - Regular reviewer and opponent of Ph.D. theses in different countries (e.g., Uppsala University, Sweden; Tampere University of Technology, Finland; Oulu University, Finland; University of Navarra, Spain)
  - Main organizer of tutorials on benchmarking in biomedical image analysis at established conferences (ISBI 2016, NEUBIAS 2017, MICCAI 2017)
  - Main organizer of a specialized international summer school on "Advanced Methods in Biomedical Image Analysis" in Brno in 2011, 2017 and 2020 (most teachers and participants from abroad, see https://ambia.fi.muni.cz/)
  - Hosting of international students during exchanges or internships (so far 4 from India, 2 from Spain, 1 from Japan)
• Supervision of students:
  Bachelor level: 7 defended
  Master level: 18 defended
  Ph.D. level: 10 defended

Scientific and Research Activities

• Biomedical image acquisition
  - Image formation and detection in biomedical imaging
  - Multi-modal and multi-dimensional (including temporal) imaging
  - Optimization and automation of computerized image acquisition
• Biomedical image analysis
  - Object detection, segmentation and tracking in biomedical images
  - Benchmarking of biomedical image analysis algorithms
  - Machine learning and artificial intelligence in biomedical imaging
  
• Biological and clinical applications
  - Computer analysis of cells, tissues and organs
  - Modeling of spatiotemporal behavior of analyzed objects
  - Learning from images of healthy versus cancer cells and tissues

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:
  2021 - 2024: "Classification of brain tumors using advanced techniques of multimodal diffusion MRI data", Czech Health Research Council, Grant No. NU21-08-00359
  2020 - 2022: "National Infrastructure for Biological and Medical Imaging Czech-BioImaging", Czech Ministry of Education, Large Infrastructure Projects No. LM2018129 and CZ.02.1.01/0.0/0.0/18_046/0016045
  2017 - 2019: "Optimization 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 - 2020: "National Infrastructure for Biological and Medical Imaging Czech-BioImaging", 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, Boards and Panels

• International:
  2020 - present: Associate Editor, journal Biological Imaging (Cambridge Univ Press)
  2018 - present: Member, Medical Image Computing and Computer Assisted Intervention (MICCAI)
  2018 - present: Member, MICCAI Working Group on Challenges in Biomedical Image Analysis
  2016 - present: Member, IEEE & IEEE Signal Processing Society
  2010 - 2010: Member, Data analysis review panel, Academy of Finland
  2002 - present: Member, European Microscopy Society (EMS)
  2000 - 2018: Member, International Society for Advancement of Cytometry (ISAC)
• National:
  2021 - present: Coordinator, Centre for Artificial Intelligence in Oncology
  2019 - present: Fellow, AICzechia - national initiative for artificial intelligence
  2017 - 2020: 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, 2018 - present: Member, Academic Senate of Masaryk University
  2006 - 2011, 2015 - present: Member, 2009 - 2011, 2018 - 2021: Chair, Academic Senate of Faculty of Informatics of Masaryk University
  2004 - 2007, 2011 - present: Member, 2011 - 2015: Chair, Scientific Council of Faculty of Informatics of Masaryk University
  2003 - 2006: Member, Scientific Council of Faculty of Science of Masaryk University
• Conference-related:
  2020: Member of OC, Challenge Committee, Medical Image Computing and Computer-Assisted Intervention (MICCAI), Lima, Peru (virtual)
  2020: Member of OC, Challenge Chair, IEEE International Symposium on Biomedical Imaging (ISBI), Iowa, US (virtual)
  2019: General Chair of European Light Microscopy Initiative (ELMI) conference, Brno, Czech Republic
  2018 - present: Reviewer and Meta-Reviewer of Challenge Proposals, Medical Image Computing and Computer-Assisted Intervention (MICCAI)
  2018: Member of PC, BioImage Computing Workshop, European Conference on Computer Vision (ECCV)
  2017: Member of PC, BioImage Computing Workshop, International Conference on Computer Vision (ICCV)
  2016: Member of LOC, Financial Chair, IEEE International Symposium on Biomedical Imaging (ISBI), Prague, Czech Republic
  2014: Member of LOC, International Microscopy Congress (IMC), Prague, Czech Republic
  2014 - present: Associate Editor of IEEE International Symposium on Biomedical Imaging (ISBI)
  2011: Member of PC, Microscopic Image Analysis with Applications in Biology (MIAAB)
  2010: Member of PC, International Conference on Image and Signal Processing (ICISP)
  2009 - 2010: Member of PC, International Conference on Signal-Image Technology & Internet-Based Systems (SITIS)
  2008 - 2011: Member of PC, International Conference on Computer Vision Theory and Applications (VISAPP)
  2008 - 2011: Member of PC, Congress of International Society for Advancement of Cytometry (ISAC)
  2007: Member of PC, European Signal Processing Conference (EUSIPCO)
  2006 - present: Reviewer, IEEE International Symposium on Biomedical Imaging (ISBI)
  

Invited Talks, Prizes and Awards

• Selected Invited Talks:
  2018: Keynote lecture "Benchmarking of Algorithms for Biomedical Image Analysis", World Congress on Medical Physics and Biomedical Engineering, Prague
  2017: Invited lecture "The ABCs of Rigorous Bioimage Analysis: Algorithms, Benchmarks, Challenges", BioImage Informatics Conference, Banff, Canada
  2017: Invited lecture "Virtual Cell Imaging: Synthetic Image Datasets for Benchmarking Bioimage Analysis Methods", Network of European BioImage Analysts - NEUBIAS Conference, Lisboa, Portugal
  2017: Invited lecture "Reliable Cell Image Analysis", Functional Organization of the Cell Nucleus Symposium, Prague
  2016: Invited lecture "30 Years of Computerized 3D Cell Image Analysis in Fluorescence Microscopy", IEEE International Symposium on Biomedical Imaging (ISBI), Prague
  2016: Invited lecture "Quality Control in Cell Image Analysis: Choosing the best algorithm or software", Functional Organization of the Cell Nucleus Symposium, Prague
  2014: Invited lecture "Quality Control in Cell Image Segmentation and Tracking using Simulated Cell Images", International Microscopy Congress (IMC), Prague
  2014: Invited lecture "Establishment of a Benchmark for Evaluation and Comparison of Cell Segmentation and Tracking Algorithms", BioImage Informatics Conference, Leuven, Belgium
• External prizes and awards (not related to Masaryk university):
  2005: Member of the CBIA team awarded the 1st Prize in national competition Best of Biotech (for the best project in biotechnologies entitled High-resolution image cytometer focusing on the automation of cell image analysis)
  2004: Awarded CIMO Fellowship, Finland, for a three-month stay at the Dept. of Information Technology, Lappeenranta University of Technology, Finland
  2001: Awarded a 3-year grant by Volkswagen Stiftung Foundation, Germany, to investigate cell tomography image analysis
  1999: TALENT'98 Award, Czech Ministry of Education (for promoting inter-disciplinary research)
  1995: Awarded prestigious Soros/FCO Scholarship for a nine-month stay at the Dept. of Engineering Science, University of Oxford, UK
  1994: Awarded TEMPUS Scholarship for a one-semester stay at Technical University Darmstadt, Germany
• Internal prizes and awards (at Masaryk university):
  2003 - 2016: Annual Rector's Prize, Masaryk University, awarded to four Ph.D. graduates supervised by Michal Kozubek (2003: Petr Matula, 2011: Silvie Luisa Brázdilová, 2012: Ondřej Daněk, 2016: Martin Maška)
  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

• MAIER-HEIN, Lena, Annika REINKE, Patrick GODAU, Minu D TIZABI, Florian BUETTNER, Evangelia CHRISTODOULOU, Ben GLOCKER, Fabian ISENSEE, Jens KLEESIEK, Michal KOZUBEK, Mauricio REYES, Michael A RIEGLER, Manuel WIESENFARTH, A Emre KAVUR, Carole H SUDRE, Michael BAUMGARTNER, Matthias EISENMANN, Doreen HECKMANN-NOETZEL, Tim RAEDSCH, Laura ACION, Michela ANTONELLI, Tal ARBEL, Spyridon BAKAS, Arriel BENIS, Matthew B BLASCHKO, M Jorge CARDOSO, Veronika CHEPLYGINA, Beth A CIMINI, Gary S COLLINS, Keyvan FARAHANI, Luciana FERRER, Adrian GALDRAN, van Ginneken BRAM, Robert HAASE, Daniel A HASHIMOTO, Michael M HOFFMAN, Merel HUISMAN, Pierre JANNIN, Charles E KAHN, Dagmar KAINMUELLER, Bernhard KAINZ, Alexandros KARARGYRIS, Alan KARTHIKESALINGAM, Florian KOFLER, Annette KOPP-SCHNEIDER, Anna KRESHUK, Tahsin KURC, Bennett A LANDMAN, Geert LITJENS, Amin MADANI, Klaus MAIER-HEIN, Anne L MARTEL, Peter MATTSON, Erik MEIJERING, Bjoern MENZE, Karel G M MOONS, Henning MUELLER, Brennan NICHYPORUK, Felix NICKEL, Jens PETERSEN, Nasir RAJPOOT, Nicola RIEKE, Julio SAEZ-RODRIGUEZ, Clara I SANCHEZ, Shravya SHETTY, van Smeden MAARTEN, Ronald M SUMMERS, Abdel A TAHA, Aleksei TIULPIN, Sotirios A TSAFTARIS, Van Calster BEN, Gael VAROQUAUX a Paul F JAEGER. Metrics reloaded: recommendations for image analysis validation. NATURE METHODS. UNITED STATES: NATURE PORTFOLIO, 2024, roč. 21, February, s. 195-212, 30 s. ISSN 1548-7091. Dostupné z: https://dx.doi.org/10.1038/s41592-023-02151-z. URL info
• REINKE, Annika, Minu D TIZABI, Michael BAUMGARTNER, Matthias EISENMANN, Doreen HECKMANN-NÖTZEL, A Emre KAVUR, Tim RÄDSCH, Carole H SUDRE, Laura ACION, Michela ANTONELLI, Tal ARBEL, Spyridon BAKAS, Arriel BENIS, Florian BUETTNER, M Jorge CARDOSO, Veronika CHEPLYGINA, Jianxu CHEN, Evangelia CHRISTODOULOU, Beth A CIMINI, Keyvan FARAHANI, Luciana FERRER, Adrian GALDRAN, Bram van GINNEKEN, Ben GLOCKER, Patrick GODAU, Daniel A HASHIMOTO, Michael M HOFFMAN, Merel HUISMAN, Fabian ISENSEE, Pierre JANNIN, Charles E KAHN, Dagmar KAINMUELLER, Bernhard KAINZ, Alexandros KARARGYRIS, Jens KLEESIEK, Florian KOFLER, Thijs KOOI, Annette KOPP-SCHNEIDER, Michal KOZUBEK, Anna KRESHUK, Tahsin KURC, Bennett A LANDMAN, Geert LITJENS, Amin MADANI, Klaus MAIER-HEIN, Anne L MARTEL, Erik MEIJERING, Bjoern MENZE, Karel GM MOONS, Henning MÜLLER, Brennan NICHYPORUK, Felix NICKEL, Jens PETERSEN, Susanne M RAFELSKI, Nasir RAJPOOT, Mauricio REYES, Michael A RIEGLER, Nicola RIEKE, Julio SAEZ-RODRIGUEZ, Clara I SÁNCHEZ, Shravya SHETTY, Ronald M SUMMERS, Abdel A TAHA, Aleksei TIULPIN, Sotirios A TSAFTARIS, Ben Van CALSTER, Gaël VAROQUAUX, Ziv R YANIV, Paul F JÄGER a Lena MAIER-HEIN. Understanding metric-related pitfalls in image analysis validation. NATURE METHODS. UNITED STATES: NATURE PORTFOLIO, 2024, roč. 21, February, s. 182-194, 20 s. ISSN 1548-7091. Dostupné z: https://dx.doi.org/10.1038/s41592-023-02150-0. URL info
• MAŠKA, Martin, Vladimír ULMAN, Pablo DELGADO-RODRIGUEZ, Estibaliz GÓMEZ-DE-MARISCAL, Tereza NEČASOVÁ, Fidel A Guerrero PEÑA, Tsang Ing REN, Elliot M MEYEROWITZ, Tim SCHERR, Katharina LÖFFLER, Ralf MIKUT, Tianqi GUO, Yin WANG, Jan P ALLEBACH, Rina BAO, Noor M AL-SHAKARJI, Gani RAHMON, Imad Eddine TOUBAL, Kannappan PALANIAPPAN, Filip LUX, Petr MATULA, Ko SUGAWARA, Klas E G MAGNUSSON, Layton AHO, Andrew R COHEN, Assaf ARBELLE, Tal BEN-HAIM, Tammy Riklin RAVIV, Fabian ISENSEE, Paul F JÄGER, Klaus H MAIER-HEIN, Yanming ZHU, Cristina EDERRA, Ainhoa URBIOLA, Erik MEIJERING, Alexandre CUNHA, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK a Carlos ORTIZ-DE-SOLÓRZANO. The Cell Tracking Challenge: 10 years of objective benchmarking. Nature Methods. 2023, roč. 20, č. 7, s. 1010-1020. ISSN 1548-7091. Dostupné z: https://dx.doi.org/10.1038/s41592-023-01879-y. URL info
• MAIER-HEIN, Lena, Annika REINKE, Michal KOZUBEK, Anne L. MARTEL, Tal ARBEL, Matthias EISENMANN, Allan HANBURY, Pierre JANNIN, Henning MÜLLER, Sinan ONOGUR, Julio SAEZ-RODRIGUEZ, Bram VAN GINNEKEN, Annette KOPP-SCHNEIDER a Bennett A. LANDMAN. BIAS: Transparent reporting of biomedical image analysis challenges. Medical Image Analysis. Elsevier, 2020, roč. 66, č. 101796, s. 1-7. ISSN 1361-8415. Dostupné z: https://dx.doi.org/10.1016/j.media.2020.101796. URL info
• MACHÁLKOVÁ, Markéta, Barbora PAVLATOVSKÁ, Jan MICHÁLEK, Adam PRUŠKA, Karel ŠTĚPKA, Tereza NEČASOVÁ, Katarzyna Anna RADASZKIEWICZ, Michal KOZUBEK, Jan ŠMARDA, Jan PREISLER a Jarmila NAVRÁTILOVÁ. Drug Penetration Analysis in 3D Cell Cultures Using Fiducial-Based Semiautomatic Coregistration of MALDI MSI and Immunofluorescence Images. Analytical Chemistry. American Chemical Society, 2019, roč. 91, č. 21, s. 13475-13484. ISSN 0003-2700. Dostupné z: https://dx.doi.org/10.1021/acs.analchem.9b02462. URL info
• MAIER-HEIN, Lena, Matthias EISENMANN, Annika REINKE, Sinan ONOGUR, Marko STANKOVIC, Patrick SCHOLZ, Tal ARBEL, Hrvoje BOGUNOVIC, Andrew BRADLEY, Aaron CARASS, Carolin FELDMANN, Alejandro FRANGI, Peter FULL, Bram VAN GINNEKEN, Allan HANBURY, Katrin HONAUER, Michal KOZUBEK, Bennett LANDMAN, Keno MÄRZ, Oskar MAIER, Klaus MAIER-HEIN, Bjoern MENZE, Henning MÜLLER, Peter NEHER, Wiro NIESSEN, Nasir RAJPOOT, Gregory SHARP, Korsuk SIRINUKUNWATTANA, Stefanie SPEIDEL, Christian STOCK, Danail STOYANOV, Abdel Aziz TAHA, Fons VAN DER SOMMEN, Ching-Wei WANG, Marc-André WEBER, Guoyan ZHENG, Pierre JANNIN a Annette KOPP-SCHNEIDER. Why rankings of biomedical image analysis competitions should be interpreted with care. Nature Communications. Nature Publishing Group, 2018, roč. 9, č. 5217, s. 1-13. ISSN 2041-1723. Dostupné z: https://dx.doi.org/10.1038/s41467-018-07619-7. 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
• KOZUBEK, Michal. Challenges and Benchmarks in Bioimage Analysis. Online. In DeVos WH, Munck S, Timmermans JP. Focus on Bio-Image Informatics. Berlin: Springer, 2016, s. 231-262. Advances in Anatomy, Embryology and Cell Biology 219. ISBN 978-3-319-28547-4. Dostupné z: https://dx.doi.org/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. Dostupné z: https://dx.doi.org/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", 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
• 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. Dostupné z: https://dx.doi.org/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. Dostupné z: https://dx.doi.org/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. Dostupné z: https://dx.doi.org/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. Dostupné z: https://dx.doi.org/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", 8 s. 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. Dostupné z: https://dx.doi.org/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. Dostupné z: https://dx.doi.org/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. 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. Image acquisition and its automation in fluorescence microscopy. In From cells to proteins: Imaging nature across dimensions. Dordrecht: Springer, 2005, s. 227-270. 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. 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. Dostupné z: https://dx.doi.org/10.1002/jemt.1080. URL 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. URL 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. Dostupné z: https://dx.doi.org/10.1007/1-4020-3616-7_13. URL 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
• 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

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