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, NEUBIAS 2022)
  - Main organizer of a specialized international summer school on "Advanced Methods in Biomedical Image Analysis" in Brno in 2011, 2017, 2020 and 2023 (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, 2 from Italy, 2 from France, 1 from Japan)
• Supervision of students:
  Bachelor level: 8 defended
  Master level: 20 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:
  2023 - 2027: "Testing and Experimentation Facility for Health AI and Robotics", EU Digital Europe Programme, Project No. 101100700.
  2023 - 2026: "National Infrastructure for Biological and Medical Imaging Czech-BioImaging", Czech Ministry of Education, Large Infrastructure Projects No. LM2023050 and CZ.02.01.01/00/23_015/0008205.
  2022 - 2025: "Structural MRI radiomic analysis for differential diagnosis of radiation injury and true progression after stereotactic radiotherapy of brain metastases", Czech Health Research Council, Grant No. NU22-03-00159.
  2021 - 2025: "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 - 2024: Associate Editor, journal Biological Imaging (Cambridge Univ Press)
  2018 - present: Member, Medical Image Computing and Computer Assisted Intervention (MICCAI)
  2018 - present: Member, MICCAI Special Interest 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 - 2024: 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:
  2025: Member of OC, Challenge Chair, Medical Image Computing and Computer-Assisted Intervention (MICCAI), Daejeon, South Korea
  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):
  2022: Annual Rector's Prize, Masaryk University (for long-term excellence in research)
  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

• ZENK, Maximilian; Ujjwal BAID; Sarthak PATI; Akis LINARDOS; Brandon EDWARDS; Micah SHELLER; Patrick FOLEY; Alejandro ARISTIZABAL; David ZIMMERER; Alexey GRUZDEV; Jason MARTIN; Russell T SHINOHARA; Annika REINKE; Fabian ISENSEE; Santhosh PARAMPOTTUPADAM; Kaushal PAREKH; Ralf FLOCA; Hasan KASSEM; Bhakti BAHETI; Siddhesh THAKUR; Verena CHUNG; Kaisar KUSHIBAR; Karim LEKADIR; Meirui JIANG; Youtan YIN; Hongzheng YANG; Quande LIU; Cheng CHEN; Qi DOU; Pheng-Ann HENG; Xiaofan ZHANG; Shaoting ZHANG; Muhammad Irfan KHAN; Mohammad Ayyaz AZEEM; Mojtaba JAFARITADI; Esa ALHONIEMI; Elina KONTIO; Suleiman A KHAN; Leon MAECHLER; Ivan EZHOV; Florian KOFLER; Suprosanna SHIT; Johannes C PAETZOLD; Timo LOEHR; Benedikt WIESTLER; Himashi PEIRIS; Kamlesh PAWAR; Shenjun ZHONG; Zhaolin CHEN; Munawar HAYAT; Gary EGAN; Mehrtash HARANDI; Isik Polat ECE; Gorkem POLAT; Altan KOCYIGIT; Alptekin TEMIZEL; Anup TULADHAR; Lakshay TYAGI; Raissa SOUZA; Nils D FORKERT; Pauline MOUCHES; Matthias WILMS; Vishruth SHAMBHAT; Akansh MAURYA; Shubham Subhas DANANNAVAR; Rohit KALLA; Vikas Kumar ANAND; Ganapathy KRISHNAMURTHI; Sahil NALAWADE; Chandan GANESH; Ben WAGNER; Divya REDDY; Yudhajit DAS; Fang F YU; Baowei FEI; Ananth J MADHURANTHAKAM; Joseph MALDJIAN; Gaurav SINGH; Jianxun REN; Wei ZHANG; Ning AN; Qingyu HU; Youjia ZHANG; Ying ZHOU; Vasilis SIOMOS; Giacomo TARRONI; Jonathan PASSERRAT-PALMBACH; Ambrish RAWAT; Giulio ZIZZO; Swanand Ravindra KADHE; Jonathan P EPPERLEIN; Stefano BRAGHIN; Yuan WANG; Renuga KANAGAVELU; Qingsong WEI; Yechao YANG; Yong LIU; Krzysztof KOTOWSKI; Szymon ADAMSKI; Bartosz MACHURA; Wojciech MALARA; Lukasz ZARUDZKI; Jakub NALEPA; Yaying SHI; Hongjian GAO; Salman AVESTIMEHR; Yonghong YAN; Agus S AKBAR; Ekaterina KONDRATEVA; Hua YANG; Zhaopei LI; Hung-Yu WU; Johannes ROTH; Camillo SAUERESSIG; Alexandre MILESI; Quoc D NGUYEN; Nathan J GRUENHAGEN; Tsung-Ming HUANG; Jun MA; Har Shwinder H SINGH; Nai-Yu PAN; Dingwen ZHANG; Ramy A ZEINELDIN; Michal FUTREGA; Yading YUAN; Gian Marco CONTE; Xue FENG; Quan D PHAM; Yong XIA; Zhifan JIANG; Huan Minh LUU; Mariia DOBKO; Alexandre CARRE; Bair TUCHINOV; Hassan MOHY-UD-DIN; Saruar ALAM; Anup SINGH; Nameeta SHAH; Weichung WANG; Chiharu SAKO; Michel BILELLO; Satyam GHODASARA; Suyash MOHAN; Christos DAVATZIKOS; Evan CALABRESE; Jeffrey RUDIE; Javier VILLANUEVA-MEYER; Soonmee CHA; Christopher HESS; John MONGAN; Madhura INGALHALIKAR; Manali JADHAV; Umang PANDEY; Jitender SAINI; Raymond Y HUANG; Ken CHANG; Minh-Son TO; Sargam BHARDWAJ; Chee CHONG; Marc AGZARIAN; Michal KOZUBEK; Filip LUX; Jan MICHÁLEK; Petr MATULA; Miloš KEŘKOVSKÝ; Tereza KOPŘIVOVÁ; Marek DOSTÁL; Václav VYBÍHAL; Marco C PINHO; James HOLCOMB; Marie METZ; Rajan JAIN; Matthew D LEE; Yvonne W LUI; Pallavi TIWARI; Ruchika VERMA; Rohan BAREJA; Ipsa YADAV; Jonathan CHEN; Neeraj KUMAR; Yuriy GUSEV; Krithika BHUVANESHWAR; Anousheh SAYAH; Camelia BENCHEQROUN; Anas BELOUALI; Subha MADHAVAN; Rivka R COLEN; Aikaterini KOTROTSOU; Philipp VOLLMUTH; Gianluca BRUGNARA; Chandrakanth J PREETHA; Felix SAHM; Martin BENDSZUS; Wolfgang WICK; Abhishek MAHAJAN; Carmen BALANA; Jaume CAPELLADES; Josep PUIG; Yoon Seong CHOI; Seung-Koo LEE; Jong Hee CHANG; Sung Soo AHN; Hassan F SHAYKH; Alejandro HERRERA-TRUJILLO; Maria TRUJILLO; William ESCOBAR; Ana ABELLO; Jose BERNAL; Jhon GOMEZ; Pamela LAMONTAGNE; Daniel S MARCUS; Mikhail MILCHENKO; Arash NAZERI; Bennett LANDMAN; Karthik RAMADASS; Kaiwen XU; Silky CHOTAI; Lola B CHAMBLESS; Akshitkumar MISTRY; Reid C THOMPSON; Ashok SRINIVASAN; J Rajiv BAPURAJ; Arvind RAO; Nicholas WANG; Ota YOSHIAKI; Toshio MORITANI; Sevcan TURK; Joonsang LEE; Snehal PRABHUDESAI; John GARRETT; Matthew LARSON; Robert JERAJ; Hongwei LI; Tobias WEISS; Michael WELLER; Andrea BINK; Bertrand POUYMAYOU; Sonam SHARMA; Tzu-Chi TSENG; Saba ADABI; Xavier Falcao ALEXANDRE; Samuel B MARTINS; Bernardo C A TEIXEIRA; Flavia SPRENGER; David MENOTTI; Diego R LUCIO; Simone P NICLOU; Olivier KEUNEN; Ann-Christin HAU; Enrique PELAEZ; Heydy FRANCO-MALDONADO; Francis LOAYZA; Sebastian QUEVEDO; Richard MCKINLEY; Johannes SLOTBOOM; Piotr RADOJEWSKI; Raphael MEIER; Roland WIEST; Johannes TRENKLER; Josef PICHLER; Georg NECKER; Andreas HAUNSCHMIDT; Stephan MECKEL; Pamela GUEVARA; Esteban TORCHE; Cristobal MENDOZA; Vera FRANCO; Elvis RIOS; Eduardo LOPEZ; Sergio A VELASTIN; Joseph CHOI; Stephen BAEK; Yusung KIM; Heba ISMAEL; Bryan ALLEN; John M BUATTI; Peter ZAMPAKIS; Vasileios PANAGIOTOPOULOS; Panagiotis TSIGANOS; Sotiris ALEXIOU; Ilias HALIASSOS; Evangelia I ZACHARAKI; Konstantinos MOUSTAKAS; Christina KALOGEROPOULOU; Dimitrios M KARDAMAKIS; Bing LUO; Laila M POISSON; Ning WEN; Martin VALLIERES; Mahdi Ait Lhaj LOUTFI; David FORTIN; Martin LEPAGE; Fanny MORON; Jacob MANDEL; Gaurav SHUKLA; Spencer LIEM; Gregory S ALEXANDRE; Joseph LOMBARDO; Joshua D PALMER; Adam E FLANDERS; Adam P DICKER; Godwin OGBOLE; Dotun OYEKUNLE; Olubunmi ODAFE-OYIBOTHA; Babatunde OSOBU; Hikima Mustapha SHU'AIBU; Mayowa SONEYE; Farouk DAKO; Adeleye DORCAS; Derrick MURCIA; Eric FU; Rourke HAAS; John A THOMPSON; David Ryan ORMOND; Stuart CURRIE; Kavi FATANIA; Russell FROOD; Amber L SIMPSON; Jacob J PEOPLES; Ricky HU; Danielle CUTLER; Fabio Y MORAES; Anh TRAN; Mohammad HAMGHALAM; Michael A BOSS; James GIMPEL; Kattil Veettil DEEPAK; Kendall SCHMIDT; Lisa CIMINO; Cynthia PRICE; Brian BIALECKI; Sailaja MARELLA; Charles APGAR; Andras JAKAB; Marc-Andre WEBER; Errol COLAK; Jens KLEESIEK; John B FREYMANN; Justin S KIRBY; Lena MAIER-HEIN; Jake ALBRECHT; Peter MATTSON; Alexandros KARARGYRIS; Prashant SHAH; Bjoern MENZE; Klaus MAIER-HEIN a Spyridon BAKAS. Towards fair decentralized benchmarking of healthcare AI algorithms with the Federated Tumor Segmentation (FeTS) challenge. Nature communications. BERLIN: NATURE PORTFOLIO, 2025, roč. 16, č. 1, s. 1-20. ISSN 2041-1723. Dostupné z: https://doi.org/10.1038/s41467-025-60466-1. URL info
• 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://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, č. 2, s. 182-194, 20 s. ISSN 1548-7091. Dostupné z: https://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://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://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://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://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://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://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://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://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://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://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://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://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://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://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://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://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://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

2025/09/11