Automated Multi-view 3D Image Acquisition in Human Genome Research. - Michal Kozubek 001; Petr Matula; Heinz Eipel; Michael Hausmann (3DPVT, 2002)

High-Resolution Cytometry Network Project: Towards Remote a d Distributed Acquisition, Processing and Visualisation of 3D Image Data in Human Genome Research. - Michal Kozubek 001; Petr Matula; Pavel Matula; Petr Mejzlík (3DPVT, 2002)

High-Resolution Cytometry Network Project: Client/Server System for 3D Optical Microscope Data Storage and Analysis. - Pavel Matula; Petr Matula; Michal Kozubek 001; Petr Mejzlík (3DPVT, 2004)

Fast Marching 3D Reconstruction of Interphase Chromosomes. - Pavel Matula; Jan Hubený; Michal Kozubek 001 (ECCV Workshops CVAMIA and MMBIA, 2004)

Applications of Image Registration in Human Genome Research. - Petr Matula; Michal Kozubek 001; Pavel Matula (ECCV Workshops CVAMIA and MMBIA, 2004)

Automated Confocal Microscopy: The Way of Achieving both Quality and Quantity in 3D Image Cytometry. - Michal Kozubek 001; Petr Matula; Pavel Matula (ISBI, 2004)

Fast point-based 3-D alignment of live cells. - Petr Matula; Michal Kozubek 001; Vladimír Dvorák (IEEE Trans. Image Process., 2006)

A Comparison of Fast Level Set-Like Algorithms for Image Segmentation in Fluorescence Microscopy. - Martin Maska; Jan Hubený; David Svoboda; Michal Kozubek 001 (ISVC (2), 2007)

Acquiarium: Free Software for the Acquisition and Analysis of 3D Images of Cells in Fluorescence Microscopy. - Pavel Matula; Martin Maska; Ondrej Danek; Petr Matula; Michal Kozubek 001 (ISBI, 2009)

Segmentation of Touching Cell Nuclei Using a Two-Stage Graph Cut Model. - Ondrej Danek; Pavel Matula; Carlos Ortiz-de-Solorzano; Arrate Muñoz-Barrutia; Martin Maska; Michal Kozubek 001 (SCIA, 2009)

A Two-Phase Segmentation of Cell Nuclei Using Fast Level Set-Like Algorithms. - Martin Maska; Ondrej Danek; Carlos Ortiz-de-Solorzano; Arrate Muñoz-Barrutia; Michal Kozubek 001; Ignacio Fernández García (SCIA, 2009)

A Fast Level Set-Like Algorithm for Region-Based Active Contours. - Martin Maska; Pavel Matula; Ondrej Danek; Michal Kozubek 001 (ISVC (3), 2010)

Simultaneous Tracking of Multiple Objects Using Fast Level Set-Like Algorithm. - Martin Maska; Pavel Matula; Michal Kozubek 001 (MEMICS, 2010)

Smooth Chan-Vese segmentation via graph cuts. - Ondrej Danek; Pavel Matula; Martin Maska; Michal Kozubek 001 (Pattern Recognit. Lett., 2012)

A benchmark for comparison of cell tracking algorithms. - Martin Maska; Vladimír Ulman; David Svoboda; Pavel Matula; Petr Matula; Cristina Ederra; Ainhoa Urbiola; Tomás España; Subramanian Venkatesan 001; Deepak M. W. Balak; Pavel Karas; Tereza Bolcková; et al. (Bioinform., 2014)

Characterization of the role of collagen network structure and composition in cancer cell migration. - María Anguiano; Carlos Castilla; Martin Maska; Cristina Ederra; Javier Fernández-Marqués; Rafael Peláez; Ana Rouzaut; Arrate Muñoz-Barrutia; Michal Kozubek 001; Carlos Ortiz-de-Solorzano (EMBC, 2015)

Quantification of the 3D collagen network geometry in confocal reflection microscopy. - Martin Maska; Cristina Ederra; Javier Fernández-Marqués; Arrate Muñoz-Barrutia; Michal Kozubek 001; Carlos Ortiz-de-Solorzano (ICIP, 2015)

Quantitative Bioimaging: Signal Processing in Light Microscopy [From the Guest Editors]. - Arrate Muñoz-Barrutia; Jelena Kovacevic; Michal Kozubek 001; Erik Meijering; Braham Parvin (IEEE Signal Process. Mag., 2015)

Toward a Morphodynamic Model of the Cell: Signal processing for cell modeling. - Carlos Ortiz-de-Solorzano; Arrate Muñoz-Barrutia; Erik Meijering; Michal Kozubek 001 (IEEE Signal Process. Mag., 2015)

Multimodal Simulations in Live Cell Imaging. - David Svoboda; Michal Kozubek 001 (SASHIMI@MICCAI, 2017)

Image-based surrogate biomarkers for molecular subtypes of colorectal cancer. - Vlad Popovici; Eva Budinska; Ladislav Dusek; Michal Kozubek 001; Fred Bosman (Bioinform., 2017)

Automatic Fusion of Segmentation and Tracking Labels. - Cem Emre Akbas; Vladimír Ulman; Martin Maska; Florian Jug; Michal Kozubek 001 (ECCV Workshops (6), 2018)

How to Exploit Weaknesses in Biomedical Challenge Design and Organization. - Annika Reinke; Matthias Eisenmann; Sinan Onogur; Marko Stankovic 002; Patrick Scholz 001; Peter M. Full; Hrvoje Bogunovic; Bennett A. Landman; Oskar Maier; Bjoern H. Menze; Gregory C. Sharp; Korsuk Sirinukunwattana; et al. (MICCAI (4), 2018)

Is the winner really the best? A critical analysis of common research practice in biomedical image analysis competitions. - Lena Maier-Hein; Matthias Eisenmann; Annika Reinke; Sinan Onogur; Marko Stankovic 002; Patrick Scholz 001; Tal Arbel; Hrvoje Bogunovic; Andrew P. Bradley; Aaron Carass; Carolin Feldmann; Alejandro F. Frangi; et al. (CoRR, 2018)

CytoPacq: a web-interface for simulating multi-dimensional cell imaging. - David Wiesner; David Svoboda; Martin Maska; Michal Kozubek 001 (Bioinform., 2019)

Condensed U-Net (Cu-Net): An Improved U-Net Architecture for Cell Segmentation Powered by 4x4 Max-Pooling Layers. - Cem Emre Akbas; Michal Kozubek 001 (ISBI, 2020)

BIAS: Transparent reporting of biomedical image analysis challenges. - Lena Maier-Hein; Annika Reinke; Michal Kozubek 001; Anne L. Martel; Tal Arbel; Matthias Eisenmann; Allan Hanbury; Pierre Jannin; Henning Müller; Sinan Onogur; Julio Saez-Rodriguez; Bram van Ginneken; et al. (Medical Image Anal., 2020)

Common Limitations of Image Processing Metrics: A Picture Story. - Annika Reinke; Matthias Eisenmann; Minu Dietlinde Tizabi; Carole H. Sudre; Tim Rädsch; Michela Antonelli; Tal Arbel; Spyridon Bakas; M. Jorge Cardoso; Veronika Cheplygina; Keyvan Farahani; Ben Glocker; et al. (CoRR, 2021)

Metrics reloaded: Pitfalls and recommendations for image analysis validation. - Lena Maier-Hein; Annika Reinke; Evangelia Christodoulou; Ben Glocker; Patrick Godau; Fabian Isensee; Jens Kleesiek; Michal Kozubek 001; Mauricio Reyes 001; Michael A. Riegler; Manuel Wiesenfarth; Michael Baumgartner 001; et al. (CoRR, 2022)

Biomedical image analysis competitions: The state of current participation practice. - Matthias Eisenmann; Annika Reinke; Vivienn Weru; Minu Dietlinde Tizabi; Fabian Isensee; Tim J. Adler; Patrick Godau; Veronika Cheplygina; Michal Kozubek 001; Sharib Ali; Anubha Gupta; Jan Kybic; et al. (CoRR, 2022)

Why is the Winner the Best? - Matthias Eisenmann; Annika Reinke; Vivienn Weru; Minu Dietlinde Tizabi; Fabian Isensee; Tim J. Adler; Sharib Ali; Vincent Andrearczyk; Marc Aubreville; Ujjwal Baid; Spyridon Bakas; Niranjan Balu; et al. (CVPR, 2023)

Understanding metric-related pitfalls in image analysis validation. - Annika Reinke; Minu Tizabi; Michael Baumgartner 001; Matthias Eisenmann; Doreen Heckmann-Nötzel; A. Emre Kavur; Tim Rädsch; Carole H. Sudre; Laura Ación; Michela Antonelli; Tal Arbel; Spyridon Bakas; et al. (CoRR, 2023)

Why is the winner the best? - Matthias Eisenmann; Annika Reinke; Vivienn Weru; Minu Dietlinde Tizabi; Fabian Isensee; Tim J. Adler; Sharib Ali; Vincent Andrearczyk; Marc Aubreville; Ujjwal Baid; Spyridon Bakas; Niranjan Balu; et al. (CoRR, 2023)

Brain MRI Screening Tool with Federated Learning. - Roman Stoklasa; Ioannis Stathopoulos; Efstratios Karavasilis; Efstathios P. Efstathopoulos; Marek Dostál; Milos Kerkovský; Michal Kozubek 001; Luigi Serio (CoRR, 2023)

Gravitational Cell Detection and Tracking in Fluorescence Microscopy Data. - Nikomidisz Eftimiu; Michal Kozubek 001 (ISBI, 2024)

Brain MRI Screening Tool with Federated Learning. - Roman Stoklasa; Ioannis Stathopoulos; Efstratios Karavasilis; Efstathios Efstathopoulos; Marek Dostál; Milos Kerkovský; Michal Kozubek 001; Luigi Serio (ISBI, 2024)

DeepFuse: A multi-rater fusion and refinement network for computing silver-standard annotations. - Cem Emre Akbas; Vladimír Ulman; Martin Maska; Michal Kozubek 001 (Comput. Biol. Medicine, 2025)

False Promises in Medical Imaging AI? Assessing Validity of Outperformance Claims. - Evangelia Christodoulou; Annika Reinke; Pascaline Andrè; Patrick Godau; Piotr Kalinowski; Rola Houhou; Selen Erkan; Carole H. Sudre; Ninon Burgos; Sofiène Boutaj; Sophie Loizillon; Maëlys Solal; et al. (CoRR, 2025)