Gravitational Cell Detection and Tracking in Fluorescence Microscopy Data - Nikomidisz Eftimiu; Michal Kozubek (IEEE International Symposium on Biomedical Imaging, ISBI 2024, Athens, Greece, May 27-30, 2024, 2024)

Brain MRI Screening Tool with Federated Learning - Roman Stoklasa; Ioannis Stathopoulos; Efstratios Karavasilis; Efstathios Efstathopoulos; Marek Dostál; Milos Kerkovský; Michal Kozubek; Luigi Serio (IEEE International Symposium on Biomedical Imaging, ISBI 2024, Athens, Greece, May 27-30, 2024, 2024)

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. (IEEE/CVF Conference on Computer Vision and Pattern Recognition, CVPR 2023, Vancouver, BC, Canada, June 17-24, 2023, 2023)

Understanding metric-related pitfalls in image analysis validation - Annika Reinke; Minu Tizabi; Michael Baumgartner; 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; Luigi Serio (CoRR, 2023)

Gravitational cell detection and tracking in fluorescence microscopy data - Nikomidisz Eftimiu; Michal Kozubek (CoRR, 2023)

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; Mauricio Reyes; Michael A. Riegler; Manuel Wiesenfarth; Michael Baumgartner; 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; Sharib Ali; Anubha Gupta; Jan Kybic; et al. (CoRR, 2022)

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)

BIAS: Transparent reporting of biomedical image analysis challenges - Lena Maier-Hein; 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; et al. (Medical Image Anal., 2020)

Condensed U-Net (Cu-Net): An Improved U-Net Architecture for Cell Segmentation Powered by 4x4 Max-Pooling Layers - Cem Emre Akbas; Michal Kozubek (17th IEEE International Symposium on Biomedical Imaging, ISBI 2020, Iowa City, IA, USA, April 3-7, 2020, 2020)

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

BIAS: Transparent reporting of biomedical image analysis challenges - Lena Maier-Hein; 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; et al. (CoRR, 2019)

Automatic Fusion of Segmentation and Tracking Labels - Cem Emre Akbas; Vladimír Ulman; Martin Maska; Florian Jug; Michal Kozubek (Computer Vision - ECCV 2018 Workshops - Munich, Germany, September 8-14, 2018, Proceedings, Part VI, 2018)

How to Exploit Weaknesses in Biomedical Challenge Design and Organization - Annika Reinke; Matthias Eisenmann; Sinan Onogur; Marko Stankovic; Patrick Scholz; Peter M. Full; Hrvoje Bogunovic; Bennett A. Landman; Oskar Maier; Bjoern H. Menze; Gregory C. Sharp; Korsuk Sirinukunwattana; et al. (Medical Image Computing and Computer Assisted Intervention - MICCAI 2018 - 21st International Conference, Granada, Spain, September 16-20, 2018, Proceedings, Part IV, 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; Patrick Scholz; Tal Arbel; Hrvoje Bogunovic; Andrew P. Bradley; Aaron Carass; Carolin Feldmann; Alejandro F. Frangi; et al. (CoRR, 2018)

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

Multimodal Simulations in Live Cell Imaging - David Svoboda; Michal Kozubek (Simulation and Synthesis in Medical Imaging - Second International Workshop, SASHIMI 2017, Held in Conjunction with MICCAI 2017, Québec City, QC, Canada, September 10, 2017, Proceedings, 2017)

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

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; Carlos Ortiz-de-Solorzano (37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2015, Milan, Italy, August 25-29, 2015, 2015)

Quantification of the 3D collagen network geometry in confocal reflection microscopy - Martin Maska; Cristina Ederra; Javier Fernández-Marqués; Arrate Muñoz-Barrutia; Michal Kozubek; Carlos Ortiz-de-Solorzano (2015 IEEE International Conference on Image Processing, ICIP 2015, Quebec City, QC, Canada, September 27-30, 2015, 2015)

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; Deepak M. W. Balak; Pavel Karas; Tereza Bolcková; et al. (Bioinform., 2014)

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

Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science, MEMICS 2010, Selected Papers, October 22-24, 2010, Mikulov, Czech Republic - Ludek Matyska; Michal Kozubek; Tomás Vojnar; Pavel Zemcík; David Antos (Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, 2011)

A Fast Level Set-Like Algorithm for Region-Based Active Contours - Martin Maska; Pavel Matula; Ondrej Danek; Michal Kozubek (Advances in Visual Computing - 6th International Symposium, ISVC 2010, Las Vegas, NV, USA, November 29 - December 1, 2010, Proceedings, Part III, 2010)

Simultaneous Tracking of Multiple Objects Using Fast Level Set-Like Algorithm - Martin Maska; Pavel Matula; Michal Kozubek (Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science, MEMICS 2010, Selected Papers, October 22-24, 2010, Mikulov, Czech Republic, 2010)

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 (Proceedings of the 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Boston, MA, USA, June 28 - July 1, 2009, 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; Ignacio Fernández García (Image Analysis, 16th Scandinavian Conference, SCIA 2009, Oslo, Norway, June 15-18, 2009. Proceedings, 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 (Image Analysis, 16th Scandinavian Conference, SCIA 2009, Oslo, Norway, June 15-18, 2009. Proceedings, 2009)

A Comparison of Fast Level Set-Like Algorithms for Image Segmentation in Fluorescence Microscopy - Martin Maska; Jan Hubený; David Svoboda; Michal Kozubek (Advances in Visual Computing, Third International Symposium, ISVC 2007, Lake Tahoe, NV, USA, November 26-28, 2007, Proceedings, Part II, 2007)

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

High-Resolution Cytometry Network Project: Client/Server System for 3D Optical Microscope Data Storage and Analysis - Pavel Matula; Petr Matula; Michal Kozubek; Petr Mejzlík (2nd International Symposium on 3D Data Processing, Visualization and Transmission (3DPVT 2004), 6-9 September 2004, Thessaloniki, Greece, 2004)

Applications of Image Registration in Human Genome Research - Petr Matula; Michal Kozubek; Pavel Matula (Computer Vision and Mathematical Methods in Medical and Biomedical Image Analysis, ECCV 2004 Workshops CVAMIA and MMBIA, Prague, Czech Republic, May 15, 2004, Revised Selected Papers, 2004)

Fast Marching 3D Reconstruction of Interphase Chromosomes - Pavel Matula; Jan Hubený; Michal Kozubek (Computer Vision and Mathematical Methods in Medical and Biomedical Image Analysis, ECCV 2004 Workshops CVAMIA and MMBIA, Prague, Czech Republic, May 15, 2004, Revised Selected Papers, 2004)

Automated Confocal Microscopy: The Way of Achieving both Quality and Quantity in 3D Image Cytometry - Michal Kozubek; Petr Matula; Pavel Matula (Proceedings of the 2004 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Arlington, VA, USA, 15-18 April 2004, 2004)

Automated Multi-view 3D Image Acquisition in Human Genome Research - Michal Kozubek; Petr Matula; Heinz Eipel; Michael Hausmann (1st International Symposium on 3D Data Processing Visualization and Transmission (3DPVT 2002), 19-21 June 2002, Padova, Italy, 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; Petr Matula; Pavel Matula; Petr Mejzlík (1st International Symposium on 3D Data Processing Visualization and Transmission (3DPVT 2002), 19-21 June 2002, Padova, Italy, 2002)