Michal Kozubek

According to our database, Michal Kozubek authored at least 35 papers between 2002 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

Gravitational cell detection and tracking in fluorescence microscopy data.

Nikomidisz Eftimiu, Michal Kozubek

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

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, Sophia Bano, Jorge Bernal, Sebastian Bodenstedt, Alessandro Casella, Veronika Cheplygina, Marie Daum, Marleen de Bruijne, Adrien Depeursinge, Reuben Dorent, Jan Egger, David G. Ellis, Sandy Engelhardt, Melanie Ganz, Noha M. Ghatwary, Gabriel Girard, Patrick Godau, Anubha Gupta, Lasse Hansen, Kanako Harada, Mattias P. Heinrich, Nicholas Heller, Alessa Hering, Arnaud Huaulmé, Pierre Jannin, Ali Emre Kavur, Oldrich Kodym, Michal Kozubek, Jianning Li, Hongwei Bran Li, Jun Ma, Carlos Martín-Isla, Bjoern H. Menze, J. Alison Noble, Valentin Oreiller, Nicolas Padoy, Sarthak Pati, Kelly Payette, Tim Rädsch, et al.

CoRR, 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, Arriel Benis, Matthew B. Blaschko, Florian Büttner, M. Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A. Cimini, Gary S. Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Robert Haase, Daniel A. Hashimoto, Michael M. Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Hannes Kenngott, Jens Kleesiek, Florian Kofler, Thijs Kooi, Annette Kopp-Schneider, Michal Kozubek, Anna Kreshuk, Tahsin M. Kurç, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus H. Maier-Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern H. Menze, Karel G. M. Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M. Rafelski, Nasir M. Rajpoot, Mauricio Reyes, Michael A. Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I. Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M. Summers, Abdel A. Taha, Aleksei Tiulpin, Sotirios A. Tsaftaris, Ben Van Calster, Gaël Varoquaux, Manuel Wiesenfarth, Ziv R. Yaniv, Paul F. Jäger, Lena Maier-Hein

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, Sophia Bano, Jorge Bernal, Sebastian Bodenstedt, Alessandro Casella, Veronika Cheplygina, Marie Daum, Marleen de Bruijne, Adrien Depeursinge, Reuben Dorent, Jan Egger, David G. Ellis, Sandy Engelhardt, Melanie Ganz, Noha M. Ghatwary, Gabriel Girard, Patrick Godau, Anubha Gupta, Lasse Hansen, Kanako Harada, Mattias P. Heinrich, Nicholas Heller, Alessa Hering, Arnaud Huaulmé, Pierre Jannin, A. Emre Kavur, Oldrich Kodym, Michal Kozubek, Jianning Li, Hongwei Bran Li, Jun Ma, Carlos Martín-Isla, Bjoern H. Menze, J. Alison Noble, Valentin Oreiller, Nicolas Padoy, Sarthak Pati, Kelly Payette, Tim Rädsch, Jonathan Rafael-Patino, Vivek Singh Bawa, Stefanie Speidel, Carole H. Sudre, Kimberlin M. H. van Wijnen, Martin Wagner, D. Wei, Amine Yamlahi, Moi Hoon Yap, C. Yuan, Maximilian Zenk, A. Zia, David Zimmerer, Dogu Baran Aydogan, Binod Bhattarai, Louise Bloch, Raphael Brüngel, J. Cho, C. Choi, Q. Dou, Ivan Ezhov, Christoph M. Friedrich, C. Fuller, Rebati Raman Gaire, Adrian Galdran, Álvaro García-Faura, Maria Grammatikopoulou, S. Hong, Mostafa Jahanifar, I. Jang, Abdolrahim Kadkhodamohammadi, I. Kang, Florian Kofler, S. Kondo, Hugo Jaco Kuijf, M. Li, M. Luu, Tomaz Martincic, Pedro Morais, Mohamed A. Naser, Bruno Oliveira, David Owen, S. Pang, J. Park, S. Park, Szymon Plotka, Élodie Puybareau, Nasir M. Rajpoot, K. Ryu, Numan Saeed, Adam Shephard, Pengcheng Shi, Dejan Stepec, Ronast Subedi, Guillaume Tochon, Helena R. Torres, Hélène Urien, João L. Vilaça, Kareem A. Wahid, H. Wang, J. Wang, L. Wang, X. Wang, Benedikt Wiestler, Marek Wodzinski, F. Xia, J. Xie, Z. Xiong, S. Yang, Y. Yang, Z. Zhao, Klaus H. Maier-Hein, Paul F. Jäger, Annette Kopp-Schneider, Lena Maier-Hein

Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2023

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, J. Alison Noble, Carlos Ortiz-de-Solórzano, Samiksha Pachade, Caroline Petitjean, Daniel Sage, Donglai Wei, Elizabeth Wilden, Deepak Alapatt, Vincent Andrearczyk, Ujjwal Baid, Spyridon Bakas, Niranjan Balu, Sophia Bano, Vivek Singh Bawa, Jorge Bernal, Sebastian Bodenstedt, Alessandro Casella, Jinwook Choi, Olivier Commowick, Marie Daum, Adrien Depeursinge, Reuben Dorent, Jan Egger, Hannah Eichhorn, Sandy Engelhardt, Melanie Ganz, Gabriel Girard, Lasse Hansen, Mattias P. Heinrich, Nicholas Heller, Alessa Hering, Arnaud Huaulmé, Hyunjeong Kim, Bennett A. Landman, Hongwei Bran Li, Jianning Li, Jun Ma, Anne L. Martel, et al.

CoRR, 2022

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, Matthias Eisenmann, Doreen Heckmann-Nötzel, A. Emre Kavur, Tim Rädsch, Minu Dietlinde Tizabi, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Peter Bankhead, Arriel Benis, M. Jorge Cardoso, Veronika Cheplygina, Beth A. Cimini, Gary S. Collins, Keyvan Farahani, Bram van Ginneken, Daniel A. Hashimoto, Michael M. Hoffman, Merel Huisman, Pierre Jannin, Charles E. Kahn, Alexandros Karargyris, Alan Karthikesalingam, Hannes Kenngott, Annette Kopp-Schneider, Anna Kreshuk, Tahsin M. Kurç, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus H. Maier-Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern H. Menze, David Moher, Karel G. M. Moons, Henning Müller, Felix Nickel, Brennan Nichyporuk, Jens Petersen, Nasir M. Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clarisa Sánchez Gutiérrez, Shravya Shetty, Maarten van Smeden, Carole H. Sudre, Ronald M. Summers, Abdel A. Taha, Sotirios A. Tsaftaris, Ben Van Calster, Gaël Varoquaux, Paul F. Jäger

CoRR, 2022

2021

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, Doreen Heckmann-Nötzel, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Jens Kleesiek, Tahsin M. Kurç, Michal Kozubek, Bennett A. Landman, Geert Litjens, Klaus H. Maier-Hein, Bjoern H. Menze, Henning Müller, Jens Petersen, Mauricio Reyes, Nicola Rieke, Bram Stieltjes, Ronald M. Summers, Sotirios A. Tsaftaris, Bram van Ginneken, Annette Kopp-Schneider, Paul Jäger, Lena Maier-Hein

CoRR, 2021

2020

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, Annette Kopp-Schneider, Bennett A. Landman

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

Proceedings of the 17th IEEE International Symposium on Biomedical Imaging, 2020

2019

CytoPacq: a web-interface for simulating multi-dimensional cell imaging.

David Wiesner, David Svoboda, Martin Maska, Michal Kozubek

Bioinform., 2019

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, Peter M. Full, Bram van Ginneken, Allan Hanbury, Katrin Honauer, Michal Kozubek, Bennett A. Landman, Keno März, Oskar Maier, Klaus H. Maier-Hein, Bjoern H. Menze, Henning Müller, Peter F. Neher, Wiro J. Niessen, Nasir M. Rajpoot, Gregory C. 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, Annette Kopp-Schneider

CoRR, 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, Stefanie Speidel, Fons van der Sommen, Guoyan Zheng, Henning Müller, Michal Kozubek, Tal Arbel, Andrew P. Bradley, Pierre Jannin, Annette Kopp-Schneider, Lena Maier-Hein

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2018, 2018

Automatic Fusion of Segmentation and Tracking Labels.

Cem Emre Akbas, Vladimír Ulman, Martin Maska, Florian Jug, Michal Kozubek

Proceedings of the Computer Vision - ECCV 2018 Workshops, 2018

2017

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

Proceedings of the Simulation and Synthesis in Medical Imaging, 2017

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

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

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

Proceedings of the 2015 IEEE International Conference on Image Processing, 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

Proceedings of the 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2015

2014

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, Markéta Streitová, Craig Carthel, Stefano Coraluppi, Nathalie Harder, Karl Rohr, Klas E. G. Magnusson, Joakim Jaldén, Helen M. Blau, Oleh Dzyubachyk, Pavel Krízek, Guy M. Hagen, David Pastor-Escuredo, Daniel Jimenez-Carretero, María J. Ledesma-Carbayo, Arrate Muñoz-Barrutia, Erik Meijering, Michal Kozubek, Carlos Ortiz-de-Solorzano

Bioinform., 2014

2012

Smooth Chan-Vese segmentation via graph cuts.

Ondrej Danek, Pavel Matula, Martin Maska, Michal Kozubek

Pattern Recognit. Lett., 2012

2010

Simultaneous Tracking of Multiple Objects Using Fast Level Set-Like Algorithm.

Martin Maska, Pavel Matula, Michal Kozubek

Proceedings of the Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science, 2010

A Fast Level Set-Like Algorithm for Region-Based Active Contours.

Martin Maska, Pavel Matula, Ondrej Danek, Michal Kozubek

Proceedings of the Advances in Visual Computing - 6th International Symposium, 2010

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

Proceedings of the Image Analysis, 16th Scandinavian Conference, 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

Proceedings of the Image Analysis, 16th Scandinavian Conference, 2009

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, 2009

2007

A Comparison of Fast Level Set-Like Algorithms for Image Segmentation in Fluorescence Microscopy.

Martin Maska, Jan Hubený, David Svoboda, Michal Kozubek

Proceedings of the Advances in Visual Computing, Third International Symposium, 2007

2006

Fast point-based 3-D alignment of live cells.

Petr Matula, Michal Kozubek, Vladimír Dvorák

IEEE Trans. Image Process., 2006

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, 2004

Applications of Image Registration in Human Genome Research.

Petr Matula, Michal Kozubek, Pavel Matula

Proceedings of the Computer Vision and Mathematical Methods in Medical and Biomedical Image Analysis, 2004

Fast Marching 3D Reconstruction of Interphase Chromosomes.

Pavel Matula, Jan Hubený, Michal Kozubek

Proceedings of the Computer Vision and Mathematical Methods in Medical and Biomedical Image Analysis, 2004

High-Resolution Cytometry Network Project: Client/Server System for 3D Optical Microscope Data Storage and Analysis.

Pavel Matula, Petr Matula, Michal Kozubek, Petr Mejzlík

Proceedings of the 2nd International Symposium on 3D Data Processing, 2004

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

Proceedings of the 1st International Symposium on 3D Data Processing Visualization and Transmission (3DPVT 2002), 2002

Automated Multi-view 3D Image Acquisition in Human Genome Research.

Michal Kozubek, Petr Matula, Heinz Eipel, Michael Hausmann

Proceedings of the 1st International Symposium on 3D Data Processing Visualization and Transmission (3DPVT 2002), 2002