On Simulating 3D Fluorescent Microscope Images. - David Svoboda; Marek Kasík; Martin Maska; Jan Hubený; Stanislav Stejskal; Michal Zimmermann (CAIP, 2007)

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)

A Fast Level Set-Like Algorithm with Topology Preserving Constraint. - Martin Maska; Pavel Matula (CAIP, 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 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)

A Simple Topology Preserving Max-Flow Algorithm for Graph Cut Based Image Segmentation. - Ondrej Danek; Martin Maska (MEMICS, 2010)

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

Fast tracking of fluorescent cells based on the Chan-Vese model. - Martin Maska; Arrate Muñoz-Barrutia; Carlos Ortiz-de-Solorzano (ISBI, 2012)

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

Automatic quantification of filopodia-based cell migration. - Martin Maska; Xabier Morales; Arrate Muñoz-Barrutia; Ana Rouzaut; Carlos Ortiz-de-Solorzano (ISBI, 2013)

Segmentation and Shape Tracking of Whole Fluorescent Cells Based on the Chan-Vese Model. - Martin Maska; Ondrej Danek; Saray Garasa; Ana Rouzaut; Arrate Muñoz-Barrutia; Carlos Ortiz-de-Solorzano (IEEE Trans. Medical Imaging, 2013)

On proper simulation of phenomena influencing image formation in fluorescence microscopy. - David Svoboda; Vladimír Ulman; Ludek Matyska; Martin Maska; Jan Bella; Stanislav Stejskal (ICIP, 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 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)

Automatic Detection and Segmentation of Exosomes in Transmission Electron Microscopy. - Karel Stepka; Martin Maska; Jakub Jozef Pálenik; Vendula Pospíchalová; Anna Kotrbová; Ladislav Ilkovics; Dobromila Klemová; Ales Hampl; Vítezslav Bryja; Pavel Matula (ECCV Workshops (1), 2016)

Particle Tracking Accuracy Measurement Based on Comparison of Linear Oriented Forests. - Martin Maska; Pavel Matula (ICCV Workshops, 2017)

Model-based generation of synthetic 3D time-lapse sequences of motile cells with growing filopodia. - Dmitry V. Sorokin; Igor Peterlík; Vladimír Ulman; David Svoboda; Martin Maska (ISBI, 2017)

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

Segmentation of actin-stained 3D fluorescent cells with filopodial protrusions using convolutional neural networks. - Carlos Castilla; Martin Maska; Dmitry V. Sorokin; Erik Meijering; Carlos Ortiz-de-Solorzano (ISBI, 2018)

Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Multiple Mutually Interacting Motile Cells with Filopodia. - Igor Peterlík; David Svoboda; Vladimír Ulman; Dmitry V. Sorokin; Martin Maska (SASHIMI@MICCAI, 2018)

FiloGen: A Model-Based Generator of Synthetic 3-D Time-Lapse Sequences of Single Motile Cells With Growing and Branching Filopodia. - Dmitry V. Sorokin; Igor Peterlík; Vladimír Ulman; David Svoboda; Tereza Necasová; Katsiarina Morgaenko; Lívia Eiselleová; Lenka Tesarová; Martin Maska (IEEE Trans. Medical Imaging, 2018)

Toward Robust Fully 3D Filopodium Segmentation and Tracking in Time-Lapse Fluorescence Microscopy. - Martin Maska; Tereza Necasová; David Wiesner; Dmitry V. Sorokin; Igor Peterlík; Vladimír Ulman; David Svoboda (ICIP, 2019)

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

3-D Quantification of Filopodia in Motile Cancer Cells. - Carlos Castilla; Martin Maska; Dmitry V. Sorokin; Erik Meijering; Carlos Ortiz-de-Solorzano (IEEE Trans. Medical Imaging, 2019)

BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows. - Ulysse Rubens; Romain Mormont; Lassi Paavolainen; Volker Bäcker; Benjamin Pavie; Leandro A. Scholz; Gino Michiels; Martin Maska; Devrim Ünay; Graeme Ball; Renaud Hoyoux; Rémy Vandaele; et al. (Patterns, 2020)

Datasets used in "3-D quantification of filopodia in motile cancer cells" IEEE Transactions on Medical Imaging 38(3), 862-872 (2019). - Carlos Castilla; Martin Maska; Dmitry V. Sorokin; Erik Meijering; Carlos Ortiz-de-Solorzano (IEEE DataPort, 2022)

Segmentation and Tracking of Mammary Epithelial Organoids in Brightfield Microscopy. - Lucia Hradecká; David Wiesner; Jakub Sumbal; Zuzana Sumbalova Koledova; Martin Maska (IEEE Trans. Medical Imaging, 2023)

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)