doc. RNDr. Martin Maška, Ph.D.

Curriculum Vitae

Basic Personal Data

• Martin Maška
  born on March 17, 1983 in Brno, Czech Republic
  

Workplace

• Centre for Biomedical Image Analysis
  Department of Visual Computing
  Faculty of Informatics, Masaryk University
  Botanická 68a, 602 00 Brno, Czech Republic

Current Position

• Associate Professor (6/2021 - present):
  - the co-principal investigator of a mid-term project "ERK Signaling Code of Epithelial Morphogenesis and Cancer", Grant Agency of Masaryk University, 4/2021–12/2023
  - a team member in a mid-term project "Segmentation and Tracking of Cells with Complex Shapes", Czech Science Foundation, 1/2021 - 12/2023
  - a team member of a mid-term project "National Research Infrastructure for Biological and Medical Imaging", Ministry of Education of the Czech Republic, 1/2020 - 12/2022
  - the co-principal investigator of a mid-term project "Deciphering the Mechanisms of Mammary Epithelial Branched Pattern Formation Through Iterative Biological and Mathematical Modelling", Grant Agency of Masaryk University, 3/2019–12/2021

Education and Academic Qualifications

• 2021: Associate Professor, Informatics, Masaryk University, Thesis: "Object Tracking in Bioimage Data"
• 2011: Ph.D., Informatics, Masaryk University, Thesis: "Fast Level Set-Like Algorithms in Fluorescence Microscopy"
• 2009: RNDr., Informatics, Masaryk University, Thesis: "Fast Approximations of Implicit Active Contours in Fluorescence Microscopy"
• 2006: M.S., Informatics, Masaryk University, Thesis: "Image Segmentation Using Fast Approximation of Implicit Active Surfaces" (in Czech)

Professional Experience

• Scientific Researcher (7/2015 - 5/2021):
  - Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University
  - a team member of a mid-term project "Benchmarking of Algorithms for Cell Segmentation and Tracking", Ministry of Education of the Czech Republic, 6/2017 - 4/2020
  - a team member of a mid-term project "Multi-modal Live Cell Image Segmentation and Tracking", Czech Science Foundation, 1/2017 - 12/2019
  - the principal investigator of a mid-term project "Development of Reliable Methods for Automated Quantitative Characterization of Cell Motility in Fluorescence Microscopy", Czech Science Foundation, 1/2016 - 12/2018
  - a team member of a long-term project "Dynamics and Organization of Chromosomes in the Cell Cycle and during Differentiation under Normal and Pathological Conditions", Czech Science Foundation, 1/2012 - 12/2018
• Postdoctoral Research Fellow (1/2013 - 6/2015):
  - Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University
  - a team member of a mid-term project "Employment of Newly Graduated Doctors of Science for Scientific Excellence", Ministry of Education of the Czech Republic, 7/2012 - 6/2015
• Postdoctoral Research Fellow (7/2011 - 12/2012):
  - Cancer Imaging Laboratory, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
  - a team member of a mid-term project "Characterization of Cellular Migratory Patterns Using 4D Imaging", Spanish Science and Innovation Ministry, 1/2010 - 12/2012
• Research and Development worker (2/2011 - 6/2011):
  - Cancer Imaging Laboratory, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
  - a team member of a mid-term project "Characterization of Cellular Migratory Patterns Using 4D Imaging", Spanish Science and Innovation Ministry, 1/2010 - 12/2012
• Research and Development worker (7/2006 - 12/2010):
  - Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University
  - a team member of a long-term project "Marker Determination, Screening and Early Diagnostics of Cancer Diseases Using Highly Automated Processing of Multidimensional Biomedical Images", Ministry of Education of the Czech Republic, 7/2006 - 6/2011

Pedagogical Activities

• 2023-present: Digital Geometry
• 2018-2022: Introduction to PhD Study
• 2017-2021: Seminar on Foundations of Programming
• 2016-present: Seminar on Mathematical Foundations of Computer Science
• 2016-2017: Domain Specific Development in C/C++
• 2014-present: Seminar on Introduction to Digital Image Processing
• 2013-present: Seminar on Digital Image Processing
• 2013-present: Image Processing Project
• 2013-present: Seminar on Advanced Methods of Digital Image Processing
• 2013-present: Advisor of master theses
• 2011-present: Advisor of bachelor theses
• 2007: Seminar on Design of Algorithms I

Scientific and Research Activities

• Optical microscopy image analysis:
  - image segmentation, object tracking, implicit active contours, PDE-based methods
• Benchmarking of bioimage analysis workflows:
  - Cell Tracking Challenge
  - Particle Tracking Challenge
• Scientometric data and peer-reviewing

Academical Stays

• 2017: Center for Applied Medical Research, University of Navarra, Pamplona, Spain (1 month, short-term research stay)
• 2014: Center for Applied Medical Research, University of Navarra, Pamplona, Spain (3 months, short-term research stay)
• 2011-2012: Center for Applied Medical Research, University of Navarra, Pamplona, Spain (18 months, postdoctoral research stay)
• 2010: Center for Applied Medical Research, University of Navarra, Pamplona, Spain (3 months, Erasmus)
• 2009: Image Acquisition and Analysis in Microscopy, Academy of Sciences of the Czech Republic, Prague, Czech Republic (1 week)
• 2008: 16th Summer School on Image Processing, Vienna University of Technology, Vienna, Austria (2 weeks)
• 2008: Center for Applied Medical Research, University of Navarra, Pamplona, Spain (4 months, Erasmus)
• 2007: Special Semester on Quantitative Biology analyzed by Mathematical Methods, Workshop on Bioimaging II / PDEs, Johann Radon Institute for Computational and Applied Mathematics, Linz, Austria (1 week)

Elected Membership in Scientific Societies and Editorial Boards

• 2021-present: Associate Editor of IEEE Transactions on Medical Imaging
• 2020-present: Associate Editor of BMC Bioinformatics
• 2017-2022: Bio Imaging and Signal Processing Technical Committee

Scientific Awards

• 2016: Masaryk University Rector’s Award for Outstanding Research Results Achieved by Young Scientists under 35

Selected Publications

• HRADECKÁ, Lucia, David WIESNER, Jakub SUMBAL, Zuzana SUMBALOVÁ KOLEDOVÁ a Martin MAŠKA. Segmentation and Tracking of Mammary Epithelial Organoids in Brightfield Microscopy. IEEE Transactions on Medical Imaging. 2023, roč. 42, č. 1, s. 281-290. ISSN 0278-0062. Dostupné z: https://dx.doi.org/10.1109/TMI.2022.3210714. 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://dx.doi.org/10.1038/s41592-023-01879-y. URL info
• RUBENS, Ulysse, Romain MORMONT, Lassi PAAVOLAINEN, Volker BÄCKER, Benjamin PAVIE, Leandro A. SCHOLZ, Gino MICHIELS, Martin MAŠKA, Devrim ÜNAY, Graeme BALL, Renaud HOYOUX, Rémy VANDAELE, Ofra GOLANI, Stefan G. STANCIU, Natasa SLADOJE, Perrine PAUL-GILLOTEAUX, Raphaël MARÉE a Sébastien TOSI. BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows. Patterns. Cell Press, 2020, roč. 1, č. 3, s. 1-10. ISSN 2666-3899. Dostupné z: https://dx.doi.org/10.1016/j.patter.2020.100040. URL info
• CASTILLA, Carlos, Martin MAŠKA, Dmitry SOROKIN, Erik MEIJERING a Carlos ORTIZ-DE-SOLÓRZANO. 3-D Quantification of Filopodia in Motile Cancer Cells. IEEE Transactions on Medical Imaging. IEEE, 2019, roč. 38, č. 3, s. 862-872. ISSN 0278-0062. Dostupné z: https://dx.doi.org/10.1109/TMI.2018.2873842. URL info
• MAŠKA, Martin, Tereza NEČASOVÁ, David WIESNER, Dmitry SOROKIN, Igor PETERLÍK, Vladimír ULMAN a David SVOBODA. Toward Robust Fully 3D Filopodium Segmentation and Tracking in Time-Lapse Fluorescence Microscopy. Online. In 26th IEEE International Conference on Image Processing. Taipei: IEEE, 2019, s. 819-823. ISBN 978-1-5386-6249-6. Dostupné z: https://dx.doi.org/10.1109/ICIP.2019.8803721. URL info
• WIESNER, David, David SVOBODA, Martin MAŠKA a Michal KOZUBEK. CytoPacq: A web-interface for simulating multi-dimensional cell imaging. Bioinformatics. Oxford University Press, 2019, roč. 35, č. 21, s. 4531-4533. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btz417. URL info
• KOTRBOVÁ, Anna, Karel ŠTĚPKA, Martin MAŠKA, Juraj PÁLENIK, Ladislav ILKOVICS, Dobromila KLEMOVÁ, Marek KRAVEC, František HUBATKA, Zankruti DAVE, Aleš HAMPL, Vítězslav BRYJA, Pavel MATULA a Vendula POSPÍCHALOVÁ. TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images. Journal of Extracellular Vesicles. Taylor and Francis Ltd., 2019, roč. 8, č. 1, s. 1-13. ISSN 2001-3078. Dostupné z: https://dx.doi.org/10.1080/20013078.2018.1560808. Full Text info
• GÓMEZ-DE-MARISCAL, Estibaliz, Martin MAŠKA, Anna KOTRBOVÁ, Vendula POSPÍCHALOVÁ, Pavel MATULA a Arrate MUÑOZ-BARRUTIA. Deep-Learning-Based Segmentation of Small Extracellular Vesicles in Transmission Electron Microscopy Images. Scientific Reports. 2019, roč. 9, č. 13211, s. 1-10. ISSN 2045-2322. Dostupné z: https://dx.doi.org/10.1038/s41598-019-49431-3. URL info
• CASTILLA, Carlos, Martin MAŠKA, Dmitry SOROKIN, Erik MEIJERING a Carlos ORTIZ-DE-SOLORZANO. Segmentation of Actin-Stained 3D Fluorescent Cells with Filopodial Protrusions using Convolutional Neural Networks. Online. In 15th IEEE International Symposium on Biomedical Imaging. Washington: IEEE, 2018, s. 413-417. ISBN 978-1-5386-3636-7. Dostupné z: https://dx.doi.org/10.1109/ISBI.2018.8363605. URL info
• SOROKIN, Dmitry, Igor PETERLÍK, Vladimír ULMAN, David SVOBODA, Tereza NEČASOVÁ, Katsiarina MORGAENKO, Lívia EISELLEOVÁ, Lenka TESAŘOVÁ a Martin MAŠKA. FiloGen: A Model-Based Generator of Synthetic 3-D Time-Lapse Sequences of Single Motile Cells with Growing and Branching Filopodia. IEEE Transactions on Medical Imaging. IEEE, 2018, roč. 37, č. 12, s. 2630-2641. ISSN 0278-0062. Dostupné z: https://dx.doi.org/10.1109/TMI.2018.2845884. URL info
• PETERLÍK, Igor, David SVOBODA, Vladimír ULMAN, Dmitry SOROKIN a Martin MAŠKA. Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Multiple Mutually Interacting Motile Cells with Filopodia. Online. In Simulation and Synthesis in Medical Imaging. Cham: Springer, 2018, s. 71-79. ISBN 978-3-030-00535-1. Dostupné z: https://dx.doi.org/10.1007/978-3-030-00536-8_8. URL info
• ANGUIANO, María, Carlos CASTILLA, Martin MAŠKA, Cristina EDERRA, Rafael PELÁEZ, Xabier MORALES, Gorka MUÑOZ-ARRIETA, Maite MUJIKA, Michal KOZUBEK, Arrate MUÑOZ-BARRUTIA, Ana ROUZAUT, Sergio ARANA, José Manuel GARCIA-AZNAR a Carlos ORTIZ-DE-SOLORZANO. Characterization of three-dimensional cancer cell migration in mixed collagen-Matrigel scaffolds using microfluidics and image analysis. PLoS ONE. 2017, roč. 12, č. 2, s. 1-24. ISSN 1932-6203. Dostupné z: https://dx.doi.org/10.1371/journal.pone.0171417. URL info
• SOROKIN, Dmitry, Igor PETERLÍK, Vladimír ULMAN, David SVOBODA a Martin MAŠKA. Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Motile Cells with Growing Filopodia. Online. In 14th IEEE International Symposium on Biomedical Imaging. Melbourne: IEEE, 2017, s. 822-826. ISBN 978-1-5090-1172-8. Dostupné z: https://dx.doi.org/10.1109/ISBI.2017.7950644. URL info
• MAŠKA, Martin a Pavel MATULA. Particle Tracking Accuracy Measurement Based on Comparison of Linear Oriented Forests. Online. In 16th IEEE International Conference on Computer Vision Workshops. Venice: IEEE, 2017, s. 11-17. ISBN 978-1-5386-1034-3. Dostupné z: https://dx.doi.org/10.1109/ICCVW.2017.8. 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://dx.doi.org/10.1038/nmeth.4473. URL info
• ŠTĚPKA, Karel, Martin MAŠKA, Jakub Jozef PÁLENIK, Vendula POSPÍCHALOVÁ, Anna KOTRBOVÁ, Ladislav ILKOVICS, Dobromila KLEMOVÁ, Aleš HAMPL, Vítězslav BRYJA a Pavel MATULA. Automatic Detection and Segmentation of Exosomes in Transmission Electron Microscopy. In Gang Hua, Hervé Jégou. Computer Vision -- ECCV 2016 Workshops: Amsterdam, The Netherlands, October 8-10 and 15-16, 2016, Proceedings, Part I. Cham, Switzerland: Springer International Publishing, 2016, s. 318-325. ISBN 978-3-319-46603-3. Dostupné z: https://dx.doi.org/10.1007/978-3-319-46604-0_23. http://dx.doi.org/10.1007/978-3-319-46604-0_23 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://dx.doi.org/10.1371/journal.pone.0144959. URL info
• MAŠKA, Martin, Cristina EDERRA, Javier FERNÁNDEZ-MARQUÉS, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK a Carlos ORTIZ-DE-SOLÓRZANO. Quantification of the 3D Collagen Network Geometry in Confocal Reflection Microscopy. Online. In 22nd IEEE International Conference on Image Processing. Québec City: IEEE, 2015, s. 1791-1794. ISBN 978-1-4799-8339-1. Dostupné z: https://dx.doi.org/10.1109/ICIP.2015.7351109. URL info
• ANGUIANO, María, Carlos CASTILLA, Martin MAŠKA, Cristina EDERRA, Javier FERNÁNDEZ-MARQUÉS, Rafael PELÁEZ, Ana ROUZAUT, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK a Carlos ORTIZ-DE-SOLÓRZANO. Characterization of the Role of Collagen Network Structure and Composition in Cancer Cell Migration. Online. In 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. Milano: IEEE, 2015, s. 8139-8142. ISBN 978-1-4244-9271-8. Dostupné z: https://dx.doi.org/10.1109/EMBC.2015.7320283. URL 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://dx.doi.org/10.1093/bioinformatics/btu080. URL info
• CHENOUARD, Nicolas, Ihor SMAL, Fabrice DE CHAUMONT, Martin MAŠKA, Ivo F SBALZARINI, Yuanhao GONG, Janick CARDINALE, Craig CARTHEL, Stefano CORALUPPI, Mark WINTER, Andrew R COHEN, William J GODINEZ, Karl ROHR, Yannis KALAIDZIDIS, Liang LIANG, James DUNCAN, Hongying SHEN, Yingke XU, Klas E G MAGNUSSON, Joakim JALDÉN, Helen M BLAU, Perrine PAUL-GILLOTEAUX, Philippe ROUDOT, Charles KERVRANN, François WAHARTE, Jean-Yves TINEVEZ, Spencer L SHORTE, Joost WILLEMSE, Katherine CELLER, Gilles P VAN WEZEL, Han-Wei DAN, Yuh-Show TSAI, Carlos ORTIZ-DE-SOLÓRZANO, Jean-Christophe OLIVO-MARIN a Erik MEIJERING. Objective Comparison of Particle Tracking Methods. Nature Methods. 2014, roč. 11, č. 3, s. 281-289. ISSN 1548-7091. Dostupné z: https://dx.doi.org/10.1038/nmeth.2808. URL info
• SVOBODA, David, Vladimír ULMAN, Luděk MATYSKA, Martin MAŠKA, Ján BELLA a Stanislav STEJSKAL. On Proper Simulation of Phenomena Influencing Image Formation in Fluorescence Microscopy. In 2014 IEEE International Conference on Image Processing. Neuveden: IEEE Signal Processing Society, 2014, s. 3944-3948. ISBN 978-1-4799-5750-7. Dostupné z: https://dx.doi.org/10.1109/ICIP.2014.7025801. URL info
• MAŠKA, Martin, Ondřej DANĚK, Saray GARASA, Ana ROUZAUT, Arrate MUÑOZ-BARRUTIA a Carlos ORTIZ-DE-SOLÓRZANO. Segmentation and Shape Tracking of Whole Fluorescent Cells Based on the Chan-Vese Model. IEEE Transactions on Medical Imaging. 2013, roč. 32, č. 6, s. 995-1006. ISSN 0278-0062. Dostupné z: https://dx.doi.org/10.1109/TMI.2013.2243463. URL info
• MAŠKA, Martin, Xabier MORALES, Arrate MUÑOZ-BARRUTIA, Ana ROUZAUT a Carlos ORTIZ-DE-SOLÓRZANO. Automatic Quantification of Filopodia-Based Cell Migration. Online. In 10th IEEE International Symposium on Biomedical Imaging. San Francisco: IEEE, 2013, s. 668-671. ISBN 978-1-4673-6454-6. Dostupné z: https://dx.doi.org/10.1109/ISBI.2013.6556563. 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://dx.doi.org/10.1016/j.patrec.2012.03.013. URL info
• MAŠKA, Martin, Arrate MUÑOZ-BARRUTIA a Carlos ORTIZ-DE-SOLÓRZANO. Fast Tracking of Fluorescent Cells Based on the Chan-Vese Model. Online. In 9th IEEE International Symposium on Biomedical Imaging. Barcelona: IEEE, 2012, s. 1316–1319. ISBN 978-1-4577-1857-1. URL info
• DANĚK, Ondřej a Martin MAŠKA. A Simple Topology Preserving Max-Flow Algorithm for Graph Cut Based Image Segmentation. Online. In Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (Selected Papers). Saarbrücken, Warden: Schloss Dagstuhl Publishing, 2011, s. 19-25. ISBN 978-3-939897-22-4. URL info
• MAŠKA, Martin, Pavel MATULA a Michal KOZUBEK. Simultaneous Tracking of Multiple Objects Using Fast Level Set-Like Algorithm. Online. In Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (Selected Papers). Saarbrücken, Wadern: Schloss Dagstuhl Publishing, 2011, s. 69-76. ISBN 978-3-939897-22-4. URL info
• MAŠKA, Martin, Pavel MATULA, Ondřej DANĚK a Michal KOZUBEK. A Fast Level Set-Like Algorithm for Region-Based Active Contours. Online. In 6th International Symposium on Visual Computing. Berlin, Heidelberg: Springer-Verlag, 2010, s. 387-396. ISBN 978-3-642-17276-2. Dostupné z: https://dx.doi.org/10.1007/978-3-642-17277-9_40. URL info
• STEJSKAL, Stanislav, Irena KRONTORÁD KOUTNÁ, Pavel MATULA, Zdeněk RUČKA, Ondřej DANĚK, Martin MAŠKA a Michal KOZUBEK. The role of chromatin condensation during granulopoiesis in the regulation of gene cluster expression. Epigenetics. USA: Landes Bioscience, 2010, roč. 5, č. 8, s. 759-767. ISSN 1559-2294. Dostupné z: https://dx.doi.org/10.4161/epi.5.8.13183. URL info
• MAŠKA, Martin, Pavel MATULA a Michal KOZUBEK. Simultaneous Tracking of Multiple Objects Using Fast Level Set-Like Algorithm. In 6th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno: NOVPRESS, 2010, s. 117-125. ISBN 978-80-87342-10-7. info
• DANĚK, Ondřej a Martin MAŠKA. A Simple Topology Preserving Max-Flow Algorithm for Graph Cut Based Image Segmentation. In 6th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno: NOVPRESS, 2010, s. 45-52. ISBN 978-80-87342-10-7. info
• MAŠKA, Martin a Pavel MATULA. A Fast Level Set-Like Algorithm with Topology Preserving Constraint. Online. In 13th International Conference on Computer Analysis of Images and Patterns. Berlin, Heidelberg: Springer-Verlag, 2009, s. 930-938. ISBN 978-3-642-03766-5. Dostupné z: https://dx.doi.org/10.1007/978-3-642-03767-2_113. URL info
• DANĚK, Ondřej, Pavel MATULA, Carlos ORTIZ-DE-SOLÓRZANO, Arrate MUÑOZ-BARRUTIA, Martin MAŠKA a Michal KOZUBEK. Segmentation of Touching Cell Nuclei using a Two-Stage Graph Cut Model. In 16th Scandinavian Conference on Image Analysis. Berlin, Heidelberg: Springer-Verlag, 2009, s. 410-419. ISBN 978-3-642-02229-6. Dostupné z: https://dx.doi.org/10.1007/978-3-642-02230-2_42. URL info
• MAŠKA, Martin, Ondřej DANĚK, Carlos ORTIZ-DE-SOLÓRZANO, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK a Ignacio FERNÁNDEZ GARCÍA. A Two-Phase Segmentation of Cell Nuclei Using Fast Level Set-Like Algorithms. Online. In 16th Scandinavian Conference on Image Analysis. Berlin, Heidelberg: Springer-Verlag, 2009, s. 390-399. ISBN 978-3-642-02229-6. Dostupné z: https://dx.doi.org/10.1007/978-3-642-02230-2_40. URL 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
• SVOBODA, David, Marek KAŠÍK, Martin MAŠKA, Jan HUBENÝ, Stanislav STEJSKAL a Michal ZIMMERMANN. On Simulating 3D Fluorescent Microscope Images. In Computer Analysis of Images and Patterns. Berlin, Heidelberg: Springer-Verlag, 2007, s. 309-316. ISBN 978-3-540-74271-5. URL info
• MAŠKA, Martin, Jan HUBENÝ, David SVOBODA a Michal KOZUBEK. A Comparison of Fast Level Set-Like Algorithms for Image Segmentation in Fluorescence Microscopy. Online. In 3rd International Symposium on Visual Computing. Berlin, Heidelberg: Spinger-Verlag, 2007, s. 571-581. ISBN 978-3-540-76855-5. URL info

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