RNDr. Martin Maška, Ph.D.


Office: A312
Botanická 554/68a
602 00 Brno

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Phone: +420 549 49 5774
E‑mail:
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Curriculum Vitae

Basic Personal Data
  • Martin Maška
    born on March 17, 1983 in Brno, Czech Republic
Workplace
  • Centre for Biomedical Image Analysis
    Faculty of Informatics, Masaryk University
    Botanická 68a, 602 00 Brno, Czech Republic
Current Position
  • Research Assistant:
    - 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
Education and Academic Qualifications
  • 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
  • Research Assistant (7/2015 - 12/2015):
    - Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University
    - engaged as a team member in 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
    - engaged as a team member in a mid-term project "Automated Analysis of Electron Microscopy Images for the Use in Biology and Medicine", Grant Agency of Masaryk University, 3/2014 - 12/2016
    - engaged as a team member in a mid-term project "Development of New MUS81 Nuclease Inhibitors as Chemical Biology Probe with Clinical Progression", Grant Agency of Masaryk University, 3/2015 - 12/2017
  • Postdoctoral Research Fellow (1/2013 - 6/2015):
    - Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University
    - engaged as a team member in 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
    - engaged as a team member in 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
    - engaged as a team member in 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
    - engaged as a team member in 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
  • 2017-present: Seminar on Foundations of Programming
  • 2016-present: Seminar on Mathematical Foundations of Computer Science
  • 2016-present: 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
  • Automation of image acquisition and analysis:
    - participation in a team project "Acquiarium" aimed at the development of an image acquisition and analysis software for automated fluorescence microscopy
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)
Professional Activities
  • Special Session Co-Organization:
    - Cell Tracking Challenge (ISBI 2013, ISBI 2014, ISBI 2015), Particle Tracking Challenge (ISBI 2012)
  • Review Activities:
    - Bioinformatics, BioTechniques, Cytometry Part A, IEEE International Symposium on Biomedical Imaging, IEEE Transactions on Biomedical Engineering, IEEE Transactions on Medical Imaging, Journal of Microscopy, Nature Methods
Scientific Awards
  • 2016: Masaryk University Rector’s Award for Outstanding Research Results Achieved by Young Scientists under 35
Selected Publications
  • 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. "e0171417". ISSN 1932-6203. doi: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. In 14th IEEE International Symposium on Biomedical Imaging. Melbourne: IEEE, 2017. s. 822-826, 5 s. ISBN 978-1-5090-1172-8. info
  • MAŠKA, Martin a Pavel MATULA. Particle Tracking Accuracy Measurement Based on Comparison of Linear Oriented Forests. In 16th IEEE International Conference of Computer Vision Workshops. Venice: IEEE, 2017. s. 11-17, 7 s. 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, 8 s. ISBN 978-3-319-46603-3. doi: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". ISSN 1932-6203. doi: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. In 22nd IEEE International Conference on Image Processing. Québec City: IEEE, 2015. s. 1791-1794, 4 s. ISBN 978-1-4799-8339-1. doi: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. In 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. Milano: IEEE, 2015. s. 8139-8142, 4 s. ISBN 978-1-4244-9271-8. doi: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. doi: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. doi: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, 5 s. ISBN 978-1-4799-5750-7. doi: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. doi: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. In 10th IEEE International Symposium on Biomedical Imaging. San Francisco: IEEE, 2013. s. 668-671, 4 s. ISBN 978-1-4673-6454-6. doi: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. doi: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. In 9th IEEE International Symposium on Biomedical Imaging. Barcelona: IEEE, 2012. s. 1316–1319, 4 s. 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. In Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (Selected Papers). Saarbrücken, Warden: Schloss Dagstuhl Publishing, 2011. s. 19-25, 7 s. 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. In Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (Selected Papers). Saarbrücken, Wadern: Schloss Dagstuhl Publishing, 2011. s. 69-76, 8 s. 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. In 6th International Symposium on Visual Computing. Berlin, Heidelberg: Springer-Verlag, 2010. s. 387-396, 10 s. ISBN 978-3-642-17276-2. doi: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. doi: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, 9 s. 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, 8 s. ISBN 978-80-87342-10-7. info
  • MAŠKA, Martin a Pavel MATULA. A Fast Level Set-Like Algorithm with Topology Preserving Constraint. In 13th International Conference on Computer Analysis of Images and Patterns. Berlin, Heidelberg: Springer-Verlag, 2009. s. 930-938, 9 s. ISBN 978-3-642-03766-5. doi: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, 10 s. ISBN 978-3-642-02229-6. doi: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. In 16th Scandinavian Conference on Image Analysis. Berlin, Heidelberg: Springer-Verlag, 2009. s. 390-399, 10 s. ISBN 978-3-642-02229-6. doi: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. In IEEE International Symposium on Biomedical Imaging. Boston: IEEE, 2009. s. 1138-1141, 4 s. 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, 8 s. 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. In 3rd International Symposium on Visual Computing. Berlin, Heidelberg: Spinger-Verlag, 2007. s. 571-581, 11 s. ISBN 978-3-540-76855-5. URL info

2017/08/15

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