Curriculum Vitae

Curriculum vitae

Person Identification

• RNDr. Ondřej Daněk, Ph.D.
  born March 21, 1983 in Boskovice, Czech Republic, single, 1 child
• e-mail: ondrej.danek@gmail.com
• www: http://www.ondrej-danek.net

Workplace

• Centre for Biomedical Image Analysis
  Faculty of Informatics
  Masaryk University
  Botanicka 68a
  602 00 Brno, Czech Republic

Current Position

• Research and development worker
• Engaged as a team member into 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

Education and Academic Qualifications

• 2007 - 2012: Ph.D., Faculty of Informatics, Masaryk University, Brno; topic: "Applications of Graph Cut Optimization in Fluorescence Microscopy"
• 2009: RNDr. in Informatics, Faculty of Informatics, Masaryk University, Brno; thesis: "Applications of Graph Cut Optimization in Fluorescence Microscopy"
• 2004 - 2007: Mgr. (master's degree), Faculty of Informatics, Masaryk University, Brno; thesis: "Voxel-based registration of images of cells"
• 2004 - 2007: Bc. (bachelor's degree), Faculty of Economics and Administration, Masaryk University, Brno; thesis: "E-commerce security"
• 2001 - 2004: Bc. (bachelor's degree), Faculty of Informatics, Masaryk University, Brno; thesis: "Improving capabilities of 3D image viewer", graduated with honours
• 1993 - 2001: Secondary grammar school, Rájec – Jestřebí; graduated with honours

Employment Summary

• 2007 - 2012: Research and development worker, Faculty of Informatics, Masaryk University, Brno
• 2005 - 2006: Consultant, Telefónica O2 Czech Republic, a.s., Brno

Scientific and Research Activities

• Biomedical image processing:
  - segmentation
  - graph cut optimization
• Automation of optical microscopy
  - participation on a team project "Acquiarium" aimed at the development of image acquisition software for automated fluorescence microscopy

Skills

• Operating systems:
  - Windows (all versions)
  - Linux (Fedora, OpenSuse, Ubuntu)
  - Unix (Solaris, IRIX, BSD)
• Programming languages:
  - experienced: C/C++, Pascal, Basic, Assembler
  - basic: Java
• Libraries:
  - wxWidgets, OpenGL, SDL
• Applications:
  - MS Visual Studio, Matlab, Maple, Subversion
  - MS Office, OpenOffice, TeX, Photoshop
• Web technologies:
  - HTML, XHTML, CSS
  - PHP, MySql

Internship and stays for the purpose of study or work

• 2010: Centro de investigación médica aplicada, Universidad de Navarra, Pamplona, Spain; three months stay
• 2008: Centro de investigación médica aplicada, Universidad de Navarra, Pamplona, Spain; four months stay
• 2007: Acquisition and Analysis of Images in Microscopy, Academy of Sciences of the Czech Republic, one week course
• 2010/04/08 – 2010/07/09: Center for Applied Medical Research (CIMA), Pamplona, ESP
• 2008/01/17 – 2008/05/15: University of Navarra, Pamplona, ESP

Languages

• Czech - mother tongue
• English - advanced; passed czech "Basic state exam" (B2 level)
• German - beginner
• Spanish - beginner

Appreciation of Scientific Community

• 2004: Awarded annual dean's prize for excellent study results, Faculty of Informatics, Masaryk University, Brno
• 2009: Annual award for best talk presented on Informatics seminar, Masaryk University, Brno
• 2010: Best student paper award: "Graph Cuts and Approximation of the Euclidean Metric on Anisotropic Grids", VISAPP International Conference on Computer Vision Theory and Applications, Angers, France

Interests

• Travelling, tourism
• Music - both classical and popular, playing piano and guitar
• Sport - both active and passive
• IT - theory, programming, freeware games development, hardware
• Mathematics - history, unsolved problems
• Economics - investment, business, management
• Literature - Pratchett, Verne, King, comics
• Theatre - playing and watching (especially czech Jára da Cimrman)
• Movies - italian comedies (Fantozzi), horrors and a lot more
• Cell phones

Selected Publications

• DANĚK, Ondřej, Pavel MATULA, Martin MAŠKA and 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, vol. 33, No 10, p. 1405-1410. ISSN 0167-8655. Available from: https://dx.doi.org/10.1016/j.patrec.2012.03.013. URL info
• DANĚK, Ondřej and Pavel MATULA. An Improved Riemannian Metric Approximation for Graph Cuts. In 16th International Conference on Discrete Geometry for Computer Imagery. Berlin, Heidelberg: Springer-Verlag, 2011, p. 71-82. ISBN 978-3-642-19866-3. Available from: https://dx.doi.org/10.1007/978-3-642-19867-0_6. URL info
• DANĚK, Ondřej and Pavel MATULA. On Euclidean Metric Approximation via Graph Cuts. In Computer Vision, Imaging and Computer Graphics. Theory and Applications. Berlin, Heidelberg: Springer-Verlag, 2011, p. 125-134, 11 pp. ISBN 978-3-642-25381-2. Available from: https://dx.doi.org/10.1007/978-3-642-25382-9_9. URL info
• DANĚK, Ondřej and 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, p. 19-25. ISBN 978-3-939897-22-4. URL info
• STIXOVÁ, Lenka, Eva BÁRTOVÁ, Pavel MATULA, Ondřej DANĚK, Soňa LEGARTOVÁ and Stanislav KOZUBEK. Heterogeneity in the kinetics of nuclear proteins and trajectories of substructures associated with heterochromatin. Epigenetics & Chromatin. 2011, vol. 4, No 5, p. 1-17. ISSN 1756-8935. Available from: https://dx.doi.org/10.1186/1756-8935-4-5. URL info
• DANĚK, Ondřej and Pavel MATULA. Graph Cuts and Approximation of the Euclidean Metric on Anisotropic Grids. In VISAPP International Conference on Computer Vision Theory and Applications. Portugal: Institute for Systems and Technologies of Information, Control and Communication, 2010, p. 68-73. ISBN 978-989-674-028-3. info
• STEJSKAL, Stanislav, Irena KRONTORÁD KOUTNÁ, Pavel MATULA, Zdeněk RUČKA, Ondřej DANĚK, Martin MAŠKA and Michal KOZUBEK. The role of chromatin condensation during granulopoiesis in the regulation of gene cluster expression. Epigenetics. USA: Landes Bioscience, 2010, vol. 5, No 8, p. 759-767. ISSN 1559-2294. Available from: https://dx.doi.org/10.4161/epi.5.8.13183. URL info
• STEJSKAL, Stanislav, Pavel MATULA, Ondřej DANĚK, Martin MAŠKA, Irena KRONTORÁD KOUTNÁ and Michal KOZUBEK. A novel approach to evaluation of the spatial relationship of fluorescent signals in ImunnoFISH analysis of different kind. In Advances in Molecular and Cancer Biology, 2010. Brno: muni PRESS, 2010, p. 39-41. ISBN 978-80-210-5312-0. info
• DANĚK, Ondřej, Pavel MATULA, Carlos ORTIZ-DE-SOLÓRZANO, Arrate MUÑOZ-BARRUTIA, Martin MAŠKA and 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, p. 410-419. ISBN 978-3-642-02229-6. Available from: 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 and 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, p. 390-399. ISBN 978-3-642-02229-6. Available from: https://dx.doi.org/10.1007/978-3-642-02230-2_40. URL info
• MATULA, Pavel, Martin MAŠKA, Ondřej DANĚK, Petr MATULA and 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, p. 1138-1141. ISBN 978-1-4244-3932-4. URL info

2017/12/31