Benchmarking in Biomedical Image Analysis

Main research field

• Ulman V, Maška M, Magnusson KEG, Ronneberger O, Haubold C, Harder N, Matula P, Matula P, Svoboda D, Radojevic M, Smal I, Rohr K, Jaldén J, Blau HM, Dzyubachyk O, Lelieveldt B, Xiao P, Li Y, Cho S, Dufour AC, Olivo-Marin J, Reyes-Aldasoro CC, Solis-Lemus JA, Bensch R, Brox T, Stegmaier J, Mikut R, Wolf S, Hamprecht FA, Esteves T, Quelhas P, Demirel Ö, Malmström L, Jug F, Tomancak P, Meijering E, Munoz-Barrutia A, Kozubek M, Ortiz-de-Solorzano C. An objective comparison of cell-tracking algorithms. Nature Methods, Macmillan Publishers Limited, part of Springer Nature, 2017, vol. 14, no. 12, p. 1141-1152. ISSN 1548-7091. doi:10.1038/nmeth.4473.
• Kozubek M. Challenges and Benchmarks in Bioimage Analysis. Advances in Anatomy, Embryology and Cell Biology, Springer, 2016, vol. 219, p. 231-262. ISSN 0301-5556. doi:10.1007/978-3-319-28549-8_9.
• Štěpka K, Matula P, Matula P, Woerz S, Rohr K, Kozubek M. Performance and Sensitivity Evaluation of 3-D Spot Detection Methods in Confocal Microscopy. Cytometry Part A, John Wiley & Sons, 2015, 87A, No 8, p. 759-772. ISSN 1552-4922. doi:10.1002/cyto.a.22692.
• Matula P, Maška M, Sorokin D, Matula P, Ortiz-de-Solórzano C, Kozubek M. Cell tracking accuracy measurement based on comparison of acyclic oriented graphs. PLoS ONE, 2015, vol. 10, No 12, p. "e0144959". ISSN 1932-6203. doi:10.1371/journal.pone.0144959.
• Maška M, Ulman V, Svoboda D, Matula P, Matula P, Ederra C, Urbiola A, Espana T, Venkatesan S, Balak DMW, Karas P, Bolcková T, Štreitová M, Carthel C, Coraluppi S, Harder N, Rohr K, Magnusson KEG, Jaldén J, Blau HM, Dzyubachyk O, Křížek P, Hagen GM, Pastor-Escuredo D, Jimenez-Carretero D, Ledesma-Carbayo MJ, Munoz-Barrutia A, Meijering E, Kozubek M, Ortiz-de-Solorzano C. A Benchmark for Comparison of Cell Tracking Algorithms. Bioinformatics, 2014, vol. 30, no. 11, p. 1609-1617. ISSN 1367-4803. doi:10.1093/bioinformatics/btu080.

Modeling and Simulations in Cell Imaging

The second main research field

• Svoboda D, Kozubek M. Multimodal Simulations in Live Cell Imaging. In Tsaftaris S., Gooya A., Frangi A., Prince J. Simulation and Synthesis in Medical Imaging. MICCAI/LABELS, LNCS 10557. Neuveden: Springer, 2017. p. 89-98, ISBN 978-3-319-68126-9. doi:10.1007/978-3-319-68127-6_10.
• Ulman V, Svoboda D, Nykter M, Kozubek M, Ruusuvuori P. Virtual cell imaging: A review on simulation methods employed in image cytometry. Cytometry Part A, John Wiley & Sons, 2017, vol. 89, no. 12., p. 1057-1072. ISSN 1552-4922. doi:10.1002/cyto.a.23031.
• Ortiz-de-Solórzano C, Munoz-Barrutia A, Meijering E, Kozubek M. Toward a Morphodynamic Model of the Cell. IEEE Signal Processing Magazine, New York: IEEE, 2015, vol. 32, No 1, p. 20-29. ISSN 1053-5888. doi:10.1109/MSP.2014.2358263.
• Svoboda D, Kozubek M, Stejskal S. Generation of Digital Phantoms of Cell Nuclei and Simulation of Image Formation in 3D Image Cytometry. Cytometry Part A, John Wiley & Sons, Inc., 2009, 75A, No 6, p. 494-509. ISSN 1552-4922. doi:10.1002/cyto.a.20714.

Image Acquisition and Analysis in Optical Microscopy

• Brázdilová, SL, Kozubek, M. Image Division Technique in Pre-acquisition Analysis of Information Content for Automated Microscopy. Journal of Microscopy, Oxford : Blackwell Science, 242, 3, p. 279-289. ISSN 0022-2720. 2011.
• Brázdilová, SL, Kozubek, M. Information Content Analysis in Automated Microscopy Imaging using an Adaptive Autofocus Algorithm for Multimodal Functions. Journal of Microscopy, Oxford : Blackwell Science, 236, 3, p. 194-202. ISSN 0022-2720. 2009.
• Matula, P, Maška, M, Daněk, O, Matula, P., Kozubek, M. 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. p. 1138-1141. ISBN 978-1-4244-3932-4.
• Matula, P, Matula, P, Kozubek, M, Dvořák, V. Fast Point-Based 3D Alignment of Live Cells. IEEE Transactions on Image Processing, 15, 8, p. 2388-2396. ISSN 1057-7149. 2006.
• Kozubek, M, Matula, P, Matula, P, Kozubek, S. Automated acquisition and processing of multidimensional image data in confocal in vivo microscopy. Microscopy research and technique, USA : Wiley-Liss, 64, 2, p. 164-175. ISSN 1059-910X. 2004.
• Kozubek, M, Matula, P, Matula, P. Automated confocal microscopy: The way of achieving both quality and quantity in 3D image cytometry. In International Symposium on Biomedical Imaging. Arlington, USA : IEEE, 2004. p. 69-72. ISBN 0-7803-8389-3.
• Kozubek, M, Matula, P, Matula, P. The power of computerized light microscopy. Imaging & Microscopy, Darmstadt : GIT Verlag, 4, 2, p. 25-28. ISSN 1439-4243. 2002.
• Kozubek, M. Theoretical versus experimental resolution in optical microscopy. Microscopy research and technique, USA : Wiley-Liss, 53, 2, p. 157-166. ISSN 1059-910X. 2001.
• Kozubek, M, Kozubek, S, Lukášová, E, Bártová, E, Skalníková, M, Matula, P, Matula, P, Jirsová, P, Gaňová, A, Koutná, I. Combined confocal and wide-field high-resolution cytometry of FISH-stained cells. Cytometry, New York : International Society for Analytical Cyt, 45, 1, p. 1-12. ISSN 0196-4763. 2001.
• Kozubek, M, Matula, P. An efficient algorithm for measurement and correction of chromatic aberrations in fluorescence microscopy. Journal of Microscopy, Oxford : Blackwell Science, 200, 3, p. 206-217. ISSN 0022-2720. 2000.
• Kozubek, M, Kozubek, S, Lukášová, E, Marečková, A, Bártová, E. - Skalníková, M, Jergová, A. High-resolution cytometry of FISH dots in interphase cell nuclei. Cytometry, New York : International Society for Analytical Cyt, 36, 4, p. 279-293. ISSN 0196-4763. 1999.

Structural Illumination in Optical Microscopy

(in collaboration with Scanning Optical Microscopy Group, Dept.of Eng.Science, University of Oxford, England)

• Schrader, M, Kozubek, M, Hell, S, Wilson, T. Optical transfer functions of 4Pi confocal microscopes : theory and experiment. Optics Letters, 22, 7, p. 436-438. ISSN 0146-9592. 1997.
• Juškaitis, R, Wilson, T, Neil, M, Kozubek, M. Efficient real-time confocal microscopy with white light sources. Nature, 383, 6603, p. 804-806. ISSN 0028-0836. 1996.
• Wilson, T, Juškaitis, R, Neil, M, Kozubek, M. Confocal microscopy by aperture correlation. Optics Letters, 21, 23, p. 1879-1881. ISSN 0146-9592. 1996.
• Wilson, T, Juškaitis, R, Neil, M, Kozubek, M. An aperture correlation approach to confocal microscopy. In Three-Dimensional Microscopy: Image Acquisition and Processing IV. Bellingham : SPIE, 1997. p. 21-24. ISBN 0-8194-2395-5.
• Wilson, T, Juškaitis, R, Neil, M, Kozubek, M. SCAM - a new form of confocal microscope. In 3D Imaging Sciences in Microscopy. Oxford : Oxford University, 1996.

Micro-Axial Tomography in Optical Microscopy

(in collaboration with Applied Optics and Information Processing Group, Kirchhoff Institute of Physics, University of Heidelberg, Germany)

• Staier F, Eipel H, Matula P, Evsikov AV, Kozubek M, Cremer Ch, Hausmann M. Micro axial tomography: A miniaturized, versatile stage device to overcome resolution anisotropy in fluorescence light microscopy. Rev. Sci. Instrum., USA: American Institute of Physica, 2011, vol. 82, No 9, p. "093701-1"-"093701-8". ISSN 0034-6748.
• Matula, P, Kozubek, M, Staier, F, Hausmann, M. Precise 3D image alignment in micro-axial tomography. Journal of Microscopy, Oxford : Blackwell Science, 209, 2, p. 126-142. ISSN 0022-2720. 2003.
• Kozubek, M, Skalníková, M, Matula, P, Bártová, E, Rauch, J, Neuhaus, F, Eipel, H, Hausmann, M. Automated micro axial tomography of cell nuclei after specific labelling by fluorescence in situ hybridisation. Micron, Amsterdam : Elsevier, 33, 7, p. 655-665. ISSN 0968-4328. 2002.
• Kozubek, M, Matula, P, Eipel, H, Hausmann, M. Automated multi-view 3D image acquisition in human genome research. In 3D data processing, visualization and transmission. Los Alamitos : IEEE Computer Society, 2002. p. 91-98. ISBN 0-7695-1521-5.

Image Analysis in Clinical Applications

(in collaboration with Imaging Core Facility, Centre for Applied Medical Research, University of Navarra, Spain)

• Anguiano M, Castilla C, Maška M, Ederra C, Peláez R, Morales X, Munoz-Arrieta G, Mujika M, Kozubek M, Munoz-Barrutia A, Rouzaut A, Arana S, Garcia-Aznar JM, Ortiz-de-Solorzano C. 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.
• Maška M, Ederra C, Fernández-Marqués J, Munoz-Barrutia A, Kozubek M, Ortiz-de-Solórzano C. Quantification of the 3D Collagen Network Geometry in Confocal Reflection Microscopy. In 22nd IEEE International Conference on Image Processing. Québec City: IEEE, 2015. p. 1791-1794. ISBN 978-1-4799-8339-1. doi:10.1109/ICIP.2015.7351109.
• Anguiano M, Castilla C, Maška M, Ederra C, Fernández-Marqués J, Peláez R, Rouzaut A, Munoz-Barrutia A, Kozubek M, Ortiz-de-Solórzano C. 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. p. 8139-8142. ISBN 978-1-4244-9271-8. doi:10.1109/EMBC.2015.7320283.
• Maška M, Daněk O, Ortiz-de-Solórzano C, Munoz-Barrutia A, Kozubek M, Fernández García I. 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. p. 390-399. ISBN 978-3-642-02229-6. doi:10.1007/978-3-642-02230-2_40.
• Daněk O, Matula P, Ortiz-de-Solórzano C, Munoz-Barrutia A, Maška M, Kozubek M. 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. doi:10.1007/978-3-642-02230-2_42.

Clinical Applications

(in collaboration with Faculty of Medicine, Masaryk University, Brno)

• Stejskal, S, Koutná, I, Matula, P, Ručka, Z, Daněk, O, Maška, M, Kozubek, M. The role of chromatin condensation during granulopoiesis in the regulation of gene cluster expression. Epigenetics, USA: Landes Bioscience, 5, 8, p. 759-767. ISSN 1559-2294. 2010.
• Šimara, P, Koutná, I, Stejskal, S, Krontorád, P, Ručka, Z, Peterková, M, Kozubek, M. Combination of mRNA and protein microarray analysis in complex cell profiling. Neoplasma, Bratislava, Slovensko : AEPress, s.r.o., 2/2009, 56, p. 141-149. ISSN 0028-2685. 2009.
• Peterková, M, Koutná, I, Tesařová, L, Potěšilová, M, Kozubek, M, Hrabčáková, V, Klabusay, M, Doubek, M, Mayer, J. Microarray analysis using limited amount of cells. Folia Biologica (Praha), 2009, 55, p. 53-60. ISSN 0015-5500. 2009.
• Koutná, I, Krontorád, P, Svoboda, Z, Bártová, E, Kozubek, M, Kozubek, S. New insights into gene positional clustering and its properties supported by large-scale analysis of various differentiation pathways. Genomics, United States : Elsevier Science Inc, 89, 1, p. 81-88. ISSN 0888-7543. 2007.
• Jansová, E, Koutná, I, Krontorád, P, Svoboda, Z, Křivánková, S, Žaloudík, J, Kozubek, M, Kozubek, S. Comparative transcriptome maps: a new approach to the diagnosis of colorectal carcinoma patients using cDNA microarrays. Clinical Genetics, Denmark : Blackwell Munksgaard, 69, 3, p. 218-227. ISSN 0009-9163. 2006.
• Koutná, I, Klabusay, M, Hrabčáková, V, Krontorád, P, Svoboda, Z, Kozubek, M, Mayer, J. Evaluation of CD34+ - and Lin- -selected cells from peripheral blood stem cell grafts of patients with lymphoma during differentiation in culture ex vivo using a cDNA microarray technique. Experimental hematology, Netherlands : Elsevier Science Inc, 34, 7, p. 832-840. ISSN 0301-472X. 2006.
• Lukášová, E, Kozubek, S, Falk, M., Kozubek, M, Žaloudík, J, Vagunda, V, Pavlovský, Z. Topography of genetic loci in the nuclei of cells of colorectal carcinoma and adjacent tissue of colonic epithelium. Chromosoma, Berlin : Springer-Verlag, 112, 5, p. 221-230. ISSN 0009-5915. 2004.
• Koutná, I, Kozubek, S, Žaloudík, J, Kozubek, M, Lukášová, E, Matula, P, Bártová, E, Skalníková, M, Cafourková, A, Jirsová, P. Topography of genetic loci in tissue samples: towards new diagnostic tool using interphase FISH and high-resolution image analysis techniques. Analytical Cellular Pathology, Amsterdam : IOS Press, 20, 4, p. 173-185. ISSN 0921-8912. 2000.

Biological Applications

(in collaboration with Institute of Biophysics, Czech Academy of Sciences, Brno)

• Taslerová, R, Kozubek, S, Lukášová, E, Jirsová, P, Bártová, E. - Kozubek, M. Arrangement of chromosome 11 and 22 territories, EWSR1 and FLI-1 genes, and other genetic elements of these chromosomes in human lymphocytes and Ewing sarcoma cells. Human Genetics, 112, 2, p. 143-155. ISSN 0340-6717. 2003.
• Amrichová, J, Lukášová, E, Kozubek, S, Kozubek, M. Nuclear and territorial topography of chromosome telomeres in human lymphocytes. Experimental Cell Research, Elsevier Science, USA, 289, 1, p. 11-26. ISSN 0014-4827. 2003.
• Kozubek, S, Lukášová, E, Jirsová, P, Koutná, I, Kozubek, M, Gaňová, A, Bártová, E, Falk, M, Taslerová, R. 3D Structure of the human genome: Order in randomness. Chromosoma, Berlin : Springer-Verlag, 111, 5, p. 321-331. ISSN 0009-5915. 2002.
• Bártová, E, Kozubek, S, Jirsová, P, Kozubek, M, Gajová, H, Lukášová, E, Skalníková, M, Gaňová, A, Koutná, I, Hausmann, M. Nuclear structure and gene activity in human differentiated cells. Journal of Structural Biology, San Diego,USA : Academic Press, 139, 2, p. 76-89. ISSN 1047-8477. 2002.
• Falk, M, Lukášová, E, Kozubek, S, Kozubek, M. Topography of genetic elements of X-chromosome relative to the cell nucleus and to the chromosome X territory determined for human lymphocytes. Gene, Amsterdam : Elsevier, 292, 1, p. 13-24. ISSN 0378-1119. 2002.
• Lukášová, E, Kozubek, S, Kozubek, M, Falk, M, Amrichová, J. The 3D structure of human chromosomes in cell nuclei. Chromosome Research, Dordrecht : Kluwer Academic, 10, 7, p. 535-548. ISSN 0967-3849. 2002.
• Jirsová, P, Kozubek, S, Bártová, E, Kozubek, M, Lukášová, E, Gaňová, A, Koutná, I, Skalníková, M. Spatial distribution of selected genetic loci in nuclei of human leukemia cells after irradiation. Radiation Research, 155, 2, p. 311-319. ISSN 0033-7587. 2001.
• Gaňová, A, Lukášová, E, Kozubek, S, Kozubek, M, Govorun, R, Koutná, I, Bártová, E, Skalníková, M, Jirsová, P, Paseková, R, Krasavin, E. Exchange aberrations among 11 chromosomes of human lymphocytes induced by gamma-rays. International Journal of Radiation Biology, 77, 4, p. 419-429. ISSN 0955-3002. 2001.
• Bártová, E, Kozubek, S, Jirsová, P, Kozubek, M, Lukášová, E, Skalníková, M, Gaňová, A, Koutná, I, Paseková, R. Higher-order chromatin structure of human granulocytes. Chromosoma, Berlin : Springer-Verlag, 110, 5, p. 360-370. ISSN 0009-5915. 2001.
• Bártová, E, Kozubek, S, Kozubek, M, Jirsová, P, Lukášová, E, Skalníková, M, Buchníčková, K. The influence of the cell cycle, differentiation and irradiation on the nuclear location of the ABL, BCR and C-MYC genes in human leukemic cells. Leukemia Research, 24, 3, p. 233-241. ISSN 0145-2126. 2000.
• Bártová, E, Kozubek, S, Kozubek, M, Jirsová, P, Lukášová, E, Skalníková, M, Cafourková, A, Koutná, I. Nuclear topography of the c-myc gene in human leukemic cells. Gene, Amsterdam : Elsevier, 244, 1, p. 1-11. ISSN 0378-1119. 2000.
• Kozubek, S, Lukášová, E, Amrichová, J, Kozubek, M, Lišková, A. - Šlotová, J. Influence of cell fixation on chromatin topography. Analytical Biochemistry, San Diego : Academic Press, 282, 1, p. 29-38. ISSN 0003-2697. 2000.
• Skalníková, M, Kozubek, S, Lukášová, E, Bártová, E, Jirsová, P, Cafourková, A, Koutná, I, Kozubek, M. Spatial arrangement of genes, centromeres and chromosomes in human blood cell nuclei and its changes during the cell cycle, differentiation and after irradiation. Chromosome Research, Dordrecht : Kluwer Academic, 8, 6, p. 487-499. ISSN 0967-3849. 2000.
• Kozubek, S, Lukášová, E, Marečková, A, Skalníková, M, Kozubek, M, Bártová, E, Kroha, V, Krahulcová, E, Šlotová, J. The topological organization of chromosomes 9 and 22 in cell nuclei has a determinative role in the induction of t(9,22) translocations and in the pathogenesis of t(9,22) leukemias. Chromosoma, Berlin : Springer-Verlag, 108, 7, p. 426-435. ISSN 0009-5915. 1999.
• Lukášová, E, Kozubek, S, Kozubek, M, Kroha, V, Marečková, A, Skalníková, M, Bártová, E, Šlotová, J. Chromosomes participating in translocations typical of malignant hemoblastoses are also involved in exchange aberrations induced by fast neutrons. Radiation Research, 151, 4, p. 375-384. ISSN 0033-7587. 1999.
• Kozubek, S, Lukášová, E, Rýznar, L, Kozubek, M, Govorun, R, Krasavin, E, Horneck, G. Distribution of ABL and BCR genes in cell nuclei of normal and irradiated lymphocytes. Blood, 89, 12, p. 4537-4545. ISSN 0006-4971. 1997.
• Lukášová, E, Kozubek, S, Kozubek, M, Kjeronská, J, Rýznar, L. - Horáková, J, Krahulcová, E, Horneck, G. Localisation and distance between ABL and BCR genes in interphase nuclei of bone marrow cells of control donors and patients with chronic myeloid leukemia. Human Genetics, 100, 5/6, p. 525-535. ISSN 0340-6717. 1997.

Book Chapters

• Kozubek, M. Image acquisition and its automation in fluorescence microscopy. In From cells to proteins: Imaging nature across dimensions. Dordrecht : Springer, 2005. p. 227-270, 44 pp. NATO Science Series. ISBN 1-4020-3615-9.
• Kozubek, M. FISH Imaging. In Confocal and two-photon microscopy: Foundations, applications, and advances. New York : Wiley-Liss, 2001. p. 389-429. ISBN 0-471-40920-0.

Earlier Books

(not related to current research)

• Ochranova, R, Kozubek, M.  Object Oriented Programming in Turbo Pascal,  Masaryk University Press, 1993, in Czech
• Kozubek, M, Kozubek, S.  Ozone Hole - a Danger for Mankind?,  CCB Brno, 1993, in Czech, free copy