Image Acquisition and Analysis in Optical Microscopy

Main research field

• Brázdilová, SL. - Kozubek, M. Image Division Technique in Pre-acquisition Analysis of Information Content for Automated Microscopy. Journal of Microscopy, Oxford : Blackwell Science. ISSN 0022-2720. In press.
• 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., 75A, 6, p. 494-509, ISSN 1552-4922. 2009.
• 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)

• 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)

• 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. LNCS 5575. ISBN 978-3-642-02229-6.
• 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. LNCS 5575. ISBN 978-3-642-02229-6.

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