Experimental Biophotonics - Radim Chmelík

Research areas

• advanced light (holographic, multimodal) microscopy (ALM) – innovative technologies
• evaluation of live cell behaviour using ALM
• analysis of micro- and nanostructures using ALM

Main objectives

Research and development of analytical and measurement methods

Experimental Biophotonics focus on advanced light microscopy techniques and methodologies applied to the study of nano- and microstructures characteristics and interactions with living cells including assessments of possible cytotoxicity and cancer cell diagnostics.

Content of research

Research and development of analytical and measurement methods

Advanced light microscopy – innovative technologies

• theoretical study of imaging processes in advanced, especially holographic and confocal light microscopy, simulation and experimental verification of results
• investigation of coherence effects, optical and coherence vortices in holographic imaging, imaging in turbid media by coherence gating
• development of coherence controlled and SLM optical systems for holographic and multimodal (correlative) microscopy
• development of advanced image-processing methods for holographic reconstruction, quantitative phase evaluation, dynamic phase differences, pattern and process recognition

Evaluation of live cell behaviour & analysis of micro- and nanostructures

• biophysics of quantitative evaluation of live cell behaviour developed with coherence- controlled holographic microscopy (CCHM)
• subtoxic impact/toxicity of nanomaterials assessment by measurement of intracellular dry mass translocation with CCHM
• in vitro qualification of cancer cell malignancy with CCHM classification of cell behaviour patterns
• observation and validation of nanostructure properties and their interactions with living cells with advanced light microscopy

Research group SITE

list / cards

Name and position	E-mail	Phone
Matěj Týč Junior researcher		+420 54114 2789
Alena Vojkůvková Administrative Support		+420 54114 2833
Pavel Veselý Senior Researcher
Lukáš Kvasnica Junior researcher		+420 54114 2816
Prof. Jiří Komrska Senior researcher		+420 54114 2826
Pavel Kolman, Ph.D. Junior Researcher		+420 54114 2816, +420 723 124 504
Hana Uhlířová, Ph.D. Junior researcher		+420 54114 2833
Prof. Jiří Petráček Senior Researcher		+420 54114 2764, +420 726 812 764
Martin Antoš, Ph.D. Junior Researcher		+420 54114 2778, +420 726 812 778
Petr Bouchal, Ph.D. Junior researcher		+420 54114 2778
Zbyněk Dostál Junior researcher		+420 54114 2833, +420 54114 2778
Prof. Radim Chmelík, Ph.D. Senior Researcher		+420 54114 2795, +420 604 072 795
Lenka Štrbková Ph.D. student		+420 54114 2789
Daniel Zicha senior researcher
Veronika Jůzová Technician
Michala Slabá Ph.D. student		+420 54114 2833
Aneta Křížová Ph.D. student		+420 54114 2789
Tereza Chmelíková Ph.D. student
Lucie Klusoňová Ph.D. student
Michala Slabá

SELECTED PUBLICATIONS

2017

• BABOCKY, J; KRIZOVA, A; STRBKOVA, L; KEJIK, L; LIGMAJER, F; HRTON, M; DVORAK, P; TYC, M; COLLAKOVA, J; KRAPEK, V; KALOUSEK, R; CHMELIK, R; SIKOLA, T, 2017:Quantitative 3D Phase Imaging of Plasmonic Metasurfaces. ACS PHOTONICS 4 (6), p. 1389 - 1397.
• BOUCHAL, P; STRBKOVA, L; DOSTAL, Z; BOUCHAL, Z, 2017:Vortex topographic microscopy for full-field reference-free imaging and testing. OPTICS EXPRESS 25 (18), p. 21428 - 21443.
• STRBKOVA, L; ZICHA, D; VESELY, P; CHMELIK, R, 2017:Automated classification of cell morphology by coherence-controlled holographic microscopy. JOURNAL OF BIOMEDICAL OPTICS 22 (8)
• UHLÍŘOVÁ, H; PEIFANG, T; KILIC, K; THUNEMANN, M; SRIDHAR, V; BARTSCH, H; DALE, A; DEVOR, A; SAISAN, P, 2017:Neurovascular Network Explorer 2.0: A Database of 2-Photon Single Vessel Diameter Measurements from Mouse SI Cortexin Response To Optogenetic Stimulation. Frontiers in Neuroinformatics (11)

2016

• STRBKOVA, L; MANAKHOV, A; ZAJICKOVA, L; STOICA, A; VESELY, P; CHMELIK, R, 2016:The adhesion of normal human dermal fibroblasts to the cyclopropylamine plasma polymers studied by holographic microscopy. SURFACE & COATINGS TECHNOLOGY 295 , p. 70 - 77.
• UHLIROVA, H; KILIC, K; TIAN, PF; SAKADZIC, S; GAGNON, L; THUNEMANN, M; DESJARDINS, M; SAISAN, PA; NIZAR, K; YASEEN, MA; HAGLER, DJ; VANDENBERGHE, M; DJUROVIC, S; ANDREASSEN, OA; SILVA, GA; MASLIAH, E; KLEINFELD, D; VINOGRADOV, S; BUXTON, RB; EINEVOLL, GT; BOAS, DA; DALE, AM; DEVOR, A, 2016:The roadmap for estimation of cell-type-specific neuronal activity from non-invasive measurements. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 371 (1705)
• UHLIROVA, H; KILIC, K; TIAN, PF; THUNEMANN, M; DESJARDINS, M; SAISAN, PA; SAKADZIC, S; NESE, TV; MATEO, C; CHENG, Q; WELDY, KL; RAZOUX, F; VANDENBERGHE, M; CREMONESI, JA; FERRI, CGL; NIZAR, K; SRIDHAR, VB; STEED, TC; ABASHIN, M; FAINMAN, Y; MASLIAH, E; DJUROVIC, S; ANDREASSEN, OA; SILVA, GA; BOAS, DA; KLEINFELD, D; BUXTON, RB; EINEVOLL, GT; DALE, AM; DEVOR, A, 2016:Cell type specificity of neurovascular coupling in cerebral cortex. ELIFE 5
• ZEMANOVA, J; HYLSE, O; COLLAKOVA, J; VESELY, P; OLTOVA, A; BORSKY, M; ZAPRAZNA, K; KASPARKOVA, M; JANOVSKA, P; VERNER, J; KOHOUTEK, J; DZIMKOVA, M; BRYJA, V; JASKOVA, Z; BRYCHTOVA, Y; PARUCH, K; TRBUSEK, M, 2016:Chk1 inhibition significantly potentiates activity of nucleoside analogs in TP53-mutated B-lymphoid cells. ONCOTARGET 7 (38), p. 62091 - 62106.
• ZEMANOVA, J; HYLSE, O; COLLAKOVA, J; VESELY, P; OLTOVA, A; PARUCH, K; TRBUSEK, M, 2016:CHECKPOINT KINASE 1 INHIBITION POTENTIATES APOPTOSIS AND INFLICTS MITOTIC FAILURE IN CLL-DERIVED MEC-1 CELL LINE. HAEMATOLOGICA 101 , p. 425 - 425.

2015

• COUVRAT-DESVERGNES, G; SALAMA, A; LE BERRE, L; EVANNO, G; VIKLICKY, O; HRUBA, P; VESELY, P; GUERIF, P; DEJOIE, T; ROUSSE, J; NICOT, A; BACH, JM; ANG, E; FOUCHER, Y; BROUARD, S; CASTAGNET, S; GIRAL, M; HARB, J; PERREAULT, H; CHARREAU, B; LORENT, M; SOULILLOU, JP, 2015:Rabbit antithymocyte globulin-induced serum sickness disease and human kidney graft survival. JOURNAL OF CLINICAL INVESTIGATION 125 (12), p. 4655 - 4665.
• KRIZOVA, A; COLLAKOVA, J; DOSTAL, Z; KVASNICA, L; UHLIROVA, H; ZIKMUND, T; VESELY, P; CHMELIK, R, 2015:Dynamic phase differences based on quantitative phase imaging for the objective evaluation of cell behavior. JOURNAL OF BIOMEDICAL OPTICS 20 (11)
• PLOSCHNER, M; KOLLAROVA, V; DOSTAL, Z; NYLK, J; BARTON-OWEN, T; FERRIER, DEK; CHMELIK, R; DHOLAKIA, K; CIZMAR, T, 2015:Multimode fibre: Light-sheet microscopy at the tip of a needle. SCIENTIFIC REPORTS 5
• SALAMA, A; COUVRAT-DESVERGNES, G; LE BERRE, L; EVANNO, G; VIKLICKY, O; HRUBA, P; VESELY, P; GUERIF, P; DEJOIE, T; NICOT, AB; BACH, JM; BROUARD, S; CASTAGNET, S; GIRAL, M; HARB, J; FOUCHER, Y; LORENT, M; SOULILLOU, JP, 2015:INCREASED LATE GRAFT LOSS IN KIDNEY RECIPIENTS WITH SERUM SICKNESS DISEASE FOLLOWING ANTI-THYMOCYTE GLOBULIN INDUCTION: RELATION WITH AN ANTI-NEU5GC RESPONSE. TRANSPLANTATION 99 (11), p. S137 - S138.
• TRUNEC, M; MACA, K; CHMELIK, R, 2015:Polycrystalline alumina ceramics doped with nanoparticles for increased transparency. JOURNAL OF THE EUROPEAN CERAMIC SOCIETY 35 (3), p. 1001 - 1009.

2014

• BOUCHAL, P; BOUCHAL, Z, 2014:Non-iterative holographic axial localization using complex amplitude of diffraction-free vortices. OPTICS EXPRESS 22 (24), p. 30200 - 30216.
• BUSBY, SA; ROBB, A; LANG, S; TAKEUCHI, Y; VESELY, P; SCOBIE, L, 2014:Antibiotic susceptibility and resistance of Staphylococcus aureus isolated from fresh porcine skin xenografts: Risk to recipients with thermal injury. BURNS 40 (2), p. 288 - 294.
• LOST'AK, M; CHMELIK, R; SLABA, M; SLABY, T, 2014:Coherence-controlled holographic microscopy in diffuse media. OPTICS EXPRESS 22 (4), p. 4180 - 4195.
• MESTAK, O; MATOUSKOVA, E; SPURKOVA, Z; BENKOVA, K; VESELY, P; MESTAK, J; MOLITOR, M; POMBINHO, A; SUKOP, A, 2014:Mesenchymal Stem Cells Seeded on Cross-Linked and Noncross-Linked Acellular Porcine Dermal Scaffolds for Long-Term Full-Thickness Hernia Repair in a Small Animal Model. ARTIFICIAL ORGANS 38 (7), p. 572 - 579.

2013

• BOUCHAL, P; BOUCHAL, Z, 2013:Concept of coherence aperture and pathways toward white light high-resolution correlation imaging. NEW JOURNAL OF PHYSICS 15
• BOUCHAL, P; BOUCHAL, Z, 2013:Wide-field common-path incoherent correlation microscopy with a perfect overlapping of interfering beams. JOURNAL OF THE EUROPEAN OPTICAL SOCIETY-RAPID PUBLICATIONS 8 (13011)
• MATOUSKOVA, M; VESELY, P; DANIEL, P; MATTIUZZO, G; HECTOR, RD; SCOBIE, L; TAKEUCHI, Y; HEJNAR, J, 2013:Role of DNA Methylation in Expression and Transmission of Porcine Endogenous Retroviruses. JOURNAL OF VIROLOGY 87 (22), p. 12110 - 12120.
• NIZAR, K; UHLIROVA, H; TIAN, PF; SAISAN, PA; CHENG, Q; REZNICHENKO, L; WELDY, KL; STEED, TC; SRIDHAR, VB; MACDONALD, CL; CUI, JX; GRATIY, SL; SAKADZIC, S; BOAS, DA; BEKA, TI; EINEVOLL, GT; CHEN, J; MASLIAH, E; DALE, AM; SILVA, GA; DEVOR, A, 2013:In vivo Stimulus-Induced Vasodilation Occurs without IP3 Receptor Activation and May Precede Astrocytic Calcium Increase. JOURNAL OF NEUROSCIENCE 33 (19), p. 8411 - 8422.
• ROSEL, D; BRABEK, J; VESELY, P; FERNANDES, M, 2013:Drugs for solid cancer: the productivity crisis prompts a rethink. ONCOTARGETS AND THERAPY 6 , p. 767 - 777.
• SCOBIE, L; PADLER-KARAVANI, V; LE BAS-BERNARDET, S; CROSSAN, C; BLAHA, J; MATOUSKOVA, M; HECTOR, RD; COZZI, E; VANHOVE, B; CHARREAU, B; BLANCHO, G; BOURDAIS, L; TALLACCHINI, M; RIBES, JM; YU, H; CHEN, X; KRACIKOVA, J; BROZ, L; HEJNAR, J; VESELY, P; TAKEUC, 2013:Long-Term IgG Response to Porcine Neu5Gc Antigens without Transmission of PERV in Burn Patients Treated with Porcine Skin Xenografts. JOURNAL OF IMMUNOLOGY 191 (6), p. 2907 - 2915.
• SLABY, T; KOLMAN, P; DOSTAL, Z; ANTOS, M; LOST'AK, M; CHMELIK, R, 2013:Off-axis setup taking full advantage of incoherent illumination in coherence-controlled holographic microscope. OPTICS EXPRESS 21 (12), p. 14747 - 14762.
• TYC, M; KVASNICA, L; SLABA, M; CHMELIK, R, 2013:Numerical refocusing in digital holographic microscopy with extended-sources illumination. OPTICS EXPRESS 21 (23), p. 28258 - 28271.

2012

• ANTOS, M; COLLAKOVA, J; VESELY, P; CHMELIK, R; KRIZOVA, A, 2012:System for coherence-controlled holographic microscopy of living cells. 18TH CZECH-POLISH-SLOVAK OPTICAL CONFERENCE ON WAVE AND QUANTUM ASPECTS OF CONTEMPORARY OPTICS 8697
• BOUCHAL, P; BOUCHAL, Z, 2012:Selective edge enhancement in three-dimensional vortex imaging with incoherent light. OPTICS LETTERS 37 (14), p. 2949 - 2951.
• HENZLOVA, M; LOST'AK, M; CHMELIK, R, 2012:Theoretical study of coherence-controlled holographic microscopy in the presence of scattering media. 18TH CZECH-POLISH-SLOVAK OPTICAL CONFERENCE ON WAVE AND QUANTUM ASPECTS OF CONTEMPORARY OPTICS 8697
• CHMELIK, R, 2012:Coherent Imaging with Incoherent Light in Digital Holographic Microscopy. 18TH CZECH-POLISH-SLOVAK OPTICAL CONFERENCE ON WAVE AND QUANTUM ASPECTS OF CONTEMPORARY OPTICS 8697

2011

• CHMELIK, R, 2011:Advances in Digital Holographic Microscopy: Coherence-Controlled Microscope. HOLOGRAPHY: ADVANCES AND MODERN TRENDS II 8074

2010

• BRABEK, J; MIERKE, CT; ROSEL, D; VESELY, P; FABRY, B, 2010:The role of the tissue microenvironment in the regulation of cancer cell motility and invasion. CELL COMMUNICATION AND SIGNALING 8
• LOST'AK, M; KOLMAN, P; DOSTAL, Z; CHMELIK, R, 2010:Diffuse light imaging with a coherence controlled holographic microscope. 17TH SLOVAK-CZECH-POLISH OPTICAL CONFERENCE ON WAVE AND QUANTUM ASPECTS OF CONTEMPORARY OPTICS 7746
• TYC, M; CHMELIK, R, 2010:Numerical Refocusing of Planar Samples Unlimited. 17TH SLOVAK-CZECH-POLISH OPTICAL CONFERENCE ON WAVE AND QUANTUM ASPECTS OF CONTEMPORARY OPTICS 7746
• ZIKMUND, T; KVASNICA, L; UHLIROVA, H; LOVICAR, L; CHMELIK, R, 2010:Dynamical Deformation Compensation of Phase in Digital Holographic Microscopy. 17TH SLOVAK-CZECH-POLISH OPTICAL CONFERENCE ON WAVE AND QUANTUM ASPECTS OF CONTEMPORARY OPTICS 7746

GRANTY

• Advances incoherent holographic microscopy using photonic simulations and principles of singular optics (GA15-14612S), Czech Science Foundation - Standard Grants, 2015 - 2017
• Validation of digital holographic microscope in investigations of living cell dynamics & completion of new multifunctional instrument (GA202/08/0590), Czech Science Foundation - Standard Grants, 2008 - 2010
• Image reconstruction of three-dimensional objects by the methods of the holographic confocal microscopy (GA202/04/1410), Czech Science Foundation - Standard Grants, 2004 - 2006
• The significance of fast intracellular motile reactions in living cells (GA304/99/0368), Czech Science Foundation - Standard Grants, 1999 - 2001
• Inorganic nanomaterials and nanostructures: fabrication, characterization, properties (MSM0021630508), MEYS - Institutional Research Plan, 2005 - 2011

CURRENT RESEARCH INFRASTRUCTURE

• first generation of coherence-controlled holographic microscopes: transmitted-light system adapted for live-cell time-lapse observations (heated box, flow chambers, anti-vibration system), reflected-light system, image-processing SW for on-line holographic reconstruction and evaluation of quantitative phase contrast
• microscopes: Nikon Eclipse TI A1R MP inverted confocal system (fluorescence, DIC, RIC, Tokai-Hit stage-top incubator), Nikon Eclipse TS100 inverted phase-contrast microscope, Nikon Eclipse L150 with reflected light (BF, DF, DIC, fluorescence microscopy), Nikon Alphaphot 2, Confocal 2002 tandem-scanning reflected-light confocal microscope, NIS elements image-processing SW
• basic facilities for cell-culture (GMO approved) and sample preparation: biohazard box, thermal box, centrifuge Rotofix, phase-contrast microscope
• complete equipment for research and development in the field of advanced light microscopy: optical design and simulation software, optical tables, opto-mechanical components, optical kits, halogen, xenon and laser sources, digital cameras, SLM