Experimentální biofotonika - 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

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

seznam / vizitky

Jméno a pozice	E-mail	Telefon
Ing. Matěj Týč, Ph.D. Junior researcher		+420 54114 2789
Mgr. Alena Vojkůvková Administrativní pracovnice		+420 54114 2833
MUDr. Pavel Veselý, CSc. Senior researcher
Ing. Lukáš Kvasnica, Ph.D. Junior researcher		+420 54114 2816
prof. RNDr. Jiří Komrska, CSc. Senior researcher		+420 54114 2826
Ing. Pavel Kolman, Ph.D. Junior researcher		+420 54114 2816, +420 723 124 504
Ing. Hana Uhlířová, Ph.D. Junior researcher		+420 54114 2833
prof. RNDr. Jiří Petráček, Dr. Senior researcher		+420 54114 2764, +420 726 812 764
Ing. Martin Antoš, Ph.D. Junior researcher		+420 54114 2778, +420 726 812 778
Ing. Petr Bouchal, Ph.D. Výzkumný pracovník junior		+420 54114 2778
Ing. Zbyněk Dostál, Ph.D. junior researcher		+420 54114 2833, +420 54114 2778
prof. RNDr. Radim Chmelík, Ph.D. Senior researcher		+420 54114 2795, +420 604 072 795
Ing. Lenka Štrbková Ph.D. student		+420 54114 2789
Ing. Daniel Zicha, CSc. senior researcher
Mgr. Veronika Jůzová Technický pracovník - laborant
Ing. Michala Slabá Ph.D. student		+420 54114 2833
Ing. Aneta Křížová Ph.D. student		+420 54114 2789
Mgr. Tereza Chmelíková Ph.D. student
Mgr. Lucie Klusoňová Ph.D. student
Ing. Michala Slabá

VYBRANÉ PUBLIKACE

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

• Pokroky nekoherentní holografické mikroskopie při použití fotonických simulací a principů singulární optiky (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