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Absorption 14, 16–18, 61, 67, 85–89, 106, 136, 140, 141 473 Index a beam aberrations 332 absorption 14, 16–18, 61, 67, 85–89, beamlets 466 106, 136, 140, 141, 149, 153, 157, beam propagation 466 166, 188, 208, 212–214, 218, 223, beam splitter 311 226, 230, 236, 255, 274, 276, 348, O2 benzylcytosine (BC) 145 389, 394, 397, 408, 410–412, 416, Bessel beam 262 419, 420, 448, 449 Bessel function 38 Abbe’s diffraction limit 368 bioluminescence 95 absorption dipole moment 416 binning 106 acceptor density 426–428 biplane imaging approach 284 acceptor emission filter 431 birefringence 13 acceptor fluorophores 413 bleaching 120 acousto-optical modulator (AOM) 345 blue-shifted dye 334 Airy disk 38, 41–44, 48 Bragg condition 33 Airy disk radius 458 Braun tubes 181 Airy pattern 173, 174 bright field 31–32, 44, 45, 61, 70, 71, angle of incidence 376 73, 74 angleofrefraction 377 brightness 28, 29, 57–62, 67, 74, 76, 80 animalcules 165 astigmatic imaging approach 281–284 astigmatism 21 c ATTO647N 325, 337 camera acquisition software 456 autocollimation telescope 468 carbocyanines 275, 281 autocorrelation function (ACF) 188, cell membrane glycans 283 189, 191, 192, 199 centrosomes 287 autofluorescence 381 charge-coupled device (CCD) 26, 104, Avalanche photodiode (APD) 114 107, 112, 273, 386–387 Avogadro’s number 412 Chinese hamster ovary (CHO) 381 axial resolution 45, 47, 173–179 chromatic reflectors 18–19 chromophore 274 b click chemistry 281–283 back focal plane (BFP) 249, 472–473 cluster size 397 ballistic light 377 coherent beams 295 bandpass filter 324, 326 colliding-pulse mode-locked (CPM) Bayesian statistics 404 218 Fluorescence Microscopy: From Principles to Biological Applications, Second Edition. Edited by Ulrich Kubitscheck. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2017 by Wiley-VCH Verlag GmbH & Co. KGaA. 474 Index complementary dichroic mirror 96, 97, 102, 375 metal–oxide–semiconductor dichromatic beam splitter 468 (CMOS) 111, 112, 388 dielectric mirrors 16–17 confocal effect 346 differential interference contrast (DIC) confocality 302 13, 23 confocal laser scanning microscope interpretation 81 (CLSM) 342 optical setup 77 confocal scanning microscopy 165, differential interference microscopy 247, 261, 429 77–80 conjugation process, synthetic different lens configurations 259–260 fluorophores 142 diffraction 1, 7, 323, 324, 326, 327 continuous fluorescence coefficients 341, 342, 346 microphotolysis (CFM) 343 limit 269, 270 continuous fluorescence photobleaching pattern 33, 34, 36 343 diffusion-enhanced energy transfer continuous illumination 358 424 continuous wave (CW) 167, 172, 329 diffusion-reaction equation 351, 355 conventional dual-color imaging scheme diffusion time 188 334 digital camera, fluorescence microscopy conventional fluorescence microscopy 113 techniques 264 digitally scanned light sheet microscopy convolution 41 (DSLM) 246, 248 convolution theorem 294, 298 4,4′-diisothiocyanatostilbene-2, copper-catalyzed azide–alkyne 2′-disulfonic (DIDS) 352 cycloaddition 282 dipole–dipole distance 414 Coulombic coupling 411, 414 dipole moments 414, 416 Coulomb’s law 414, 418 Dirac delta distribution 298 coupling FRET 425 discovery, fluorescence of 91–92 critical angle 378 discriminator 172 critical illumination 28–30 dispersion 9 crystallography techniques 422 donor fluorophores 425 cut-off frequency 295, 302 donor emission spectrum 412 cyan fluorescent protein (CFP) 152, donor excitation filter 431 423 donor quantal spectrum 412 cylindrical lens 246, 248 donor quantum yield 412, 417, 431, d 438, 440 DAOSTORM 287 donor quenching (DQ) 428–429, 432 Davson–Danielli–Robertson model double helix PSF 284 341 double-sided illumination 253, 254, defocused imaging 395 258 Deinococcus radiodurans 150 doughnut-shaped depletion beam depth of field (DOF) 49, 81, 392 335 depth of focus 49, 256, 313, 392 dSTORM 275, 282 detection, PSFs 175 dual-color imaging 334 development, confocal microscopy dual-view system 375 169 dynamic imaging 373 Index 475 e fluorescence photobleaching techniques electrically tunable lenses (ETLs) 248, CLSMs-assisted photobleaching 256 methods electromagnetic radiation 391, 408 implementation 358–359 electronic delay 332 opportunities 359 electronic filters 103 concepts and procedures electron-multiplying charge-coupled complexity from bottom up device (EM-CCD) 109, 387 346–347 emission dipole 416, 417 principle and several modes emission spectrum 90, 99, 411 340–345 epifluorescence 98 set up 345–346 epi-illumination 31–32 continuous fluorescence equilibrium properties, fluorescence microphotolysis (CFM) emission 88–89 background and data evaluation excitation, PSFs 175 354–357 excitation filter 101 combination of 357 excitation light distribution 311–313 variants 357–358 excited state 325, 327 fluorescence recovery after exciting light intensity 99, 122–123 photobleaching (FRAP) exciting photon 89 binding 350–351 diffusion measurements f 347–350 Fermi’s golden rule 414, 416 membrane transport 351–354 field of view (FOV) 247, 248 fluorescence photon 88 finite optics setup 25 fluorescence quantum yield 136, 147 FlAsH 148 fluorescence recovery after fluid mosaic model 341 photobleaching (FRAP) 160, fluorescein 410 341 fluorescence confinement 326 fluorescent labels fluorescence correlation spectroscopy characteristics 134 (FCS) 172, 354 properties 133, 135, 142 fluorescence cross-correlation sensors in cell 160 spectroscopy (FCCS) 190 fluorescent protein (FPs) 152, 156, fluorescence depletion 326 324, 329, 337 fluorescence emission 272, 300 fluorophore 270, 407 depolarization of 428 classes of 337 fluorescence excitation 293 emission spectrum 326, 336 fluorescence filter 246 excitation 326 fluorescence intensity, measurements of kinetics 328 119–121 photoactivatable/photoconvertible fluorescence labeling 368 272 fluorescence lifetime changes 437–441 photobleaching 270, 355 fluorescence markers 157 photon number 280 fluorescence microscopy 86, 90–95, photoswitchable 273 299 property of 342 fluorescence photobleaching recovery reaction-induced photoswitching (FPR) 341 273 476 Index fluorophore (contd.) green fluorescent protein (GFP) 150, rhodamine 275 281, 368, 410 ROP 354 grid projection 295 for STED microscopy 337 stimulated emission depletion 324 h flux equation 356 hetero-FRET 413 focal lengths 251 high-pressure mercury vapor focal plane 250, 260, 471–472 arc-discharge lamps (HBO) 99 Förster distance 413, 420 burners 100 Förster equation 414–418 high-resolution information 300–301 Förster radius 399, 400 homo-FRET 414 Förster resonance energy transfer Huygens–Fresnel integral equation 35 (FRET) 155, 191, 369 Huygens wavelet 37 Fourier frequency 36 i Fourier theory 41 illumination intensity (I) 381 Fourier-transformed illumination illumination microscopy 296 pattern 299 illumination pattern 298–301, 4Pi microscopy 357 303–307, 313 Fraunhofer diffraction pattern 38 illumination photons 324 frequency-domain FLIM 443–444 illumination time 381, 382 frequency spectra 415 image brightness 57 fringe distance 315 image contrast 90–93 fringe period 313 image deconvolution 184, 462 fringe projection, see two-beam image integration time 109 interference image processing operations full quantitation 433–434 focal plane 37 full width at half-maximum (FWHM) pixel groups 461–462 175, 372 single pixels 460–461 functional magnetic resonance imaging imaging artifacts 278 (fMRI) 237 imaging contrast, measures improving 285 g immersion media 62–65 Gaussian beam 250–252 immunofluorescence 281 Gaussian filters 462 immunoglobulin G antibodies 147, Gaussian function 272, 394 282 Gaussian intensity profile 348 induced acceptor emission 429–432 Gaussian photon distribution 372 infinity space 24 Gaussian-shaped signal distribution instrument response function (IRF) 390 172 geometric-optical term 176 integrator 172 global fitting approaches 446 intensified charge-coupled device gratings 34, 37, 38, 57, 330 (ICCD) 104, 107, 109 constant 8, 33, 35 intensity-based measurements, FRET distance 299, 312 432–433 structure 34 intensity distribution 173 gray values 189, 317, 455 intensity histograms 288, 459–460 Index 477 intensity zero 332 dark-field 68 interference effects DIC 77 light rays 11 interference contrast 74 pattern 304 optical contrast methods 68 interference microscopy 77 phase contrast, see phase contrast interferometer 303, 304, 309 phase objects 67 plane 306 entrance pupil 50 setup 308 exit pupil 50, 51 interferometric imaging 284–285 field-of-view 28 intermediate image 25 high resolution objectives 65 intrinsically photoswitchable probes illumination system 28 274 beam path 30 inverted microscopes 32, 473 image path 24 in vivo/in vitro measurements, FRET magnifications 26 401 CCD 26 IrisFP 154 focal length 27 isoSTED configuration 336 magnifying glass 27 multiview imaging 257–259 j numerical aperture 27 Jablonski diagram 92, 325 telecentricity 51 wave optics and resolution 32 k light propagation 377 Köhler illumination 28–30, 379, 383, light sheet fluorescence microscopy 384 (LSFM) 246 kinetic measurements, FRET 401 light sheet illumination 254, 259, 263 kinetics, fluorescence emission 88–89 light sheet microscopy construction and working 248–249 l photobleaching and toxicity 247 Lambert radiator 58 polarization 253 Lampyris noctiluca 93 principle of 246–247 laser scanning microscopes (LSMs) 3D imaging 255–357 180, 362 water-dipping illumination lens 250 label size vs. structural resolution light sources, STED 332–333 280–282 light waves 2 lateral resolution 41, 175 circular polarized 4 coherent light sources 43 on interference 2 incoherent light sources 41 plane wave 7 optical units 47 transverse wave 3 lens alignment 468 description 3 lens classes
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