158 References

Ha, T. and Tinnefeld, P. (2012). Photophysics of fluorescence probes for single molecule biophysics

and super-​resolution imaging. Annu. Rev. Phys. Chem. 63:595–​617.

Ha, T. et al. (1996). Probing the interaction between two single molecules: Fluorescence reson­

ance energy transfer between a single donor and a single acceptor. Proc. Natl. Acad. Sci. USA

93:6264–​6268.

Ha, T. et al. (2002). Initiation and re-​initiation of DNA unwinding by the Escherichia coli Rep helicase.

Nature 419:638–​641.

Hecht, B. et al. (2000). Scanning near-​field optical microscopy with aperture probes: Fundamentals

and applications. J. Chem. Phys. 112:7761–​7774.

Hell, S.W. and Stelzer, E.H.K. (1992). Fundamental improvement of resolution with a 4Pi-​confocal

fluorescence microscope using two-​photon excitation. Opt. Commun. 93:277–​282.

Hell, S.W. and Wichmann, J. (1994). Breaking the diffraction resolution limit by stimulated

emission: Stimulated-​emission-​depletion fluorescence microscopy. Opt. Lett. 19:780–​782.

Horton, N.G. et al. (2013). In vivo three-​photon microscopy of subcortical structures within an intact

mouse brain. Nat. Photon. 7:205–​209.

Huisken, J. et al. (2004). Optical sectioning deep inside live embryos by selective plane illumination

microscopy. Science 305:1007–​1009.

Jones, S.A. et al. (2011). Fast, three-​dimensional super-​resolution imaging of live cells. Nat. Methods

8:499–​508.

Kapanidis, A.N. et al. (2005). Alternating-​laser excitation of single molecules. Acc. Chem. Res.

38:523–​533.

Keller, P.J. et al. (2008). Reconstruction of zebrafish early embryonic development by scanned light

sheet microscopy. Science 322:1065–​1069.

Kneipp, K. et al. (1997). Single molecule detection using surface-​enhanced Raman scattering (SERS).

Phys. Rev. Lett. 56:1667–​1670.

Kneipp, J. et al. (2010). Novel optical nanosensors for probing and imaging live cells. Nanomed.

Nanotechnol. Biol. Med. 6:214–​226.

Kobat, D. et al. (2011). In vivo two-​photon microscopy to 1.6-​mm depth in mouse cortex. J. Biomed.

Opt. 16:106014.

Lee, S.F. et al. (2011). Super-​resolution imaging of the nucleoid-​associated protein HU in Caulobacter

crescentus. Biophys. J. 100:L31–​L33.

Levoy, M. et al. (2009). Recording and controlling the 4D light field in a microscope using microlens

arrays. J. Microsc. 235:144–​162.

Lew, M.D. et al. (2011). Three-​dimensional superresolution colocalization of intracellular protein

superstructures and the cell surface in live Caulobacter crescentus. Proc. Natl. Acad. Sci. USA

108:E1102–​E1110.

Maestro, L.M. et al. (2010). CdSe quantum dots for two-​photon fluorescence thermal imaging. Nano

Letters 10:5109–​5115.

Magde, D., Elson, E.L., and Webb, W.W. (1972). Thermodynamic fluctuations in a reacting

system: Measurement by fluorescence correlation spectroscopy. Phys. Rev. Lett. 29:705–​708.

Marrison, J. et al. (2013). Ptychography—​A label free, high-​contrast imaging technique for live cells

using quantitative phase information. Sci. Rep. 3:2369.

Miyawaki, A. et al. (1997). Fluorescent indicators for Ca2+​ based on green fluorescent proteins and

calmodulin. Nature 388:882–​887.

Monod, J. (1971). Chance and Necessity. Vintage Books, New York.

Mortensen, K.I. et al. (2010). Optimized localization analysis for single-​molecule tracking and super-​

resolution microscopy. Nat. Methods 7:377–​381.

Park, H., Toprak, E., and Selvin, P.R. (2007). Single-​molecule fluorescence to study molecular motors.

Quart. Rev. Biophys. 40:87–​111.

Prakash, R. et al. (2012). Two-​photon optogenetic toolbox for fast inhibition, excitation and bistable

modulation. Nat. Methods 9:1171–​1179.

Qu, X., Wu, D., Mets, L., and Scherer, N.F. (2004). Nanometer-​localized multiple single-​molecule

fluorescence microscopy. Proc. Natl. Acad. Sci. USA 101:11298–​11303.

Ritter, J.G. et al. (2010). Light sheet microscopy for single molecule tracking in living tissue. PLoS One

5:e11639.