Spring 2012

ECE 564 Modern Light Microscopy

Prof. Gabriel Popescu

Text: “Introduction to Optical Microscopy” by J. Mertz (Roberts and Company, 2010)

Schedule: 11:00-12:20 T-R, 245 Everitt Lab;

Teaching Assistant:

Office Hours:

Research Projects

#	Day	Date	Topic	Supporting Material	Homework	Links	References
28	T	Jan 17	Introduction	Microscopy Milestones (Nature)		1D Fourier Transforms (ECE 460)
27	R	Jan 19	Groundwork: 2D, 3D Fourier transforms	Groundwork		ImageJ	Papoulis [1], Bracewell [2], Goodman [3]
26	T	Jan 24	Groundwork: 2D, 3D Fourier transforms		HW 1
25	R	Jan 26	Propagation of Gaussian beams	Gaussian beams			Yariv- Optical waves in crystals
24	T	Jan 31	Propagation of Gaussian beams		HW2
23	R	Feb 02	Propagation of Gaussian beams	Dispersive media			Born & Wolf [4], Jackson [5]
22	T	Feb 07	Propagation in dispersive media		HW3
21	R	Feb 9	Propagation in inhomogeneous media	Light scattering			Born & Wolf [4], van de Hulst [6], Ishimaru [7]
20	T	Feb 14	Propagation in inhomogeneous media		HW4
19	R	Feb 16	Dynamic light scattering	Dynamic Light Scattering			Berne & Pecora [8]
18	T	Feb 21	Dynamic light scattering		HW5
17	R	Feb 23	Propagation in nonlinear media				Blombergen [9], Boyd [10], Shen [11]
16	T	Feb 28	Propagation in nonlinear media	No lecture (APS Meeting)- to be rescheduled;	HW6
15	R	Mar 01	Spatial and temporal coherence	No lecture (APS Meeting)- to be rescheduled Coherence			Wolf, Mandel & Wolf [12, 13], Glauber [14], Goodman- Statistical optics [15]
14	T	Mar 06	Image characteristics	Image characteristics			Webb- Biomed. Imaging
13	R	Mar 08	Intrinsic contrast microscopy: dark field, Schlerein, phase contrast, DIC, etc	Microscopy- basics			Pluta [16]
12	T	Mar 13	Intrinsic contrast microscopy: dark field, Schlerein, phase contrast, DIC, etc		HW7
	R	Mar 15	Midterm
	T	Mar 20	Spring Break
	R	Mar 22	Spring Break
11	T	Mar 27	Confocal microscopy	Confocal; Microscopy-images;			Ch. 14
10	R	Mar 29	Optical coherence tomography	OCT			Ch. 11
9	T	Apr 03	Optical coherence tomography				Ch. 12
8	R	Apr 05	Quantitative phase microscopy				Ch. 13
7	T	Apr 10	Microrheology
6	R	Apr 12	1. Green fluorescence protein (GFP) 2. Fluorescence correlation spectroscopy (FCS) 3. Total internal reflection fluorescence (TIRF) microscopy			Research Projects Peer evaluation form
5	T	Apr 17	4. Fluorescence resonance energy transfer (FRET) 5. Fluorescence recovery after photobleaching (FRAP) 6. Fluorescence Lifetime Imaging Microscopy (FLIM)				Ch. 15
4	R	Apr 19	7. Two photon fluorescence microscopy (TPFM) 8. Second harmonic generation microscopy (SHGM) 9. Coherent anti-Stokes Raman scattering (CARS) microscopy				Ch. 16
3	T	Apr 24	10. Near-field scanning optical microscopy (NSOM) 11. Stimulated emission depletion microscopy (STED) 12. Nonlinear structured illumination microscopy				Ch. 18
2	R	Apr 26	13. Super-localization: STORM/PALM/fPALM 14. Photoacoustic microscopy (PAM)				Ch. 18
1	T	May 1	REVIEW
	R	May 3	Reading Day
	R	May 5	Reports due by email	Template.

Grading formula: Midterm 30%; Final report - 20%; Homework - 30%; Presentation 20%; Class participation - 5% .

REFERENCES

[1] A. Papoulis, The Fourier integral and its applications. New York,: McGraw-Hill, 1962.

[2] R. N. Bracewell, The Fourier transform and its applications, 3rd ed. Boston: McGraw Hill, 2000.

[3] J. W. Goodman, Introduction to Fourier optics, 2nd ed. New York: McGraw-Hill, 1996.

[4] M. Born and E. Wolf, Principles of optics : electromagnetic theory of propagation, interference and diffraction of light, 7th expanded ed. Cambridge ; New York: Cambridge University Press, 1999.

[5] J. D. Jackson, Classical electrodynamics, 3rd ed. New York: Wiley, 1999.

[6] H. C. van de Hulst, Light Scattering by Small Particles New York: Dover Publications 1981.

[7] A. Ishimaru, Electromagnetic wave propagation, radiation, and scattering. Englewood Cliffs, N.J.: Prentice Hall, 1991.

[8] B. J. Berne and R. Pecora, Dynamic Light Scattering : With Applications to Chemistry, Biology, and Phys. : Dover Publications; Unabridged edition (August 14, 2000) 2000.

[9] N. Bloembergen, Nonlinear optics; a lecture note and reprint volume. New York,: W.A. Benjamin, 1965.

[10] R. W. Boyd, Nonlinear optics, 3rd ed. Amsterdam ; Boston: Academic Press, 2008.

[11] Y. R. Shen, The principles of nonlinear optics. New York: J. Wiley, 1984.

[12] L. Mandel and E. Wolf, "Coherence Properties of Optical Fields," Reviews of Modern Physics, vol. 37, p. 231, 1965.

[13] L. Mandel and E. Wolf, Optical coherence and quantum optics. Cambridge ; New York: Cambridge University Press, 1995.

[14] R. J. Glauber, "The quantum theory of optical coherence," Physical Review, vol. 130, p. 2529, 1963.

[15] J. W. Goodman, Statistical optics. New York: Wiley, 1985.

[16] M. Pluta, Advanced light microscopy. Warszawa: Polish Scientific Publishers, 1988.