1. Microscopy is about a combination of resolution (seeing smaller and smaller things), and contrast (seeing what you want to see).
Both aspects have recently seen great advancements, with the advent of single molecule studies (in dilute solutions) and super-resolution, beating the Abbe-limit. Here, we will treat both aspects, starting with contrast agents that are either added or that occur naturally.

2. Contrast
- Polarization, birefringence
Fluorescence lifetime
Fluorescence transfer
Fluorescence recovery
Resolution/Contrast
Two Photon Microscopy
Single plane illumination
Resolution
Stimulated Emission Depletion
Structured Illumination
Total internal reflectance
Scanning near field

3. Polarization microscope
- 450
450
opt. axis d
n||
BS compensator
Polarizer
Analyzer
ellipticity f(d) = (n|| – n ) d/l
optical axes
Babinet Soleil compensator:
adjustable phase retarder

4. Results in conoscopic figures
Problem!
cholesteric liquid crystals
nematic liquid crystals

5. Twisted liquid crystal cell = polarization switch = light switch - can be used as a filter
(Kerr effect)
Used in flat screens (TV, notebooks, beamers…) ,
TFT LCD = thin film transistor liquid crystal display

6. Birefringence microscope
Birefringence modulator (Kerr effect on nematics) = tunable retardance device
full ‘index ellipsoid’ image by measuring intensities for 4 different incident polarization states

7. How to determine the sign of the phase
I = A sin2 f  A f2
I+ = A sin2 (f+a)
I- = A sin2 (f-a)
I0 = A sin2 f
a I+ - I-
f =
2 I- - 2 I0 + I+

9. Birefringence image is INDEPENDENT of orientation of optical axis
Microtubule aster image
White: 0.3nm retardance

10. movie

11. Fluorescence
Fluorescence principle
Vibrational states

12. Light basically interacts with the electrons in a given material
Light basically interacts with the electrons in a given material. The photons making up the light in Quantum mechanics can be absorbed, if there is an electron state at the energy corresponding to the absorbed energy of the photon.
Once a photon is absorbed and the electrons are excited, they can either relax via collisions and vibrations or by emitting another photon. In case the electron relaxes before emitting another photon, there is fluorescence.

13. Natural proteins for fluorescence studies
Green fluorescent protein (GFP)

14. Fluorescence lifetime microscopy (FLIM)
Lifetime image
A. GFP-tagged protein B. YFP- tagged protein C & D. Both GFP and YFP tagged proteins. The colour bars show the calibration of fluorescence lifetime from approx 2.1ns (red) to 3.0ns (dark blue).

19. Measuring viscosities using FLIM

20. Measuring temperatures using FLIM

21. Forster resonance energy transfer (FRET)
Overlap of emission and absorption spectra of flouorophores can be used to obtain information on their distance

22. FRET measures distance changes in the nanometer scale, a relevant length scale for many biomolecules.

24. Histone phosphorylation (specific for serine 28 on histone 3) in living HeLa cells undergoing cell division. Red signifies high FRET (and high phosphorylation levels), blue signifies low FRET (and low phosphorylation levels), and green is intermediate. The reporter displays a rapid increase in FRET 5-15 minutes after breakdown of the nuclear envelope.

25. Functional studies using FRET on single molecules in real time
Time record of folding and unfolding of an RNA molecule hairpin ribozyme. We attach the donor (green) and acceptor (red) dyes to the RNA so that the folded state has high FRET and the unfolded state has low FRET. We can see this beautiful two-state fluctuations in FRET values as a function of time

27. Fluorescence recovery after photobleaching (FRAP)

28. Recovery of fluorescence due to diffusion of unbleached molecules into illuminated regions after time t = d2/2Ds

29. Two photon fluorescence microscopy
Principle of 2 photon fluorescence
Radiationless decay
fluoro
2 NIR photons are absorbed simultaneously
weakest absorption
Best penetration near 1000nm

30. Typical two photon fluorescence setup
High intensity required !
2 hv excit
Fluorescence detection

32. Selective plane illumination microscopy (SPIM)

33. Scanning SPIM (DLSM)
Allows for faster scanning and induces less photons to the sample, since only a single line is illuminated. Long-time imaging becomes possible.

34. Movie of Zebrafish embryo nuclei

35. Stimulated emission depletion (STED) microscopy

36. Typical setup

39. Standing wave illumination microscopy (SWIM)

40. Also beats the Abbe limit

41. Total internal reflection (fluorescence) microscopy TIRMz
Evanescent light wave I0, decays exponentially with distance z from surface I0 ~ exp(-az)
Fluorescence intensity I(z) ~ I0
z(t) ~ - ln I(t), fluctuating position
Distribution p(z) ~ exp (-F(z)/kT)
Typical potential energy curves of a negatively charged polystyrene sphere(R=5 µm) close to an equally charged glass surface as a function of the separation distance between the glass and the particle surface. For large particle-surface separations the interaction potential is dominated by gravity which can be seen in the linear behavior of the potential curve in this regime, whereas at small separations the repulsive Coulomb interaction dominates. The potential curves are plotted for particles with different weights

42. Optical near field microscope (SNOM)
D < l
“near field “

43. Recap Microscopy is all about resolution AND contrast.
Birefringence gives information on molecular properties.
Fluorescence lifetime and transfer can be used as contrast agents.
Contrast (and resolution) enhancement can be obtained by two-photon excitation and single plane illumination.
Resolution increase is possible by using structured illumination and ingeneous fluorescence excitation.

44. Photoelasticity