2. Optical Microscopy 2.1 Principles A microscope is in principle

2. Optical Microscopy
2.1 Principles
A microscope is in principle nothing else than a simple lens system for magnifying
small objects. The first lens, called the objective, has a short focal length (a few mm),
and creates an image of the object in the intermediate image plane. This image in turn
can be looked at with another lens, the eye piece, which can provide further
Figure 2.1 : Principle scheme of an optical microscope. The objective lens has a much shorter focal
length than the eye-piece, in order to magnify the intermediate image (usually by a factor 40-100).
The resolution of the image is limited by diffraction. The Abbe-Rayleigh criterion
states that, for a wavelength  , the smallest distance d min resolvable between two
point sources in the object plane, as deduced from diffraction theory, is :
d min  1.22 
2 NA
where NA  n  sin  is called numerical aperture of the objective lens. n is the index
of refraction in the object space, and  half the maximal angle under which the
objective lens collects light from the object. This relation is equivalent to a Fourier (or
Heisenberg) relation applied to space and transverse wavevector K  n
sin  . The
numerical aperture should be as large as possible for two different reasons :
i) the spatial resolution improves for larger NA
ii) the collection efficiency, i.e. the brightness of the image, increases very quickly
with NA, quadratically for small apertures. The fraction of light collected for an
isotropic light source is :
 1
 1  cos   
4 2
1 1  1  NA / n 2  .
2 
Figure 2.2 : Variation of the collection
solid angle with numerical aperture NA.
The increase is quadratic for low NA, and
becomes even steeper for larger NA’s.
Therefore, the main difficulty in manufacturing microscope objectives is to achieve a
good correction of all aberrations (spherical, chromatic) also for off-axis rays with
angles which can be larger than 60°. This is achieved by assembling a large number
of lenses (sometimes more than 10), which have to be anti-reflection-coated for a
good luminosity. Good microscope objectives are therefore quite advanced and
expensive pieces of technology. Immersion oil objectives reach a NA of 1.4,
corresponding to collection angles of 70° or more.
An ideal microscope lens will therefore image a point source as an Airy pattern, if a
circular iris or diaphragm limits the aperture. The point-spread function (PSF) has
therefore the classical form of the diffraction spot from a round hole. If the light
collected is a Gaussian beam instead, the PSF is a Gaussian spot.
Figure 2.3: Angular
distribution of the
field in the lens
aperture and Fourier
transform intensity
distribution in the
image plane (pointspread function)
In the axial direction, the size of the PSF is approximately :
, and is known as the
depth-of-focus or Rayleigh length. The 3D appearance of the PSF is thus an elongated
(prolate, or cigar-shaped) ellipsoid. Decreasing this length is the third reason why the
numerical aperture should be as high as possible. A shorter Rayleigh length means a
stronger rejection of out-of-focus sources of background.
The numerical aperture is inversely proportional to the object refraction index.
Therefore, it is of advantage to collect light through glass, or through high-index oil,
whenever possible. Special water-immersion objectives are used for biological
samples. To fully benefit from high index, the index must of course be matched
between sample and objective glass. This is achieved thanks to immersion oil. A
further advantage of immersion is the higher efficiency of fluorescence collection. An
air gap leads to light losses by total internal reflection at the interface from high- to
low-index media.
Figure 2.4 : Importance of
immersion to collect light from an
emitter in a high-index medium. In
the case of an air gap, much light
is lost by total internal reflection at
the air-sample interface.
For emitters placed at an air-glass interface, the situation is even worse, as a large
fraction of the emitted light (up to 90%) is sent into the high-index material.
Collecting emission on the air side therefore entails a big loss of intensity.
2.2. Correction of aberrations
The ideal microscope objective would image a planar object onto a plane field
(aplanetism), without distortion, and without change in image with wavelength
(achromatism). To achieve this, the following aberrations must be corrected :
i) chromatic aberrations from the dispersion of glasses (their refractive index is larger
for blue than for red light). Even with well-corrected objectives, the focus often
moves by some microns when the wavelength varies over the visible spectrum.
ii) geometrical aberrations : spherical (change of focal point with distance from axis),
coma, due to changes of the image point with ray direction, field curvature (image
focussing is not obtained on a plane but on a curved surface), field distortion
(pincushion or barrel images), etc.
Figure 2.5 : Some geometrical aberrations : spherical aberration (left), leading to coma for off axis
rays (middle). Focussing on a spherical field (left) instead of a planar one, image deformation as a
pincushion or barrel (right)
Simple spherical lenses made out of ordinary dispersive glass suffer from all these
aberrations and cannot fulfil the requirements of the ideal lens for large numerical
apertures. For example, a plano-convex lens has spherical aberrations which are
minimized by placing the convex surface on the side of the parallel beam. Aspheric
singlets used in CD readers correct in principle perfectly for their focus, but they work
only at one wavelength and have strong chromatic aberrations. To approximate the
ideal lens’ requirements, one uses combinations of spherical lenses possessing various
radii of curvature, thicknesses, and materials, and one varies their positions. To design
objectives and other multilens systems, special codes calculate imaging with rays far
from paraxial for arbitrary systems of lenses. A good objective may contain as much
as 10 lenses, which have to be positioned with specifications as narrow as microns for
some of them. The air-glasses interfaces have to be anti-reflection coated to reduce
reflection losses, and small gaps between the lenses are bridged with a high-index
medium, usually UV-polymerizable glue, after the respective position of the lenses
has been adjusted by hand. Therefore, objective lenses are expensive and sensitive
optical components.
Nowadays, most objectives are infinity-corrected. This means that they are not
calculated to form their image directly in the intermediate image plane, but to form an
image at infinity. Another lens called tube lens, then images the plane waves into the
intermediate image. Some manufacturers use the tube lens to correct some
aberrations. In that case, tube lens and objective must be used in combination for
optimal correction. The advantages of infinity-corrected objectives are essential in
confocal microscopy, polarization studies and spectroscopy, because plane waves are
easier to filter and manipulate than spherical waves (for example they are not
distorted by flat windows).
Figure 2.6 : Schematic principle of a microscope with infinity-corrected objective lens. The tube lens is
used to obtain the intermediate image, which can then be seen with the eye piece.
2.3. Polarization structure at the focus
The electric field of a laser wave is a vector quantity, which gives rise to a
complicated polarization structure in the case of high numerical aperture. We will
briefly discuss the polarization of the field at the focus of a linearly polarized laser
wave. For low NA, the polarization of the spot is the same as that of the incident
beam. At the focal point itself, by symmetry, the polarization is also the same. At high
NA, however, and for parts of the PSF away from the focus, interference of the
incoming rays leads to deviations from this polarization. For large incidence angle
and a linearly polarized incident beam, a simple drawing shows that the longitudinal
(i.e., axial) component of the field presents two (weak) lobes in the focal plane, with a
node in the center. The third transverse component (perpendicular to the axis and to
the incoming polarization) is even weaker and presents four lobes. By using annular
illumination, and/or by introducing phase masks in the incoming beam, the
polarization of exciting laser light at the focus can be manipulated, and can even
present a PSF with a single lobe for the longitudinal polarization. This is of great
interest to determine the 3D orientation of single absorbers, since the transverse
polarization can be probed with linearly polarized light and normal illumination.
Figure 2.7 : Polarization of light focused from a linearly polarized beam. In the center of the PSF, the
polarization is conserved (left). Away from the center, optical path differences lead to a longitudinal
component of the field (middle). By introducing a retardation plate on part of the rays, the polarization
can be manipulated, for example to obtain a strong longitudinal component with a single lobe. The
intensity distributions are schematically represented in the lower part of the figure.
A similar, but distinct problem is to find the polarization structure of a wave radiated
by a linear dipole at the focus, and collimated into a plane wave by an objective with
large numerical aperture. In the case of a dipole lying in the focal plane, it can be
shown (Fourkas Opt. Lett. 2001) that the polarization is linear throughout the field,
parallel to the dipole along the horizontal and vertical directions (N, S, E, W), and
significantly tilted in the NW, NE, SW, SE positions. In the case of a dipole
perpendicular to the focal plane, the polarization is radial.
2.4. Various microscopy methods :
There are several ways to record images with a microscope. We briefly mention the
most important ones for single-molecule studies:
i) confocal microscopy : in this method, only one point of the sample is imaged onto a
photodetector. If the sample is moved in 3 dimensions, a 3D image is recorded. To
reduce background, i.e. to insure that the signal arises only from the focus, a
diaphragm or pinhole is inserted in one of the image planes. To scan the area to be
imaged, one can move either the sample itself with piezo-electric transducers (sample
scanning), or the focus by means of tilting mirrors (beam scanning).
Figure 2.8 : Confocal microscope with sample scanning. The signal intensity is recorded as a function
of the position of the sample.
Figure 2.9 : Confocal microscope with mirror scanning . The scanning mirrors deflect the illumination
beam in two orthogonal directions. The telecentric system images the laser spot on the mirror (or
mirrors, in which case these mirrors have to be as close to each other as possible) on the entrance lens
of the objective. The backwards traveling detection beam of course is refolded by the mirror(s)
precisely onto the incoming path.
ii) wide-field imaging : in this method, a large part of the field is illuminated by an
unfocused beam (epi-illumination), and the image is formed on a multi-channel
detector such as a CCD camera or an image intensifier. In that case background arises
from emissions below and above the imaged plane of the sample. This background
can be significantly reduced by imaging Ronchi rulings in the focal plane and
subsequent composition of two or three images. Such rulings are also used in
structured-illumination microscopy to improve the resolution by a factor of up to two.
iii) To reduce the background, the excitation light can be sent at a large incidence
angle on the surface, achieving total internal reflection (TIR). Fluorescence and other
emissions can be collected either on the other side of the interface, or on the same side
as the illumination. In that case, an immersion objective with large N.A. is of course
Figure 2.10 : Illumination of a sample by total internal reflection, either with a high-index prism in the
case of a low index sample (left), or via the objective lens itself in the case of a sample close to an
interface to a lower index (air or water, right).
Confocal microscopy is particularly useful to detect single molecules. The design has
the advantage that only the focus is excited with high efficiency, and that fluorescence
arising from other points does not reach the detector. The spatial selection is therefore
performed in two steps, with equivalent performance:
- excitation selection, by focusing the laser beam on a small spot,
- detection selection, by detecting from the same area only.
Several other optical designs have been developed in the last twenty years with
various elements for excitation and collection : single mode optical fiber, parabolic
mirror, aspheric lenses, gradient index lenses, etc.
Figure 2.11 : Various elements used in single-molecule optics, besides microscope objectives.
2.5. Near-field optics :
To improve the resolution of optical microscopic images, and to reduce the selected
volume in single-molecule studies, it is of great advantage to reduce the spot size
below the Abbe diffraction limit. Optics at ranges smaller than the wavelength are
called near-field optics. To produce and analyze optical fields with variations less
than  , interaction with microscopic objects is necessary. Near-field optics thus has
to use small objects, usually tips or small apertures, to enhance or constrain the optical
field. It has therefore much in common with scanning probe microscopies (STM and
AFM): the scanning procedure, the importance of the tip, the stability requirements;
However, the slow spatial variations of the optical field make it much more difficult
to interpret and model the images obtained.
Figure 2.12 : Structure of a currently used SNOM
tip. Incident light propagates in the core of a singlemode fiber, and reaches the tip. A small part of it is
guided to the end and produces an evanescent wave
around the aperture. Part of the light is also
radiated in the far field across the aperture.
A common way to confine the optical field is to stretch an optical fiber, so as to obtain
a conical tip, and to coat it with a thin, but opaque metal layer, usually aluminum. The
end of the fiber is uncoated, and is therefore a small pinhole through which an
evanescent light wave can pass. Alternatively, the end of the fiber can be cut with an
ion milling machine (FIB). The diameter of the hole is often 50-100 nm. The
transmission decreases very rapidly with diameter, approximately like the 6th power
for small sizes. For a 20 nm diameter, the transmission does not exceed 10 6 . A
scanning near-field optical microscope (SNOM) can be used in excitation (via the
fiber) or detection (or pick-up) mode. To detect fluorescent single molecules, it is
important not to irradiate the sample too long, therefore the excitation mode is
preferable. The tip is scanned across the sample, and the total fluorescence is
collected by an auxiliary optics (a microscope objective) as a function of tip position.
While scanning, the distance between tip and surface must be kept constant. Several
methods can be used, among which shear-force AFM is very common. To detect the
weak force from the substrate, the tip is glued to a tuning fork. The presence of the
surface manifests itself by a shift and broadening of the fork’s resonance. The phase
of the oscillation can also be used as error signal for the stabilization of the tip’s
Figure 2.13 : Optical path in a SNOM where the tip
is used for excitation. Detection is done in far-field,
by means of a microscope objective. The distance of
the tip to the sample is regulated by atomic-force
microscopy, detecting the change in oscillation of
the tuning fork carrying the tip.
A SNOM gives in principles access to spatial resolutions less than 100 nm, as was
demonstrated by van Hulst’s group; However, the operation of a SNOM is much more
demanding than that of a far-field confocal microscope, and in many cases,
particulary in single-molecule studies, the increase in resolution does not justify the
additional work. Moreover, low temperatures are even more difficult, and fluorescent
objects below the surface cannot be accessed in near-field.
A recent development of near-field optics is plasmonics, in which resonances of the
metal structures for surface plasmon resonances give rise to strongly enhanced and
localized fields. These plasmonic effects will be briefly described in the last chapters
in the case of metal nanoparticles.
Exercise 2.1: Use the Gaussian beam formulas below to find the above-mentioned
depth of focus (also called Rayleigh length L  
E ( x, y, z )  E0
) in the axial direction.
 ( z ) ikz
e exp   ( z )( x 2  y 2 )  ,
 w02  2i .
 ( z)
(express the beam waist w0 as a function of the half-aperture angle  , and use the
paraxial approximation tan   sin  ).
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