Fluorescence Microscopy

Kenneth R. Spring
National Institutes of Health, Bethesda, Maryland, U.S.A.

INTRODUCTION fluorochromes (also called fluorophores), which are ex-

cited by specific wavelength irradiating light and emit
When organic or inorganic specimens absorb and sub- light of useful intensity. Fluorochromes are stains that
sequently reradiate light, the process is typically a result attach themselves to visible or subvisible structures, are
of fluorescence or phosphorescence. Fluorescence emis- often highly specific in their attachment targeting, and
sion is nearly simultaneous with the absorption of the have significant quantum yield (the photon emission/ab-
excitation light as the time delay between photon ab- sorption ratio). The growth in the use of fluorescent mic-
sorption and emission is typically less than a microsec- roscopes is closely linked to the development of hundreds
ond. When the emission persists long after the excitation of fluorochromes with known intensity curves of exci-
light is extinguished, the phenomenon is known as phos- tation and emission and well-understood biological struc-
phorescence. Stokes coined the term ‘‘fluorescence’’ in ture targets.
the middle of the 19th century when he observed that the
mineral fluorspar emitted red light when it was il-
luminated by ultraviolet (UV) excitation. Stokes noted EXCITATION AND
that the fluorescence emission always occurred at a EMISSION FUNDAMENTALS
longer wavelength than that of the excitation light. Early
investigations showed that many specimens (minerals, The basic task of the fluorescence microscope is to ir-
crystals, resins, crude drugs, butter, chlorophyll, vita- radiate the specimen with the desired wavelength and then
mins, inorganic compounds, etc.) fluoresce when irra- to separate the much weaker emitted (fluorescent) light
diated with UV light. In the 1930s, the use of fluoro- from the excitation light. Only the emission light should
chromes began in biology to stain tissue components, reach the eye or other detector so that the resulting fluor-
bacteria, or other pathogens. Some of these stains were escing areas are contrasted against a dark background.
highly specific and they stimulated the development of The detection limit is largely determined by the darkness
the fluorescence microscope. of the background. The exciting light is typically 105 or
Fluorescence microscopy has become an essential tool 106 times brighter than the emitted light.
in biology as well as in materials science as it has at- Fig. 1 is a graphical representation of the design of
tributes that are not readily available in other optical an epi-fluorescence microscope. This is basically a re-
microscopy techniques. The use of an array of fluor- flected light microscopy mode in which the wavelength
ochromes has made it possible to identify cells and sub- of the reflected light is longer than that of the excitation.
microscopic cellular components and entities with a high J.S. Ploem is credited with the development of the ver-
degree of specificity amid nonfluorescing material. The tical illuminator for reflected light fluorescence micro-
fluorescence microscope can reveal the presence of a scopy. In this device, light of a specific wavelength or set
single fluorescing molecule. In a sample, through the use of wavelengths, often in the UV, is produced by passing
of multiple staining, different probes can simultaneously light from a lamp or other source through a wavelength
identify several target molecules. Although the fluores- selective exciter filter. The desired wavelength light re-
cence microscope cannot provide spatial resolution below flects off a dichromatic (‘‘dichroic’’) mirror, through the
the diffraction limit of the respective objects, the de- microscope objective lens to the specimen. If the spe-
tection of fluorescing molecules below such limits is cimen fluoresces, the collected emission light then passes
readily achieved. through the dichromatic mirror and is subsequently fil-
There are specimens that autofluoresce when they tered by a barrier filter that blocks the excitation wave-
are irradiated and this phenomenon is exploited in the lengths. It should be noted that this is the only mode of
field of botany, petrology, and in the semiconductor in- microscopy in which the specimen, subsequent to ex-
dustry. In the study of animal tissues or pathogens, auto- citation, gives off its own light. The emitted light re-
fluorescence is often either extremely faint or nonspe- radiates spherically in all directions, regardless of the
cific. Of far greater value for such specimens are added direction of the exciting light.

548 Encyclopedia of Optical Engineering

DOI: 10.1081/E-EOE 120009628
Published 2003 by Marcel Dekker, Inc. All rights reserved.
Fluorescence Microscopy 549

Fig. 1 Cut-away diagram of an upright microscope equipped both for transmitted light and epi-fluorescence microscopy. The vertical
illuminator in the center of the diagram has the light source at one end (episcopic lamphouse) and the filter cube at the other.

Epi-fluorescence is the overwhelming choice in mo- The reflected light illuminator has, at its far end, a
dern microscopy and the reflected light vertical illumin- lamphouse containing a light source, usually a mercury or
ator is interposed between the observation viewing tubes xenon burner (the episcopic lamphouse in Fig. 1). The
and the nosepiece carrying the objectives. The illuminator light travels along the illuminator perpendicular to the
is designed to direct light onto the specimen by first optical axis of the microscope, passes through collector
passing the light through the microscope objective on the lenses and a variable, centerable aperture diaphragm, and
way toward the specimen and then using that same ob- then through a variable, centerable field diaphragm (aper-
jective to capture the emitted light. This type of illumi- tures in Fig. 1). It impinges upon the excitation filter
nator has several advantages: the objective—first serving where selection of the excitation wavelength light and
as a well-corrected condenser and then as the image- blockage of undesired wavelengths occurs. The selected
forming light gatherer—is always in correct alignment; wavelengths reach the dichromatic beamsplitting mirror.
most of the unused excitation light reaching the speci- This is a special type of interference filter that efficiently
men passes through it and travels away from the ob- reflects shorter wavelength light and efficiently passes
jective; the illuminated area is restricted to that which is longer wavelength light. The dichromatic beam splitter
observed; the full numerical aperture (n.a.) of the ob- (also sometimes called the dichroic mirror, as shown in
jective, in Koehler illumination, is utilizable; it is pos- Fig. 1) is tilted at 45° to the incoming excitation light and
sible to combine or alternate reflected light fluorescence reflects the excitation light at a 90° angle directly through
with transmitted light observation. the objective and onto the specimen. The fluorescent light
550 Fluorescence Microscopy

if the housing is inadvertently opened during operation.

The lamphouse should be sturdy enough to withstand
a possible burner explosion during operation. The lamp
socket should have adjustment screws to permit center-
ing the image of the lamp arc or halogen lamp coil to
the back aperture of the objective (in Koehler illumina-
tion, these planes are conjugate). In the light path, closer
to the lamphouse and before the excitation filter, it is
desirable to have a shutter for complete blocking of ex-
citation light as well as neutral density filters on a wheel
or slider to permit reduction of light intensity.

STOKES’ SHIFT

When electrons go from the excited state to the ground

state, there is a loss of vibrational energy. As a result, the
emission spectrum is shifted to longer wavelengths than
Fig. 2 A microscope filter cube containing the exciter and the excitation spectrum (wavelength varies inversely to
barrier filters as well as the dichromatic mirror. radiation energy). This phenomenon is known as Stokes’
Law or Stokes’ shift. The greater the Stokes’ shift, the
easier it is to separate excitation light from emission light.
emitted by the specimen is gathered by the objective, now The emission intensity peak is usually lower than the
serving in its usual image-forming function. Because the excitation peak; and the emission curve is often a mirror
emitted light consists of longer wavelengths, it is able to image of the excitation curve, but shifted to longer wave-
pass through the dichroic mirror. lengths (Fig. 3). To achieve maximum fluorescence in-
Any scattered excitation light reaching the dichroic tensity, the dye is usually excited at wavelengths near or
mirror is reflected toward the light source. Before the at the peak of the excitation curve, and the widest possible
emitted light can reach the eyepiece or detector, it is range of emission wavelengths that include the emission
incident upon and passes through the barrier or suppres- peak are selected. The selection of excitation wavelengths
sion filter. This filter blocks (suppresses) any residual and emission wavelengths is typically based on interfer-
excitation light and passes the desired longer emission ence filters. In addition, the spectral response of an optical
wavelengths. In most reflected light fluorescence illu- system will depend on such factors as glass transmission
minators, the excitation filter, dichroic mirror, and bar- and detector responsivity.
rier filter are incorporated in a cube, as illustrated in
Fig. 2. Most microscopes accommodate three or four
fluorescence cubes (on a revolving turret or on a slider
as shown in Fig. 1) and permit the user to attach re-
placement custom-made exciters, barrier filters, or di-
chroic mirrors.
The design of the illuminator should permit the user to
employ the desirable Koehler Illumination, providing
bright and even illumination across the field of view. The
corrected condensing lenses of the system ensure that the
image of the centerable aperture diaphragm is conjugate
with the back aperture of the focused objective. The
image of the prefocused, centerable field diaphragm is
conjugate with the focused specimen and the plane of the
fixed eyepiece diaphragm.
The illuminator lamphouse usually incorporates an
infrared suppression filter. The lamphouse itself should
not leak harmful UV wavelengths and, preferably, should Fig. 3 Absorption and emission spectra are shown for
incorporate a switch to automatically shut down the lamp fluorescein.
Fluorescence Microscopy 551

The separation of excitation and emission wavelengths (FRET) for studying molecular interactions and associa-
is achieved by the proper selection of filters to block or tions at distances far below the lateral resolution of the
pass specific wavelengths of the spectrum. The design of
fluorescence illuminators is based on the control of ex-
light microscope. F
citation light and emission light by readily changeable
filter insertions in the light path on the way toward the LIGHT SOURCES
specimen and then emanating from the specimen. It is
important, in view of low emission intensities, that the In most fluorescence microscopy applications, the number
light source chosen for excitation be of sufficient bright- of photons that reach the eye or detector is usually very
ness so that the relatively weak emission light can be low. This is because the collection efficiency of micro-
maximized; and that fluorochromes of satisfactory ab- scopes is less than 30% and the concentration of most
sorption and yield be chosen. fluorochromes in the optical path is low (usually mi-
The efficiency with which the fluorochrome absorbs a cromolar or nanomolar). To generate sufficient excitation
photon of the excitation light is a function of molecular light intensity to produce detectable emission, powerful
cross-section, and the likelihood of absorption is known compact light sources are needed, usually short arc lamps.
as the extinction coefficient. Larger extinction coeffi- The most common lamps are the mercury burners, rang-
cients mean that the absorption of light in a given wave- ing in wattage from 50 to 200 W and the xenon burners
length region is more likely. The quantum yield denotes ranging from 75 to 150 W. These light sources are
the ratio of the number of quanta emitted compared to powered by a direct current (d.c.) supply, furnishing
those absorbed (usually the yield is between 0.1 and enough start-up power to ignite the burner (by ionization
1.0). Quantum yields below 1 are the result of the loss of the gaseous vapor) and to keep it burning with a
of energy through nonradiative pathways (e.g., heat or minimum of flicker. The power supply should have a
photochemical reaction) rather than the reradiative path- timer to track the number of hours the burner has been in
way of fluorescence. Extinction coefficient, quantum use. Arc lamps lose efficiency and are more likely to
yield, mean luminous intensity of the light source, and shatter, if used beyond their rated lifetime. The mercury
fluorescence lifetime are all important factors that contri- burners do not provide even intensity across the spectrum
bute to the intensity and utility of fluorescence emission. from UV to infrared and much of the intensity of the
mercury burner is expended in the near UV. Prominent
peaks of intensity occur at 313, 334, 365, 406, 435, 546,
FADING and 578 nm. At other wavelengths of visible light, the
intensity is steady although not nearly so bright, but still
There are conditions that may affect the reradiation of usable. Mere lamp wattage is not the prime consideration;
light and thus reduce the intensity of fluorescence. This instead, the critical parameter is the mean luminance that
reduction of emission intensity is generally called fading takes into account the source brightness, arc geometry,
and is further subdivided into quenching and bleaching. and the angular spread of emission.
Bleaching is the irreversible decomposition of the fluor- In recent years, there has been increasing use of
escent molecules in the excited state because of their lasers, particularly the argon-ion and argon –krypton-ion
interaction with molecular oxygen. The occurrence of lasers as light sources. They have the virtues of small
bleaching is exploited in a technique known as fluor- source size, low divergence, monochromaticity, and high
escence recovery after photobleaching (FRAP), to study mean luminance. They have become essential in scan-
diffusion and motion. It is based upon bleaching a ning confocal microscopy, a technique that has proved to
sharply defined region of the specimen by an intense be a powerful tool in rendering very sharp fluorescence
burst of laser light and subsequently observing the rate images by rejecting out-of-focus light. This is accom-
and pattern of the recovery of fluorescence in the plished through point or line scanning and coincident
bleached area. Quenching reduces fluorescence intensity imaging through a conjugate aperture. Optical sections
by a variety of mechanisms involving nonradiative ener- of the specimen are stored in a computer and recon-
gy loss and frequently comes about as a result of oxi- stituted into the whole image that then can be displayed
dizing agents or the presence of salts of heavy metals or on a monitor.
halogen compounds. Sometimes quenching results from
the transfer of energy to other so-called acceptor mole-
cules physically close to the excited fluorophores, a phe- FILTER TERMINOLOGY
nomenon known as resonance energy transfer. This
particular phenomenon has become the basis of the tech- The terminology applied to fluorescence filters has be-
nique called fluorescence resonance energy transfer come a jumble as a result of various initials utilized by
552 Fluorescence Microscopy

different manufacturers to identify their filters. Basically, longer wavelength light to the barrier filter, and reflect-
there are three categories of filters: exciter filters, barrier ing any scattered excitation light back in the direction
filters, and dichromatic beam splitters (dichroic mirrors). of the lamphouse.
Fluorescence filters were formerly almost exclusively
made of colored glass or colored gelatin sandwiched be-
tween glass plates. Now, interference filters are used
THE LIGHT BUDGET
for exciter filters to pass or reject wavelengths of light
with great selectivity and high transmission. Dichromatic
It is a useful exercise to estimate the light fluxes in a
beam splitters are specialized interference filters. Barrier
typical fluorescence microscope as one obtains consid-
filters may be either made of colored glass or inter-
erable insight into the constraints that any microscopist or
ference filters.
optical engineer encounters.
The excitation source is assumed to be a 75-W xenon
Exciter Filters lamp with a mean luminous density of approximately 400
cd/mm2. When the lamp output is collected and directed
Abbreviations used by manufacturers to denote the pro- through a 490-nm interference filter (10-nm bandwidth,
perties of their filters include: UG (UV glass) and BG 75% transmission), about 2 mW of light will pass. After
(blue glass), which are glass exciter filters. KP (K is an reflection by a 90% efficient dichromatic mirror, a light of
abbreviation for kurz, short in German) and SP are short 1.8 mW enters the back aperture of the microscope
pass filters; and EX indicates an exciter filter. Some objective lens as the excitation beam. With an objective
manufacturers label their interference filters with the lens of 100
/1.4 n.a., the area of specimen illuminated
designation IF. Narrow band-pass interference filters are will be 12
10  6 cm2, assuming a circular field of view
especially helpful if the Stokes’ shift is small. of 40 mm in diameter. The light flux on the specimen is
then 1.8 mW/12
10  6 cm2 = 150 W/cm2. This cor-
responds to a flux of 0.36
1021 photons/cm2 sec, about
Barrier Filters 1000 times higher than that incident on the Earth’s surface
on a sunny day.
Acronyms or abbreviations for barrier filters include: LP The fluorescence emission that results from this light
or L for long pass filters, Y or GG for yellow or gelb flux depends on the absorption and emission character-
(German) glass, R or RG for red glass, OG or O for istics of the fluorophore, its concentration in the spe-
orange glass, K for kante, a German term for edge (filter), cimen, and the optical path length of the specimen. The
and BA for barrier filter. When the filter type is also fluorescence produced, F, is given by:
associated with a number, e.g. BA475, that designation
refers to the wavelength (in nanometers) at 50% of its
F ¼ sQI
maximum transmission.

where s is the molecular absorption cross-section, Q is

Dichromatic Beam Splitters the quantum yield, and I is the incident light flux
(0.36
1021 photons/cm2 sec, as calculated above). As-
Abbreviations used to describe and identify beam split- suming that fluorescein is the fluorophore, s = 3
10 16
ters include: CBS for a chromatic beam splitter, DM for cm2/molecule, Q = 0.99, and F = 1
105 photons/sec
a dichroic mirror, TK for ‘‘teiler kante,’’ German for molecule. For a preparation with a dye concentration of 1
edge splitter, FT for ‘‘farb teiler,’’ German for color mM/l uniformly distributed in a 40-mm diameter disk with
splitter, and RKP for reflection short pass. All of these a thickness of 10 mm (volume of 1.2
10  11 l), there are
terms should be considered interchangeable. These filters approximately 1.2
10  17 moles of dye or 7.2
106
are always the interference type. The coatings are de- molecules in the optical path. If all of the molecules were
signed to have high reflectivity for shorter wavelengths excited simultaneously, the fluorescence emission rate
and high transmission for longer wavelengths. Dichro- would be 7.2
1011 photons/sec (given by the product of
matic beam splitters are oriented at a 45° angle to the F and the number of dye molecules). How many of these
path of the excitation light entering the cube through photons would be detected and for how long could this
the reflected light fluorescence illuminator. Their func- emission rate continue?
tion is to direct the selected excitation (shorter wave- The efficiency of detection is a function of the optical
lengths) light through the objective and onto the speci- collection efficiency and the detector quantum efficiency.
men. They also have the additional functions of passing A 1.4-n.a. objective lens with 100% transmission has a
Fluorescence Microscopy 553

maximum collection efficiency, limited by the acceptance signal would be 7
1010 photons/sec or about 10% of the
angle, of 30%. The transmission efficiency of the dichro- emitted fluorescence. Even with a perfect detector (100%
matic mirror is 85% and that of the barrier filter 80%. The
overall collection efficiency is then 20% or 14
1010
quantum efficient), only 20% of the emission photons
would be detected.
F
photons/sec. If the detector is a conventional charge- The duration of emission depends on the rate of pho-
coupled device (CCD), the quantum efficiency is about todestruction as a result of bleaching. For fluorescein in
50% for the green fluorescein emission, so the detected an oxygenated solution, measurements show that each

Fig. 4 The principle and design of a total internal reflection fluorescence (TIRF) microscope using an external laser light source are
shown. The top portion shows a close-up of the specimen to which a glass cube is approximated with an intervening layer of glycerol.
The illuminating laser beam is totally reflected at the boundary between the coverslip and the aqueous buffer solution provided that it
enters the glass cube at an angle greater than the critical angle (yc).
554 Fluorescence Microscopy

molecule can only emit about 3.6
104 photons before employing an external light source is illustrated in Fig. 4.
being destroyed. In a deoxygenated environment, the In this method, a beam of light (usually an expanded
rate of photodestruction diminishes about tenfold, so beam of laser light) is directed through a prism of high
3.6
105 photons are produced per molecule. The entire refractive index, e.g. glass or sapphire, which abuts a
dye pool of 7.2
106 molecules could then produce a lower refractive index medium, e.g. glass or aqueous
minimum of 2.6
1011 photons or a maximum of solution. If the light is directed at higher than the critical
2.6
1012 photons. Assuming the emission rate of angle, the beam will be totally internally reflected at the
1
105 photons/sec molecule calculated above, fluores- interface. However, an evanescent wave develops at the
cence could continue for only 0.3 –3 sec before photo- interface by the generation of an electromagnetic field
destruction. If 10% of the photon flux were detected, a that permeates about 200 nm or less into the lower re-
signal of 7.2
1010 electrons/sec would be obtained. If fractive index space. The light intensity in the evanescent
the detector is a 1
1 K CCD camera, this signal would wave is sufficiently high to excite the fluorophores within
be distributed over 1
106 sensors, with 7.2
104 elec- it, but because of its shallow depth, the volume excited is
trons/sensor. For a scientific-grade CCD with 9
9 mm very small. The result is an extremely low-level back-
square sensors, the full well storage capacity is about ground because so little of the sample is exposed to the
8
104 electrons and the read-out noise is less than 10 excitation light.
electrons. The signal/noise ratio would then be largely TIRF can also be accomplished by a modification of
determined by photon statistical noise equal to the square the epi-illumination approach used in wide field fluor-
root of the signal, i.e. 268. Unfortunately, this high signal escence microscopy (Fig. 5). This method necessitates a
level could only continue for a very brief time before very high numerical aperture objective lens (at least 1.4,
photodestruction occurs. The compromise utilized by but preferably 1.6) and partial illumination of the
most microscopists to prolong the observation period is microscope field from one side by a small spot or more
a reduction in the incident light flux intensity so that uniform illumination by a thin annulus. High refractive
only a fraction of the fluorophore molecules in the dye index lens immersion medium and microscope cover
pool are excited and subjected to photodestruction. Thus,
the signal/noise ratio rarely equals the theoretical maxi-
mum and typically ranges between 10 and 20 in fluor-
escence microscopy.

DETECTING SINGLE MOLECULES

It is possible to detect the emissions from a single fluor-

ophore provided that the optical background and detector
noise are sufficiently low. As discussed above, a single
fluorescein molecule could emit as many as 3
105 pho-
tons before it is destroyed. Assuming a 20% collection/
detection efficiency, about 6
104 photons would be de-
tected. Investigators, using an avalanche photodiode de-
tector for these experiments, have been able to monitor
the behavior of single molecules for many seconds or
minutes. The biggest problems arise from the need to
suppress the optical background sufficiently. Because
most of the materials used in microscope lenses and filters
show some autofluorescence, efforts were initially di-
rected toward the manufacture of very low fluorescence
components. However, it soon became evident that fluor-
escence microscopic methods utilizing total internal re- Fig. 5 The basic principle of TIRF through a microscope
flection provided the desired combination of low back- objective lens is shown. Excitation laser light exiting the
ground and high exiting light flux. objective lens at angle A1, less than the critical angle, will be
Total internal reflection fluorescence (TIRF) utilizes transmitted because the effective numerical aperture is < 1.38.
the evanescent wave that is developed at the interface at Light that exits the lens at angle A2, equal to or greater than the
which light is totally internally reflected. The principle critical angle, will be totally reflected (labeled NA > 1.38).
Fluorescence Microscopy 555

glass are required for achievement of the illumination sible. The increasing use of electro-optics in fluorescence
angle resulting in total internal reflection. As shown in microscopy has lead to the development of optical twee-
Fig. 5, light rays exiting the objective lens at an angle less
than the critical angle (denoted as angle A1 in Fig. 5) are
zers capable of manipulating sub-cellular structures or
particles, the imaging of single molecules, and a wide
F
transmitted. When the angle is increased to or beyond the range of sophisticated spectroscopic applications.
critical angle (denoted as angle A2 in Fig. 5), total internal
reflection results. TIRF may be combined with other
optical methods such as FRAP and FRET as well as FURTHER READING
spectroscopy. The result is a very powerful tool for the
study of individual fluorophores and fluorescently labeled Fluorescence Microscopy
molecules. The advantages of the study of the properties
of single molecules are only beginning to be appreciated. Abramowitz, M. Fluorescence Microscopy—The Essentials;
The range of optical microscopy now extends from the Olympus-America: New York, 1993.
single molecule to the entire animal. Herman, B. Fluorescence Microscopy, 2nd Ed.; Springer-
Verlag: New York, 1998.
Periasamy, A. Methods in Cellular Imaging; Oxford U. Press:
New York, 2001.
CONCLUSION

The modern light microscope combines the power of high Confocal Microscopy
performance optical components with computerized con-
trol of the instrument and digital image acquisition to Pawley, J.B. Handbook of Biological Confocal Microscopy, 2nd
achieve a level of sophistication that far exceeds that of Ed.; Plenum Press: New York, 1995.
simple observation by the human eye. The fluorescence
microscope depends heavily on electronic imaging to
rapidly acquire information at low light levels or at
TIRF, FRAP, and other
visually undetectable wavelengths. These technical im-
Advanced Techniques
provements are not mere window dressing, but are
essential components of the light microscope as a sytem. Foskett, J.K.; Grinstein, S. Noninvasive Techniques in Cell
The days of the light microscope as a purely descriptive Biology; Wiley-Liss: New York, 1990.
instrument or plaything of the intellectual are past. At
present, optical image formation is only the first step
toward data analysis. The microscope accomplishes this General Microscopy
first step in conjunction with electronic detectors, image
processors and display devices that can be viewed as Inoué, S.; Spring, K.R. Video Microscopy, The Fundamentals,
extensions of the imaging system. Computerized control 2nd Ed.; Plenum Press: New York, 1997.
of focus, stage position, optical components, shutters, Murphy, D.B. Fundamentals of Light Microscopy and Elec-
filters, and detectors is in widespread use and enables tronic Imaging; Wiley-Liss: New York, 2001.
experimental manipulations that are not humanly pos- http://microscopy.fsu.edu.