Confocal Raman Microscopy

Marvin Minskey, who is well known as the father of artificial intelligence was also the author of another important achievement [2.25]. He built a revolutionary light microscope in the 1950s as a postdoctoral fellow at Harvard University. This instrument enabled him to view successively deeper layers in a specimen with astonishing clarity, without the

microscope as " double-focusing stage-scanning microscope " in 1961 but during the 17- years life of the patent no microscopes of similar design were manufactured. Disappointed with the lack of appreciation for his foray in the optics, he left the prototype to rust in a corner of his basement and moved on to other challenges.

To day his approach otherwise known as confocal microscopy is widely used in optical microscopy. It provides one of the significant advances in optical microscopy in the last few decades. A variety of microscopes for different purposes have been built which take advantage of this approach including confocal Raman microscopy.

The confocal setup of a Raman microscope can provide the means for "optical sectioning". This means that it has the ability to discriminate between parts of the sample which are not at the same depth and only allow the detection of scattered Raman light from molecular vibrations of a particular depth. This also provides a valuable way in Raman spectroscopy to almost eliminate the stray light (background, fluorescence) coming from outside the focal volume.

However, it should be noted that the use of the confocal method can also have some disadvantages. Since the laser light is focused on a very small point on the sample, the laser intensity is very high in that region and thus in some cases can damage the sample even at laser powers below 1 mW. This damage becomes visible under a light microscope in the form of a black snot or a "paling" of the sample at the site of the laser focus. The choice of the laser wavelength used for excitation is found to be crucial. In many cases such damage has not been observed with the use of a 632.8 nm laser. Photochemical effects may be the most plausible cause of the sample degradation at 514.5 nm. Foote [2.26] shows that DNA bases and a number of amino acids can be degraded in

"photodynamical" processes requiring the presence of light, a sensitiser and oxygen. In

such a process laser excitation brings the sensitiser via the singlet state in a long-lived triplet state. It can then react with oxygen to form reactive oxygen species that could cause the observed radiation damage through oxidation of the DNA bases or amino acids leading to lesions in these molecules.

Confocal Raman microspectrometry has been employed in many areas of science and technology. Some teams of researchers have reported the design of a new instrument or have developed the existing Raman microscopes in order to use the instrument in confocal mode for various applications [2.27-2.33], The use of fiber-optics in some of the new instruments has been reported [2.34-2.38]. It provides remote capabilities for the microscope and the ability to use multiple excitation sources and detection schemes. Biological applications of the technique include: cell biology and chromosomes [2.39- 2.45], DNA-protein complexes [2.47-2.53] and other biological applications [2.54-2.61]. The use of this technique in materials [2.62-2.66] and polymer [2.67-2.74] science has also been reported.

2.4.2.I. Theory

Raman microscopy with spatial resolution of 1 pm in the lateral plane (x, y) has been used for many years to provide information about molecular vibrations of small area of samples. However for some samples a good spatial resolution along the optical axis, z is desirable. The signal intensity recorded by the detector for a given Raman line at the wavelength X is expressed by: [2.75]

Where I0 = laser irradiance at the sample (watts unit area"1)

= differential cross-section for the analysed Raman line (cm2 . sterad'1 . molecule'1)

N = number of molecules in the probed volume, V 0 = angle of collection of the Raman light

= througthput of the instrument at the wavelength X s^ = sensitivity of the detector at the wavelength X

As a result of using the confocal approach a small volume of the sample is to be examined and thus, to compensate for the large reduction in the number of the molecules N in the probed volume, only I0 and 0 may be modified. For this reason the best way to decrease sampling volume while increasing laser irradiance and the collection angle is to use microscope objectives. Such objectives are used for both illuminating the sample and collecting the Raman scattered light. The numerical aperture (N. A.) of an objective determines the distribution of the laser field around the focus. The numerical aperture is the sine of half the angular aperture, i. e.,

Thus, microscope objectives with high-numerical aperture (NA) optics are able to focus the laser beam into a very small volume and to collect, under a wide angle, the Raman light scattered by this volume. See figure 2.3.

(2.2)

Where, N. A. = Numerical aperture with maxium value of 1. 0 = Angle of entrance.

i PLANE OF F O C U S W A IST W A IST PLANE O F FO C U S (a) (b)

Figure 2.3: Schematic diagram o f the distribution o f laser light near focus using a microscope objective with (a) high NA, (b) low NA

Table 2.1 shows the calculated values of such a relationship for the objectives which have been used for the studies in this thesis.

Objective NA 1/2 angle, 0 (deg) Depth of focus, © (pm)

lOOx 0.95 71.8 0.1

5 Ox 0.80 53.13 0.4

20x 0.46 27.39 2.4

20x (long) 0.40 23.58 3.3

lOx 0.30 17.46 6.4

When a pinhole is placed in the back focal plane of a microscope, light from planes higher or lower than focal plane are blocked by the opaque regions around the pinhole and in this way the depth resolution of the microscope can be enhanced enormously. Figure 2.4 shows the principle of confocal microscopy.

slit w idth

CCD area (4 x 5 7 6 pixels) LASER BEAM

CCD area cap tu rin g light from confocal sectio n (pinhole effect). FILTER CCD d e tecto r ENTRANCE SLIT MICROSCOPE OBJECTIVE FOCAL PLANE

Figure 2.4: Schematic diagram o f the principle o f confocal Raman microspectroscopy

Some researchers [2.73,2.42] have used pinholes with dimensions 100 and 300 pm. The pinhole has been aligned in the optical axis and along the optical axis with the aid of micrometer adjustments. The process of such optical alignment can be difficult and time- consuming. In order to reduce such difficulties Williams et al describe the use of a CCD

detector with a stigmatic Raman spectrograph [2.74], In this way the long axis of the CCD detector (576 pixels) is used to describe the spectral dimension, while the shorter axis (384 pixels) describes the image height. By using only a few pixels in the spatial direction of the detector (four pixels represent an image of 100 pm) and the spectrometer slit with width of approximately 15 pm (used to provide the primary aperture in the system), the "pinhole effect" as a small area on the CCD detector is created. This is shown in figure 2.4.

The role of the pinhole can be explained by geometrical reasoning and, and in order to keep the model for explaining this role simple, diffraction effects at the pinhole are ignored. This is a good approximation since a pinhole of greater than 100 pm has been used in these studies and thus diffraction effects at the pinhole are small [2.73]. In addition the influence of refraction, scattering, and absorption at the sample surface has been disregarded. Figure 2.5 shows the schematic of a light microscope coupled to a spectrograph. This is similar to the Renishaw Ramascope used for these studies.

Figure 2.5: The schematic diagram o f the optics in the Raman microscope with confocal setup (similar to Renishaw Ramascope). (a) sample plane, (b) objective lens, (c) microscope objective, (d) laser source, (e) beam splitter, (f) mirror reflecting the Raman light to the spectrometer, (g) slit focusing lens, (h) pinhole, fI andf2 are the focal length o f the objective and slit focusing lenses respectively, d is the distance from the focal plane o f the objective lens, Is is the diameter ofpinhole and f is the diameter o f the image o f the projected laser spot

The objective lens and the slit focusing lens are designated as L\ and L2 respectively. The smallest diameter of the laser beam is in the focal plane of the objective lens, LI [2.76] and this diameter remains approximately constant up to a certain distance from the focal plane. This is known as the waist, co (see fig 2.3). Equation 2.3 can be used to determine depth of waist which is known as depth of the focus [2.77].

Where X = wavelength of the laser light 0 - entrance half-angle

The calculated depth of focus for the objectives used in these studies are shown in table 2.1. The size of the laser spot can be expressed by s(/l ± d) where f \ is focal length of the objective lens and d is distance from in-focus plane and thus the following equations can be used to determine the diameter of the laser light around the focus;

s(f,±d) = s(f,) for 2.4

for 2.5

In a confocal arrangement a slit is placed at the back image of the microscope and an out- of-focus laser spot with size s.(/j ± d) will be imaged outside of back focal plane at a distance Z2 from the slit focusing lens, L2-(see fig 2.5). i.e.,

-1

Z, = s---

2 If, -1 (2.6)

fo -

v»i f, ± d,

Wheref y is the focal length of the slit focusing lens, L2

This image is projected on the back image plane of the microscope which is bigger than the laser spot image lying on the focal plane. The diameter of the out-of-focus projection, It on the image planef y can be calculated [2.73] by:

f,.M.[s.(f, ±d)] (2 ?)

1 z."2

Where M is the magnification power of the objective. Since the out-of-focus projection, 1^ is larger than in-focus one (see fig 2.5), by placing a pinhole with a diameter, Is less than that of If, it is possible to block most of the light coming from the regions below and above than the focal plane and allow only the light from the focal plane to reach the detector of the instrument. Equation 2.7 shows that microscope objectives with a high numerical aperture (and thus with a wide half angle of collection) can ensure (1) a very divergent beam out sid“ the focal plane and (2) a short waist. In this way the projection, If (see eqn 2.7) is enlarged from the out-of-focus laser at the back image plane and thus enhances the efficiency of the pinhole.

Figure 2.6 shows a comparison between curves obtained with confocal and conventional Raman microscopy. In this figure intensity distribution has been represented as a function of distance from the object focal plane.

400

300

100

■20-18-16-14-12-10 -8 -6 -4 -2 0 2 4 6 8 10 12 14 16 18 20

Depth (micrometer)

Figure 2.6: Comparison o f (a) confocal Raman microscopy, and (b) conventional Raman spectroscopy

In order to show the effect of microscope objectives with various magnification power and numerical aperture on confocal Raman microscopy, a simple experiment was performed [2.67], In this test the focus of the laser was stepwise (1 pm) scanned away from the surface of a silicon wafer, and the signal intensity of the fundamental vibration at 519 cnr1 was recorded. Figure 2.7 shows a plot of Raman intensity as a function of distance away

from silicon surface. From this experiment the depth resolution using different microscope objectives could be determined. The depth resolution was thus determined for the lOOx objective as 2.0 ± 0.3 pm and for the 50x objective as about 5 ± 1 pm using FWHM criterion. However, it is clear from figure 2.7 that about 90% of the scattered light is contributed from a 2 pm (with a lOOx objective) from below and above the plane of focus, but it should be noted that significant Raman scattering light is still contributed from the regions further above and below this region.

The data for the curves in figure 2.7 have been collected experimentally using the above test and thus these curves show the response of the Raman confocal microscope in practice. However it is possible to determine the theoretical response of the system and thus compare the experimental and theoretical performance of the Raman confocal microscope.

1600