Methods of soil analysis 5-269

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Methods of soil analysis 5-269...


Published 2008 Chapter 10

Scanning Electron Microscopy G. NORMAN WHITE, formerly Texas A&M University, currently Texas Commission on Environmental Quality, Austin The scanning electron microscope (SEM) has very diverse uses in the study of soils. Only those solids that decompose in a very weak electron beam or are unstable in even the slightest vacuum cannot be examined with scanning electron microscopy. The SEM has a large magnification range, allowing examination of solids with almost no magnification to imaging at well over 100,000 times. Another important feature is the large depth of field of SEM images, which appears three-dimensional and provides much more information about a specimen’s topography and surface structures than light microscopy at the same magnification. In most instruments, the specimen can be moved in the x, y, and z directions as well as rotated about the vertical axis and tilted almost 90°. These movements facilitate obtaining quality images and optimum sample information. A very close relative of the SEM is the Electron Probe Microanalyzer (EPMA). The basic optical design of an EPMA is very similar to an SEM, but the EPMA is arranged to optimize X-ray signal detection, while the SEM is optimized for visual information and only secondarily for X-rays and other electron interactions. In this chapter, the basics of scanning electron microscopy are presented, with special emphasis on maximizing the quality of data obtained from the instrument. This includes the identification of minerals with an SEM and recognition of soil features that may not otherwise be detectable. As EPMA is discussed elsewhere in this book (Guillemette, 2008), this chapter covers only examination of a sample using visual characteristics and compositional characteristics that can be detected by energy dispersive X-ray spectrometry (EDS), an accessory that is available on most SEM instruments and is almost vital for proper identification of minerals with the instrument. There are several treatises on the background and theory of scanning electron microscopy (e.g., Goldstein et al., 1992, 2003). For more detail about electron optics and SEM use, check these books or the chapter on EPMA in this volume (Guillemette, 2008, this volume). While the X-ray signal from EDS is often vital to the correct identification of minerals in soils and sediments, SEMs are not optimized to obtain quantitative compositional data. Such data can only be obtained with an SEM for the higher atomic number elements if they have a significant concentration and then only after making assumptions that need not be made with an EPMA. Obtaining good quantitative compositional data is easier with an EPMA (Guillemette, 2008, this volume). The environmental scanning electron microscope (ESEM) is a recent modification of traditional SEM. The major difference between ESEM and traditional SEM is the much Copyright © 2008 Soil Science Society of America, 677 S. Segoe Road, Madison, WI 53711, USA. Methods of Soil Analysis. Part 5. Mineralogical Methods. SSSA Book Series, no. 5.




higher specimen chamber pressures that are allowed in the ESEM. A differential pumping system allows pressures of several hundred Pa in the specimen chamber while maintaining a pressure of 1.3 × 10−11 MPa near the electron gun. The high vacuum near the electron gun makes it possible to use high intensity filaments such as a LaB6 filament and get a significant signal despite the higher sample chamber vacuum. The ESEM allows the introduction of various gases and allows the partial pressure of the gases in the chamber to reach up to 0.0027 MPa. With the addition of a peltier cooler, this pressure is sufficient to condense water on a specimen. The higher gas pressure serves the additional purpose of transmitting heat and excess electrons away from the specimen, with the result that sample coating is not needed. The ESEM exhibits its full potential in studies involving gas interactions or effects of temperature on a sample. The helpful addition of a heating stage allows the control of temperature up to 1000 °C. The ability to control atmospheres permits the study of surface–gas interactions. As the effects of heating or reactions with gases are kinetically controlled, video output allows the storage of video data for future use, in addition to photography. Instruments are only recently gaining sufficient control over the atmosphere to obtain reliable data on soil wetting because the range of humidity involved in soil wetting is too small; thus, the full potential of these instruments is to be determined in the future. SAMPLE PREPARATION FOR USE IN SOIL MINERALOGY The Importance of Coating a Sample When a sample is examined by SEM, a large number of electrons are striking the surface. If these electrons are not removed, the sample may be damaged by heating and an area with a high electric charge may result. In practice, this is most often observed as a dark area surrounded by a brightly glowing area that increases in light intensity with time during examination. This phenomenon is termed charging. The presence of sample areas that are charging is more than an inconvenience; particles may become loose from the sample and affect the valves in the vacuum system. The particles may also decompose chemically. It is impossible to examine the sample near the charging areas because the beam is affected by the electrical charge. Although examination of a sample with no conductive coating is possible at very low beam voltages, the low beam voltage renders use of EDS impossible, limits the amount of signal available for visual examination, and limits examination to relatively low magnifications. A lack of signal strength translates into a lack of contrast in the output. For that reason, most samples are coated with a thin layer of conducting material to allow removal of excess electrons to ground, thereby preventing charging. Sample coating involves the addition of a very thin layer (about 10 nm depending on the sample) of a conductive material to the surface of a sample. This layer is added in a sputter coater, a specially designed device in which high voltage is applied to a negative cathode constructed of the target material to be sputtered (typically gold or gold–palladium) in a vacuum. A diffuse cloud of positively charged ions results and they impinge on the specimen from all directions. A coating of ions condenses evenly on the specimen, placed on the anode, which is kept at ground potential. Carbon coating prepares specimens by evaporating high purity carbon under vacuum onto the specimen in a manner similar to the metal coating method. A thin layer uniformly covering the specimen is the desired result. The coating should be sufficiently thick to transmit the excess electrons, reducing problems with charging, but not so thick as to obscure morphological or chemical features on the sample. The choice of coating is very important because it affects the quality of the images produced and may interfere with some elements during EDS. Coating the sample

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Table 10–1. Commercially available elements used for coatings and elements with EDS peaks that would overlap to some degree with the coating.

Coating Al Cr Cu Au Au/Pd

Ir Ni Pd

Pt Pt/Pd

Ag Ta

X-ray peaks keV 1.487 5.411 5.947 8.041 8.907 2.1–2.2 9.7 2.1–2.2 2.838 2.99 3.172 3.328 9.7 1.9–2.1 9.2 7.472 8.265 2.838 2.99 3.172 3.328 2.0–2.1 9.44 2.0–2.1 2.838 2.99 3.172 3.328 9.44 2.984 3.348 1.775 3.149 8.145–9.341

Elements affected Mg, Al, Si V Kβ Mn Kα Ni Kβ Zn Kα P Kα, S Kα Zn Kβ P Kα, S Kα, Y Lβ, Zr Lβ Cl Kβ K Kα Zn Kβ P Kα, Y Lβ, Zr Lβ Zn Kβ Co Kα Cu Kα Cl Kβ K Kα P Kα, S Kα, Y Lβ, Zr Lβ Zn Kβ P Kα, S Kα, Y Lβ, Zr Lβ Cl Kβ K Kα P Kα, S Kα, Y Lβ, Zr Lβ I Lα K Kα, Ca Lα, In Lα, In Lβ Si Kα K Kα Ni Kα

with carbon will result in the best EDS data, but charging is potentially more of a problem and the micrographs do not have the contrast and resolution of metal-coated samples. Many metals are used for the conductive coatings. Equipment catalogs show numerous choices, including aluminum, chromium, copper, gold, gold–palladium, iridium, nickel, palladium, platinum, platinum–palladium, silver, and tantalum. The user must be careful to choose a coating that does not interfere with the interpretation of the EDS patterns if used. Table 10–1 lists potential peak interferences by coating materials in EDS. The most common metal coatings are gold, a mixture of platinum and palladium, and gold and palladium. Gold has X-ray peaks in the region just above 2 keV and between 9 and 10 keV. The second peak does not interfere with the principle peaks for any important elements, but the location of the first peak interferes with the peaks from P and S and would not be a good choice for a coating if those elements are important in your study. Platinum interferes with the same elements as gold, while palladium interferes with chlorine and potassium. Potassium is very important in the identification of micas and feldspars, so the use of gold for a metallic coating is advised for work involving those minerals.



The metallic coatings usually produce better quality micrographs, but when minerals containing S or P are to be examined, carbon coating is the best choice. Carbon does not have EDS peaks in the region above 1 keV and thus does not interfere with EDS detection of higher atomic number elements, but carbon coatings are not as efficient at removing the electrons, which may reduce the quality of the micrographs, especially at high magnifications. In addition, while the use of a sputter coater to apply metallic coatings is relatively easy even for a beginner, application of an adequate carbon coating requires experience. Sample Preparation: Peds vs. Grains vs. Thin Sections The first step in examining samples with an SEM is preparation of the sample. This step is often time-consuming and should be finished before the time scheduled for SEM examination of the sample. Do not assume that the sample can be prepared for examination in a negligible amount of time. To a great degree the type of information desired determines the method used to examine a sample with an SEM. In general, soil is prepared for SEM examination in three ways, as individual grains, peds, or as thin sections. Each method can yield different information about the sample. Examination of individual grains allows the user to obtain qualitative information about grain morphology and relative concentrations of different minerals in a similar manner to that used in petrographic microscopy for grain counts. With each method, the sample must be strongly adhered to a sample holder and coated with a metal or carbon to transmit the excess electrons and heat from the area examined. Which method is appropriate for use is the first decision to be made by an SEM user. Examination of Single Mineral Grains Examination of single grains is best done on individual size fractions. See Soukup et al. (2008, this volume) for information on particle size separation and pretreatment. More information with less preparation can be obtained by examining the finer sand fractions and the silt. These fractions have more mineralogical variability, and more grains can be placed on one sample holder. Examination of single mineral grains in a size fraction allows one to see the variability in grain morphologies. Surface morphology may reveal information about weathering intensity, environment of deposition, parent material, or past history of a soil (e.g., the discussion on Decatur soil in White and Dixon, 1998). The observation of a mineral that is present only in trace quantities within a sample is more likely during examination of grain mounts of individual grains, especially when the mineral has a morphology that contrasts strongly with the minerals that make up the majority of the sample. To prepare a sample fraction for examination: 1.

Place a conducting adhesive material on the surface of the sample holder. The standard material for such examinations in the past was double-sided tape, but an apparent change in manufacturing resulted in the tape becoming unstable in the electron beam. Several manufacturers produce metal or carbon conducting tapes or tabs that are specifically designed for this use. Liquid adhesives should be used with caution because the thickness of the adhesive is often significant when compared with the thickness of the grains, and capillary action may obscure portions of the sample.


Sprinkle a small number of grains onto the adhesive. Use a spatula with as small a surface as possible to scoop up about 1 mm3 of grains. Sprinkle the grains as evenly as possible over the adhesive surface by gently tapping the side of the spatula while holding it above the adhesive. Be careful not to add too much material. Sand grains should be well separated. When working with silt factions, you can examine the stub with a binocular microscope to check for loading. Experience will allow you

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to make this judgment by differences in the appearance of the adhesive. Too many particles can result in problems from a shadow effect. 3.

Make sure that the material is adequately adhered to the surface. Softly pushing sand grains down increases adhesion with the sample holder, but care must be taken not to avoid marring the surface of the grain. There may be features not readily observed by other methods that could be disturbed by frequent handling or manipulation, resulting in artifacts. Adhesion is rarely a problem with silt because of the higher surface area. Blow loose grains from a silt fraction SEM mount with a gas duster or remove them by tapping the mount while it is inclined at a high angle. Failure to remove poorly adhered grains will result in areas that are obscured by sample charging and the possibility of sample loss within the microscope column. In a worst case scenario, a grain lost from the sample may get caught in one of the vacuum valves, rendering the microscope inoperable. In any case, loose grains will result in areas that cannot be examined due to sample charging because the excess electrons cannot be removed when grains are poorly adhered to a conducting mount.


Coat the sample for use with either carbon or a metal coating using a sputter-coater following the manufacturers instructions. The removal of the electrons is the purpose of sample coating.

Examination of Peds Examination of peds also requires careful sample preparation. The sample needs to be dried and fixed to the sample holder, but choosing the area to be examined requires care. Peds should be examined on a fresh fracture surface to avoid artifacts due to handling or smoothing. Examination of peds allows observation of morphological features of the minerals and soil matrix itself, how peds or particles are arranged relative to each other, the presence of coatings and cutans, and the void sizes and arrangements. There are several potential problems that may be encountered when examining peds. Ideally, the ped or portion of ped examined must be sufficiently cohesive to remain intact during sample preparation and under examination in the microscope. This requires the presence of a certain amount of clay or natural cementing agent to bind the ped into a cohesive unit. As the clay content decreases, a problem with grain charging is often observed because the grain contacts are insufficient to allow the heat and electrons to diffuse from the area examined. The particles begin to become brighter with time, may begin to move, and possibly fly off the sample holder. Minerals may or may not be identifiable when viewed because areas visible by imaging are not necessarily unobstructed by other grains for the detector used for determination of composition and because the beam may penetrate the particle being observed, resulting in an apparent composition with contributions from underlying grains. It is important to recognize that the EDS characteristics observed might not entirely result from the particle that you are examining. Electrons penetrate from 2 to 5 μm or more depending on the beam kilo electron voltage. As a result, EDS patterns for very thin grains may have significant contributions from underlying grains. A less obvious problem is due to the liquid adhesive used to bind the specimen to the sample holder. This adhesive may wick up through the pores of the peds by capillary action and appear in the region that is to be examined. Without EDS, features resulting from the adhesive are hard to distinguish from features of the ped. Most conducting adhesives are either organic or contain a metal such as Ag. The researcher should always know what the EDS characteristics are for the sample adhesive to prevent mistaking the adhesive for sample features.



When preparing a ped for examination, the problem arises as to the effect of water on the fabric of the ped. If the sample is to be examined using ESEM or in an environmental cell, no drying step is needed. In a normal SEM, sample instability is likely to result from drying of the sample due to thermal expansion of the water resulting from the vacuum and the heat produced by the beam. To prepare a ped for examination: 1.

Dry the ped in an oven at 105°C or remove the free water in some other manner such as acetone displacement and drying.


Trim the ped to fit the appropriate stub size. Remove any loose grains by tapping or using a gas duster or other source of a light wind. Be careful, as many gas dusters produce too high a flow rate for this use. A smaller ped is less likely to break off the sample holder and is much less likely to have charging problems. Most microscopes have some limitations on sample size both vertically and horizontally. Too large a sample may not fit into the microscope for examination. In addition, a sample that is too tall may damage the detectors by contact or may limit the working distance.


Adhere the sample to the sample holder (stub). The method used could include a conducting adhesive tab or some type of liquid adhesive. If using a liquid adhesive, apply it only to the sample holder and allow it to begin to dry slightly before adding the sample. Check to make sure that the sample is adequately attached to the stub. Except when used in an ESEM, the sample must be strongly adhered to the holder with a conducting adhesive. Low adhesion results in more problems with charging, as does use of a nonconducting adhesive.


Coat the sample for use with either carbon or a metal coating.

Examination of a Sample Prepared as a Thin-Section or Polished Block A thin section or polished block is by nature smooth and will lack topographic relief that is common in peds or single grains. Thus, thin sections or polished blocks are often more suited to backscatter electron imaging or X-ray analysis and imaging. The benefit of using a thin section ground to a thickness of 25 to 30 μm is that the images observed in a petrographic microscope can be correlated with SEM or EDS images. Optically, a polished block can be viewed by reflected light, but it lacks the detailed fabric and mineralogical information observed in a petrographic thin section. Use of thin sections or polished blocks is more often used with EPMA than an SEM but there may be occasions when the SEM may be used to answer questions about the thinsection interpretation, for example, comparison of the distribution of Fe and Mn in Fe-Mn nodules. Thin section analysis with SEM is also useful to search for obscured sedimentary features by mapping for elements that occur in highly stable, high–specific gravity minerals such as Ti and Zr, or as a quantitative analysis tool using the EDS system. Free water in the sample must be removed before impregnation. To prepare a thin section or polished block for examination: 1.

Consolidate the sample with an impregnating agent. Epoxies are used because other resin impregnation agents such as polyester resins are unstable under the electron beam. In selecting an impregnating resin, there are several factors to consider. The first is the stability of the epoxy under the vacuum and electron beam conditions used in the microscope. All epoxies are somewhat unstable under the beam, but some are better than others. The manufacturer should provide this information. The second factor is the composition of the epoxy. Many epoxies contain elements that will show up on the EDS pattern. For example, many products contain trace amounts of Cl or S and some marine epoxies contain Si. Another factor is the viscosity of the

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fixative. If the epoxy is too viscous, it may not penetrate into the finer pores and polishing the sample may be difficult. Diluting with acetone may decrease the viscosity, but this increases the length of time needed for the epoxy to harden. A harder epoxy polishes more evenly. It is best to select an epoxy especially formulated for sample impregnation, ability to transmit electrons, and stability in an SEM. 2.

Once the sample is impregnated, produce a flat face that bisects the features of interest by cutting with a diamond saw.


Make a second cut parallel to the first to produce a 3- to 5-mm thick block. Trim the edges to accommodate the SEM sample holder. The thickness of the block is not as critical as when producing thin sections for petrographic use because only the surface will be examined. If the sample is too thick, however, there is the risk of damage to the signal detectors in the microscope.


Polish the face to be examined with increasingly smaller grit size polishes until the final polish is with a grit size much smaller than will be resolved in the sample. At the minimum, polishing should continue to
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