Optimizing thin film X-ray spectra for quantitative analysis

Energy dispersive X-ray detectors are frequently attached to electron microscopes to enable microanalysis to be performed, but because such detectors accept X-rays generated within an appreciable solid angle, the recorded spectra usually include some spurious contributions from the instrument. This paper describes instrumental modifications firstly to reduce and secondly to permit the subtraction of the residual extraneous contributions. The probable accuracy of this subtraction procedure is examined. Results are presented showing the effects of various instrumental modifications on spectra from thin specimens and demonstrate that by careful attention to experimental details it is possible to separate the spectrum due to the thin specimen alone from all other extraneous signals. Two test specimens and a number of test procedures for investigating the analytical performance of (scanning) transmission electron microscopes are presented. Sources of error and the method of their correction when the thin specimen Bremsstrahlung is used for quantitative analysis are discussed.     

Modification of an EM6G electron microscope for X-ray microanalysis

A dual purpose stage has been constructed for an EM6G 100 kV transmission electron microscope. With this stage the composition of thin films and bulk specimens can be determined by X-ray microanalysis. With thin films a change of specimen cartridge then enables a full analysis of crystal defects in the film to be made using tilt controls incorporated in the stage. Modifications to the stage to reduce background effects in X-ray microanalysis spectra are also described. The alternative use of this system in the bulk analysis of specimens by an X-ray fluorescence technique is also discussed.     

Optimal strategies for imaging thick biological specimens: exit wavefront reconstruction and energy-filtered imaging

In transmission electron microscopy (TEM) of thick biological specimens, the relationship between the recorded image intensities and the projected specimen mass density is distorted by incoherent electron–specimen interactions and aberrations of the objective lens. It is highly desirable to develop a strategy for maximizing and extracting the coherent image component, thereby allowing the projected specimen mass density to be directly related to image intensities. For this purpose, we previously used exit wavefront reconstruction to understand the nature of image formation for thick biological specimens in conventional TEM. Because electron energy-loss filtered imaging allows the contributions of inelastically scattered electrons to be removed, it is potentially advantageous for imaging thick, biological samples. In this paper, exit wavefront reconstruction is used to quantitatively analyse the imaging properties of an energy-filtered microscope and to assess its utility for thick-section microscopy. We found that for imaging thick biological specimens (> 0.5 μm) at 200 keV, only elastically scattered electrons contribute to the coherent image component. Surprisingly little coherent transfer was seen when using energy-filtering at the most probable energy loss (in this case at the first plasmon energy-loss peak). Furthermore, the use of zero-loss filtering in combination with exit wavefront reconstruction is considerably more effective at removing the effects of multiple elastic and inelastic scattering and microscope objective lens aberrations than either technique by itself. Optimization of the zero-loss signal requires operation at intermediate to high primary voltages (> 200 keV). These results have important implications for the accurate recording of images of thick biological specimens as, for instance, in electron microscope tomography.     

Mass thickness determination by electron energy loss for quantitative X-ray microanalysis in biology

As is well known, electron energy loss spectroscopy can be used to determine the relative sample thickness in the electron microscope. This paper considers how such measurements can be applied to biological samples in order to obtain the mass thickness for quantitative X-ray microanalysis. The important quantity in estimating the mass thickness from an unknown sample is the total inelastic cross section per unit mass. Models for the cross section suggest that this quantity is constant to within ±20% for most biological compounds. This is comparable with the approximation made in the continuum method for measuring mass thickness. The linearity of the energy loss technique is established by some measurements on evaporated films and quantitation is demonstrated by measurements on thin calcium standards. A significant advantage of the method is that the energy loss spectrum can be recorded at very low dose, so that mass thickness determination can be made before even the most sensitive samples suffer damage resulting in mass loss. The energy loss measurements avoid the necessity to correct the continuum measurement for stray radiation produced in the vicinity of the sample holder. Unlike the continuum method the energy loss technique requires uniform mass thickness across the probe area, but this is not usually a problem when small probes (<100 nm diameter) are used.     

Quantitative study of spurious X-ray production in thin film microanalysis

When X-ray microanalysis is performed in a TEM on a thin area of a specimen, some a priori indistinguishable spurious photons produced in other zones of this specimen are always recorded. Several mechanisms contribute to this production. For instance, some Bremsstrahlung and characteristic photons are generated by secondary and Auger electrons; a conservative upper bound to this particular contribution is calculated for several materials, and the present approach is compared to the Monte Carlo simulation. It is then shown that, in special test-specimens, the total extraneous contribution of the thick parts of the specimen to the spectra recorded in a thin zone can be measured; different instruments may now be compared in this respect. In the HB5 STEM, this total contribution remains low; its main cause is beam scattering in the specimen, not before it. Finally, an experimental procedure for estimating this bulk contribution in any specimen of interest is proposed. Calculations and experiments are illustrated for the case of gallium arsenide.     

Interfacial energies and surface-tension forces involved in the preparation of thin,flat crystals of biological macromolecules for high-resolution electron microscopy

It is generally agreed that surface-tension forces and the direct interaction between the specimen and either the air-water interface or the water-substrate interface can influence significantly the preparation of biological materials for electron microscopy. Even so, there is relatively little systematic information available that would make it possible to control surface-tension forces and interfacial energies in a quantitative fashion. The main objective in undertaking the present work has been to understand somewhat better the factors that influence the degree of specimen flatness of large, monolayer crystals of biological macromolecules. However, the data obtained in our work should be useful in understanding the preparation of specimens of biological macromolecules in general. Data collection by electron diffraction and electron microscopy at high resolution and high tilt angles requires thin crystals of biological macromolecules that are flat to at least 1°, and perhaps less than 0·2°, over areas as large as 1 μm² or more. In addition to determining empirically by electron diffraction experiments whether sufficiently flat specimens can be prepared on various types of modified or unmodified carbon support films, we have begun to use other techniques to characterize both the surfaces involved and the interaction of our specimen with these surfaces. In the specific case of large, monolayer crystals of bacteriorhodopsin prepared as glucose-embedded specimens on hydrophobic carbon films, it was concluded that the initial interfacial interaction involves adsorption of the specimen to the air-water interface rather than adsorption of the specimen to the substrate. Surface-tension forces at the air-water interface and an apparently repulsive interaction between the specimen and the hydrophobic carbon seem to be major factors influencing the specimen flatness in this case. In the more general case it seems likely that interfacial interactions with either the substrate or the air-water interface can be variously manipulated in the search to find desirable conditions of specimen preparation.     

The use of a phi(rhoz) model for simultaneous determination of composition and thickness in analytical transmission electron microscopy

X-ray microanalysis using transmission electron microscopy (TEM) offers the possibility to perform quantitative analysis with high spatial resolution. Disadvantages are its low accuracy and the problem of preparing very thin specimens and the thin film standards, needed for the analysis and calibration. To calculate composition from the measured X-ray intensities, a peak-ratio method is usually applied, based on the thin film method by Cliff and Lorimer (Proceedings of the Fifth European Congress on Electron Microscopy, 1972, p. 140). We however, applied an entirely different approach, calculating the composition using a full matrix correction method based upon a phi(rhoz) matrix correction model as they are commonly used in EPMA measurements up to 40 kV. The validity of the model under TEM conditions was checked by performing bulk analyses on AlNi and AlTi samples and thin film analyses on an AlNi TEM specimen. In principle, both thin and thick specimens as well as light elements can be analysed this way. No major changes to the TEM set-up or simplifications to the model are needed, only an accurate beam current meter is required.     

X-ray microanalysis of freeze-dried and frozen-hydrated cryosections

The elemental composition and the ultrastructure of biological cells were studied by scanning transmission electron microscopy (STEM) combined with energy dispersive X-ray microanalysis. The preparation technique involves cryofixation, cryoultramicrotomy, cryotransfer, and freeze-drying of samples. Freeze-dried cryosections 100-nm thick appeared to be appropriate for measuring the distribution of diffusible elements and water in different compartments of the cells. The lateral analytical resolution was less than 50 nm, depending on ice crystal damage and section thickness. The detection limit was in the range of 10 mmol/kg dry weight for all elements with an atomic number higher than 12; for sodium and magnesium the detection limits were about 30 and 20 mmol/kg dry weight, respectively. The darkfield intensity in STEM is linearly related to the mass thickness. Thus, it becomes possible to measure the water content in intracellular compartments by using the darkfield signal of the dry mass remaining after freeze-drying. By combining the X-ray microanalytical data expressed as dry weight concentrations with the measurements of the water content, physiologically more meaningful wet weight concentrations of elements were determined. In comparison to freeze-dried cryosections frozen-hydrated sections showed poor contrast and were very sensitive against radiation damage, resulting in mass loss. The high electron exposure required for recording X-ray spectra made reproducible microanalysis of ultrathin (about 100-nm thick) frozen-hydrated sections impossible. The mass loss could be reduced by carbon coating; however, the improvement achieved thus far is still insufficient for applications in X-ray microanalysis. Therefore, at present only bulk specimens or at least 1-μm thick sections can be used for X-ray microanalysis of frozen-hydrated biological samples.     

The application of analytical electron microscopy to the study of diseased biological tissue

A routine method is described for X-ray microanalysis of thin specimens of biological tissue containing mineral particles in cancerous growths. Such a method allows information to be obtained that relates pathological history to histology, electron microscopy and X-ray microanalysis. Classification of minerals is possible in a way that is not provided by bulk analysis. The technique provides baselines of elemental data of minerals from various sources that may be used to classify particles found present in certain tumour growths.     

Electron Beam Heating Temperature Profiles in Moderately Thick Cold Stage STEM/SEM Specimens

The analytic solution for the model of electron beam heating a moderately thick STEM/SEM specimen was used to calculate the steady state temperature profiles developed in the bulk of the specimen. For thin specimens one maximum in the temperature profile was found near the surface. The location of this maximum shifted away from the surface with increasing sample thickness. For specimens of thickness approaching the electron range two maxima were found: one close to the surface (as in thin samples) due to a ‘self-insulating’ effect, and another maximum near the sample-substrate interface—a result of very rapid increase in the energy loss by the electrons near their penetration range. These results are of particular interest for X-ray microanalysis where high beam currents are used, resulting in potentially large temperature rises in the bulk of the specimen.     

Improvement of quantitation of biological X-ray microanalysis

Absolute measurements of elemental concentrations within thin biological samples are often made by reference to a series of standards which resemble the samples in chemical and physical properties and the linear relationship between (p-b)/c and concentration. This principle requires that the chemical and physical properties of the matrix remain constant throughout a series of standards with different elemental contents and throughout different regions of the samples. Some of the changes undergone by specimens during X-ray microanalysis, e.g. loss of elements or organic mass loss, are also influenced by the composition of the matrix. A simple empirical modification to the linear (p-b)/c versus concentration relationship is presented to account for some of these effects and therefore improve quantitation of analyses.     

Low temperature techniques for X-ray microanalysis in pathology: Alternatives to cryoultramicrotomy

Many diseases are associated with a change in the distribution of diffusible ions at the cell or tissue level. These diseases can profitably be studied by X-ray microanalysis. This technique for the study of ion distribution requires the use of cryoprepared specimens. Analysis at low or medium resolution can be carried out on thick or semi-thick cryosections, or on frozenhydrated or freeze-dried embedded bulk samples. Such analyses are particularly useful in the initial stages of an investigation or when data from a large number of samples have to be acquired. Also X-ray microanalysis of cultured or single cells prepared by freeze-drying can be used to rapidly collect information on a large number of cells. Analysis at high resolution has to be carried out on thin sections: Cryosections or sections of freeze-substituted or freeze-dried embedded tissue. For the latter type of specimens, the use of low-temperature embedding methods may have important advantages.     

Development and comparison of the methods for quantitative electron probe X‐ray microanalysis analysis of thin specimens and their application to biological material

In recent years, there has been a return to the use of electron probe X‐ray microanalysis for biological studies but this has occurred at a time when the Hall programme which acted as the mainstay for biological microanalysis is no longer easily available. Commercial quantitative routines rely on the Cliff‐Lorimer method that was originally developed for materials science applications. Here, the development of these two main routines for obtaining quantitative data from thin specimens is outlined and the limitations that are likely to be met when the Cliff‐Lorimer routine is applied to biological specimens is discussed. The effects of specimen preparation on element content is briefly summarized and the problems encountered when using quantitative analysis on resin‐embedded materials emphasized.     

Evaluation of several common standards for the X-ray microanalysis of thin biological specimens

The question of the best type of standard to use for X-ray microanalysis of thin biological specimens remains unanswered. Standards embedded in an organic matrix have the advantage that they resemble biological specimens, but their composition is generally not known exactly. We compared several standards and, surprisingly, inorganic binary salts sprayed onto a supporting film were the most suitable: they corresponded closely with several other methods using organic matrices; they were easily produced; and their composition is known. Glutaraldehydeurea aminoplastic resin thin sections and thin films containing dissolved salts were problematic. The composition of the polymer appears to be variable, and the thin films did not correspond with any other standard tested. Chelex¹⁰⁰ bio-standard beads and flakes loaded with accurately determined concentrations of ions, embedded in epoxy resin and thin sectioned, tended to correspond to the results obtained with the binary salts. However, the results from some bio-standards were inexplicably aberrant. An epoxy resin standard was used for bromine, and was found to agree closely with the binary standards.     

Quantitative electron probe microanalysis of rough targets: testing the peak-to-local background method

Rough samples with topography on a scale that is much greater than the micrometer dimensions of the electron interaction volume present an extreme challenge to quantitative electron beam x-ray microanalysis with energy-dispersive x-ray spectrometry. Conventional quantitative analysis procedures for flat, bulk specimens become subject to large systematic errors due to the action of geometric effects on electron scattering and the x-ray absorption path compared with the ideal flat sample. The best practical approach is to minimize geometric effects through specimen reorientation using a multiaxis sample stage to obtain the least compromised spectrum. When rough samples must be analyzed, corrections for geometric factors are possible by the peak-to-local background (P/B) method. Correction factors as a function of photon energy can be determined by the use of reference background spectra that are either measured locally or calculated from pure element spectra and estimated compositions. Significant improvements in accuracy can be achieved with the P/B method over conventional analysis with simple normalization.     

The continuum normalization method for quantification of X-ray spectra in biological microanalysis. 1. Generalized bremsstrahlung production cross-sections and analysis using standards

The thin self-supporting biological specimens used for quantitative X-ray microanalysis are problematical because the sections are most unlikely to be uniform in thickness or density, so the intensities of the characteristic lines alone are not a good measure of composition. The method developed to overcome these problems was introduced by T. A. Hall in 1971 and uses the bremsstrahlung or continuum intensity recorded in the X-ray spectrum to normalize each characteristic line, and hence is frequently referred to as the continuum normalization (CN) procedure.
  Reformulating the CN method of quantification in terms of generalized cross-sections and calculating more accurate values of bremsstrahlung production using a formula allows us a better understanding of the options open to the analyst of biological thin sections by which the errors in the measurement may be reduced. If one chooses to use the original Hall (1971 ) method using Kramers cross-sections, the window measuring the continuum for normalization should be set in the 4–7 keV region for typical scanning electron microscope and microprobe beam energies, 20–40 kV, and above 10 keV for transmission electron microscope energies of 80 kV and above. Although it is clear that peak counts must not contribute to the white count, the window should be as wide as possible to reduce statistical errors.     

Quantitative electron probe analysis: Problems and solutions

Quantitative electron probe microanalysis of thin films was evaluated with a series of sulfur-containing proteins, and a method is given for correcting errors due to changes in detector calibration (centroid position and resolution). The correlation coefficient between the results of electron probe analysis and the stoichiometric concentrations of sulfur was 0.998. Shifts in detector calibration that affect particularly elements having overlapping peaks are shown to be correctable by including the first and second derivative of the characteristic peak in the multiple least squares fitting routine used to determine the number of characteristic X-rays in the spectrum. This method allows the accurate measurement of low concentrations of Ca in the presence of high concentrations of K normally encountered in biological specimens. A systematic small error in the quantitation of Na is reported and shown to be due to digital filtering of this region of the continuum that has a relatively high curvature; methods for correction are proposed.     

Mass determination of thin biological specimens using backscattered electrons. Application in quantitative X-ray microanalysis on an automated STEM system

The capabilities of modern computerized X-ray analysis systems can be expanded to the acquisition of various signals available in the electron probe microanalyzer, in parallel with the X-rays. These facilities allow the use of backscattered electrons for the measurement of the total specimen mass thickness, which can be used in mass fraction calculations, up to a (biological) specimen thickness of 10 micron. A mass measurement procedure based on the use of backscattered electrons may become an alternative for the X-ray continuum normalization method, often used in electron probe X-ray microanalysis. A mass measurement procedure using backscattered electrons is described, and preliminary results are given.     

Ionic composition of rat airway surface liquid determined by X-ray microanalysis

The thin layer of liquid that lines the conducting airway epithelium, the airway surface liquid (ASL), is important for mucociliary clearance. Altered ionic composition and/ or volume of the ASL play a major role in the pathology of airway diseases such as cystic fibrosis. Since the ASL is a thin layer, it has been difficult to exactly determine its composition. The present paper describes two techniques that have been developed and used to study ASL composition: X-ray microanalysis of frozen hydrated rat trachea, and an ion-exchange (dextran) bead method, where dextran beads were placed on the airway epithelium to equilibrate with the ASL; the beads were then collected under silicone oil, dried and analyzed by X-ray microanalysis. The results from both frozen-hydrated specimens and from the dextran beads showed that ASL from rat trachea is hypotonic. Concentrations of Na, P, S, and K were higher in the frozen-hydrated ASL, in which mainly the mucus layer is analyzed, compared with the dextran bead method, in which mainly the periciliary liquid is sampled. Also the composition of rat nasal fluid was investigated by the dextran bead method. This fluid was somewhat hypertonic because of a high K concentration. The ionic composition of the nasal and tracheal fluid can be manipulated by cholinergic or alpha- or beta-adrenergic stimulation. Collecting ASL with dextran beads did not disturb the integrity of the airway epithelium. The ionic composition of the collected beads remained stable for several days during storage in silicone oil. It is concluded that X-ray microanalysis is a suitable method to determine the ionic composition of ASL.     

X-ray microanalysis of wet biological specimens in the environmental scanning electron microscope. 1. Reduction of specimen distance under different atmospheric conditions

X-ray microanalysis of non-biological and biological specimens was carried out in the environmental scanning electron microscope (ESEM) under different conditions of specimen distance (the distance travelled by the electron probe within the specimen chamber) and chamber atmosphere. Using both water vapour and argon atmospheres, it was shown that reduction in specimen distance had no effect on atmospheric gas X-ray signal in either case. Unlike water vapour, increased levels of argon (up to 10 torr) caused a marked depression of specimen P/B ratios, with a decrease in both characteristic and background (continuum) counts. These effects in argon were not altered by reduction in specimen distance. Specimen distance was important in relation to beam skirting and elemental analysis. With an extended assembly (short specimen distance), beam skirting in a water-vapour atmosphere was much reduced – leading to enhanced element detectability in a discrete biological specimen (Anabaena cyclindrica).