Institute of Geophysics of the CAS, v. v. i.


Microstructural analysis

Microstructural analysis qualitatively and quantitatively describes the spatial and geometrical relations between rock components smaller than discernible by unaided eye. Depending on the components scale and nature of the investigated microstructures various microscopic techniques are applied for their visualisation and measurement. The analysis results serve for interpretation of the rock origin, of the deformation events it experienced and of the effect of the resulting microstructures on the rock physical properties.

Scanning electron microscope techniques

A scanning electron microscope (SEM) is a device using a beam of high energy electrons that interfere with a sample surface to produce and detect a variety of secondary effects carrying information on the sample surface morphology, composition and crystalline structure and orientation. For the purpose of the electron microscope analyses mentioned below we cooperate with the electron microscopy lab at the Institute of Petrology and Structural Geology of the Faculty of Sciences of the Charles University in Prague.

Backscattered and secondary electrons

For detailed observation of microstructures in petrographic thin sections or on polished or natural surfaces either the primary electrons scattered from the sample surface (backscattered electrons, BSE) or secondary electrons (SE) emitted by the sample surface can be used. The SEM images from one or the other mode are reassembled from raster measurements using grayscale to convert the detected electron count to the image gray shade. Since the scattering of the primary electrons is mainly affected by the density of the material, the BSE mode is useful for visualisation of spatial distribution of the rock forming minerals (Fig. 1a). Contrastingly, the SE mode provides high depth of field of the images and is thus suitable for visualisation of the morphology of natural (e.g. fracture) surfaces (Fig. 1b).

Figure 1. Scanning electron microscope images of a fracture surface in granite acquired using (a) backscatter electrons and (b) secondary electrons.

Electron backscatter diffraction

A rock is a natural solid aggregate of crystals (grains) of one or more minerals which in turn are homogeneous solids formed by an anorganic chemical compound ordered in unit cells forming by regular repetition a crystal lattice (Fig. 2a). The combination of the lattice parameters (the lengths of the unit cell edges and angles between them, Fig. 2b) and of the unit cell crystal system are unique for each mineral.

Figure 2. (a) Scheme showing the regular repetition of a unit cell (pink cube) forming a crystal lattice and (b) the meaning of the lattice parameters.

For measurement of the lattice parameters and of the lattice orientation the electron microscope device is used in electron backscatter diffraction (EBSD) mode. In this mode the configuration of the SEM device is characteristic by the electron beam incident at high angle to the rock specimen (Fig 3.). The interference of the electrons with the crystal lattice results in diffraction “Kikuchi” patterns (Fig. 3) the geometry and orientation of which correspond to a specific mineral and its lattice orientation.

Figure 3. (left) Electron backscatter “Kikuchi” pattern and (right) scheme of its origin by diffraction of electrons (e-) within the specimen (brown).

The orientations are usually measured on polished surfaces or thin sections with an area on the order of cm2 and drawn on maps colored in function of the crystal lattice orientation (Fig. 4).

Figure 4. (a) Polarized transmitted light micrograph of a salt rock and (b) the corresponding map of EBSD crystal lattice orientation using (c) a colour palette relating the orientation of crystallographic directions with horizontal-east direction of the map (Závada et al., 2012).

Electron microprobe

The electron microscope device is also used for chemical analysis in the mode known as electron microprobe. The analysis is based on either energy or wavelength spectrocopy of X-rays emitted from the tested material due to excitation and reequilibration within the elements electron shells provoked by the electron gun primary electrons. The energies or the equivalent wavelengths of the X-ray photons are unique for each element and thus enable its identification. To evaluate the material chemical composition relative counts of the emitted photons per element are measured in a defined time period. In this manner, the measurements can be done on a spot for precise analysis of a restrained specimen volume or in a raster or along a profile in order to reveal the distribution of the elements of interest.

Optical microscope techniques

Optical microscopy provides basic structural and indirectly also chemical information on a rock sample with low equipment costs and little sample preparation. For this method, rock specimens are prepared to the form of petrographic thin sections having 30 µm thickness and an area typically between 5 and 10 cm2 allowing observation of an ensemble of tens to thousands of grains depending on the rock grain size. The microscope Nikon Eclipse 80i at our institute is equipped for observation of petrographic thin sections in transmitted polarised light, in reflected light and in UV-excited green fluorescent light.

Plane- and cross-polarized light

Polarised light microscopy (PLM) is based on mineral-specific optical properties affecting polarised light transmitted through the thin section. One of the properties is the birefringence of optically anisotropic minerals resulting in specific interference colors when observed in cross polarised light. This property is demonstrated in Fig. 5 by sequence of 180 micrographs recorded during step-wise rotation of the specimen by 2° with respect to the microscope polarizators.

Figure 5. Sequence of micrographs demonstrating the view in cross-polarized light during the thin section rotation.

Taking advantage of the optical propertes, the PLM serves to identify the rock mineral composition and consider the rock microstructural relationships. Using digital image analysis various microstructural parameters such as grain size or grain boundary and crack orientation can be statistically quantified. 

Examples of microstructres of three basic rock types - magmatic, metamorphic and sedimentary - are shown in microphotographs in Fig. 6, for an extended number of microphotographs see our gallery of microstructures.

Figure 6. (a, c, e) Plane polarised light and (b, d, f) cross-polarised light micrographs showing (a, b) magmatic microstructure of granite, (c, d) microstructure of metamorphic contact of serpentinised peridotite (left) and carbonate rock (right) and (e, f) sedimentary microstructure of a carbonate rock.

Epoxy fluorescent light

For observation of the rock microporosity the specimens are impregnated by a fluorescent epoxy prior to preparation of the thin section. The epoxy-filled void space is then highlighted using UV light excitation of the fluorescent epoxy (Fig. 7).

Figure 7. Micrographs of granite acquired in (a) plane polarised light, (b) cross-polarised light and (c) fluorescent light (Staněk et al., 2013).

Digitalisation and numerical analysis

Digital images acquired by both electron and optical microscopes are subject to numerical analysis of geometrical parameters of the microstructural featurest of interest. For example, the grain boundaries and the impregnated microporosity network shown on Fig. 7 were digitally traced and their orientations were analysed. The orientation distributions resulting from the analysis in three mutually perpendicular thin sections are displayed in Fig. 8 by means of rose diagrams. The diagrams show that the grain boundaries and cracks except in quartz have similar orientation as the granite magmatic structure represented by preferred orientation of long axes of the grains (approximately top-left to bottom-right in the figures). In contrast, the highest proportion of cracks in quartz is oblique to the magmatic structure and subparallel to natural macroscopic fractures limiting the sampled block in terrain (horizontal in the figures).

Figure 8. Orientation distribution of grain boundary and crack microporosity in granite shown in Fig. 7. (a) Orientation of the sections with respect to the sample mesostructures and orientation distributions of (b) grain boundaries and of (c, d, e, f) cracks in three mutually perpednicular thin sections (Staněk et al., 2013).

Sources of figures

1, 6: Staněk, M.




4. Závada, P., Desbois, G., Schwedt, A., Lexa, O. & Urai, J. L. (2012). Extreme ductile deformation of fine-grained salt by coupled solution-precipitation creep and microcracking: Microstructural evidence from perennial zechstein sequence (neuhof salt mine, germany), Journal Of Structural Geology 37, 89–104, DOI: 10.1016/j.jsg.2012.01.024.

5. Machek, M.

7. Staněk M., Y. Géraud, O. Lexa, P. Špaček, S. Ulrich and Marc Diraison, (2013), Elastic anisotropy and pore space geometry of schlieren granite: direct 3-D measurements at high confining pressure combined with microfabric analysis, Geophys. J. Int., DOI: 10.1093/gji/ggt053.