SEM Laboratory

The SEM Laboratory analyses geological samples by means of user-controlled and automated scanning electron microscope (SEM). The microscope is able to generate images of polished rock sections as well as to display the topography and structure of crystals and rock-fragments like sandstones.

GEUS has acquired a ZEISS Sigma 300VP Field Emission Scanning Electron Microscope, and we can now offer to make automated mineralogy analyses on entire thin sections or polished mounts relevant for mining and exploration as well as investigations of reservoirs (oil & gas and geothermal energy).

The new instrument was installed in the autumn of 2017. The instrument is equipped with 2 Bruker Xflash 6|30 129 eV EDS detectors, an Bruker e-FlashFS EBSD detector, a 185-850 nm Light-Guide Cathodoluminescence detector, and it is able to work under variable pressure conditions, with high vacuum condition of 3.25 x 10-4 Pa and low vacuum conditions between 2-133 Pa.

The Scanning Electron Microscope contains the Mineralogic software platform for mining and reservoir rocks. With this software, are able to perform automated mineralogy on entire thin sections, polished mounts (e.g. drill cores, heavy mineral separates, cuttings samples) or parts thereof.

Analytical methods

(energy dispersive spectrometry, EDS)

The chemistry of the samples is analysed with two energy dispersive spectrometers (EDS). These detectors allow for the simultaneous measurement of major and minor elements in concentrations larger than c. 0.5 wt%. The technique can be applied on points, selected areas or for element mapping.


Point analysis with EDS detectors, showing the chemistry of individual minerals. The spectrum can be quantified. (click on the picture to view it in full size

element mapping

 Example of element mapping with EDS software. Individual mineral maps can be combined.

(Zeiss Mineralogy software)

Mineralogy of polished sections can be automatically categorised by the Zeiss Mineralogic software. Before analysis and classification of minerals, the mineral library for the analysis needs to be updated by a geologist to match the exact mineral composition for the samples in the project. During analysis, the software creates a false-coloured image based on the underlying Back-scattered electron image and the interpretation of chemical analyses (EDS) for each pixel of the image. The software includes options for mining, like liberation and interlocking analyses, and reservoir analyses, like porosity measurements.

element map

Example of an element map showing two types of pyroxene (green and wine-red), ilmenite (orange) and olivine (pink) in plagioclase (blue). Width of view: ca. 8 mm. Pixel size 10 µm.

The same software can also be used for particle analysis (Computer-controlled scanning electron microscopy, CCSEM). Here, the major and minor element chemistry, grain morphology, liberation, association and locking parameters can be determined on an individual grain basis. The technique can be applied to loose grains or heavy minerals in epoxy mounts and is often applied for provenance, mining and exploration studies.

Automated particle analysis
Automated particle analysis applying the CCSEM technique with the Zeiss Mineralogic software. The mineral classification is per particle, allowing for a faster analysis of the sample.

(Secondary electrons, SE)

With the secondary electron detectors, 3D images of structures, topography and relief of i.e., minerals, fossils, porosity, and mineral overgrowths can be made. The SEM has two SE detectors (for high vacuum and variable pressure conditions) that give birds’ eye view of the sample, and an inLense detector that views the sample exactly from above.

  Coccolith microfossil

Coccolith microfossil in porous chalk. Image taken with the InLense SE detector (view from above).

Biotite grain

Biotite grain in granite rock. Image taken with the variable pressure SE detector.

(Backscattered electrons, BSE)

The SEM’s back-scatter detector provides an image of the sample’s surface, based on the average atomic number and density of the sample. The technique is usually applied on polish sections.

Two material contrast images

Two material contrast images made with the SEM’s back-scatter detector.

(growth information, CL)

This imaging technique shows variations in trace element composition or in the temperature during crystallization. It can be applied to image zircons, apatites, diagenetic overgrowths in silicates and carbonates, healed fault zones, ore formations and other cases where growth zonations are expected.



Sandstones consisting mainly of quartz grains with quartz overgrowths, which are recognised in cathodoluminescence by a darker grey rim than the core detrital grain. A. Backscattered Electrons, B: cathodoluminescence.

Internal zonation

Internal zonation in zircon minerals, revealed by cathodoluminescence. 

(Electron backscatter diffraction, EBSD)

The electron backscatter diffraction detector (EBSD) can be use to analyse the crystallographic orientation of minerals in samples. The method is for example applied to study preferred orientations, strain in shear zones, material defects, and preferred directional growth on mineral surfaces. The method requires a final polishing step before analysis.

Orientation of quartz grains

Orientation of quartz grains in a sheared pegmatite analysed with EBSD.

GEUS has a sample preparation laboratory and an optical microscopy facility where the work on the SEM can be organised. The SEM laboratory has the option to platinum- or carbon-coat samples. Uncoated samples can be studied under low-vacuum conditions.


Mikael Pedersen
Head of Department
Mapping and Mineral Resources
Nynke Keulen
Senior Researcher
Mapping and Mineral Resources

Restrictions on access

Training is required before the Scanning Electron Microscope can be used independently. For short projects, the microscope can be booked with assistance.


Please contact the laboratory for information on prices.