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Scanning Electron Microscopy (SEM)

​​​​​​​​​​​​​​​​scanning electron microscopy western cape

Scanning Electron Microscopy (SEM) is a powerful tool for topological, morphological and chemical analysis of a broad range of samples. These data range from determining the elemental composition of certain materials to the 3D rendering of specific structures of interest in biological tissue samples. In combination with other imaging modalities, SEM offers the perfect platform for precision analysis in both the material and biological sciences. Our equipment is housed on both Stellenbosch (STB) and Tygerberg (TYG) campuses. Example data of what is achievable with our systems.​

​How to send samples for analysis:





​Register for CAF ID

  • ​Fill in and send sample submission form to SEM Unit

  • Samples must be clearly labelled with name of client and date of delivery
  • ​A turnaround time of approximately 1-2 weeks is expected

  • Results will be available via SharePoint/Google Drive or can be collected from SEM unit physically​
  • ​Samples need to be collected within a month after completion of analysis or it will be discarded​

Electron Microscopes:

Zeiss MERLIN SEM (STB):

Combining ultr​a-fast analytics and high resolution imaging, the MERLIN has wide range of beam flexibility and is fitted with a number of imaging detectors, including: an in-lens and chamber secondary (SE) detectors (nano & micron-scale imaging), an in-column energy selective backscattered (ESB) electron detector, a retractable 5 diode backscattered electron detector (BSD) (nano-BSE & 5-diode detector nano to micron imaging), a cathodoluminescence (CL) detector and a scanning transmission electron microscopy (STEM) detector. Analytical capability is also provided by the Oxford Instruments XMax 20mm2 [KJ[1] detector for high resolution spectra and high spatial resolution maps using energy dispersive X-ray spectrometry (EDS). Furthermore, the instrument has a Quorum cryostage for micro-quantitative analysis of beam-sensitive samples, as well as a facility for local charge compensation (CC) for the analysis of insulating samples.
DX elemental map of nanofibers showing contaminants in colour overlay with BSD.


Zeiss EVO MA15 SEM (STB):

The EVO is fitted with both secondary and backscattered electron detectors for imaging, as well as an Oxford Instruments XMax 20mm2 [KJ[2] Electron Dispersive X-ray (EDS) detector and Wave Dispersive X-ray Spectrometer (WDS) for analytical capabilities. It is capable of identifying and quantifying all elements in the periodic table except H, He, and Li. By following the “k‐ratio" (unknown/standard) measurement protocol development for electron‐EDS/WDS. EDS&WDS is a non-destructive analysis technique used to obtain elemental information about a range of materials by measuring characteristic x-rays within a small wavelength range. EDS/WDS analytical techniques include the following-: elemental phase mapping, linescans/traverse, spot/area, feat​ure & automate analysis.
Elemental phase map across the surface of a garnet sample. The heat map indicates high concentrations of specific elements.


ThermoFisher APREO Volumescope (TYG):

The APREO is a highly versatile SEM capable of conventional high-resolution imaging (SEM/STEM) as well as 3D volumetric acquis​ition through Serial Block-Face SEM (SBF-SEM). SBF-SEM combines in situ sectioning and imaging of resin embedded tissue within the SEM vacuum chamber in a fully automated fashion for reconstruction of structures of interest. This is especially useful for medical researchers and biologists, as cellular ultrastructure can be assessed in its 'natural' 3D confirmation. For conventional SEM, the Apreo is fitted with an Everhart-Thornley (ETD) detector (SE/BSE imaging) as well as three Trinity detectors for SE imaging, a STEM detector for nano-scale imaging, and a Directional Backscattered (DBS) detector. The APREO is also capable of low-vacuum, variable pressure SEM that allows image acquisition of certain uncoated samples.
Serial block-face (SBF) SEM 3D rendering of melanin containing cells in lizard skin samples. 
Melanin indicated in purple, cell nuclei in 
white and translucent colours indicate 
individual cells within the tissue.


Support Equipment:

Leica EM UC7 ultra-microtome (TYG)

Zeiss Axio & Stereo Light Microscopes (STB)

Tousimis Critical Point Dryer (TYG)

Gold/Carbon Sputter coaters (TYG & STB)