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Challenges and victories at the SEM unit during lockdown
Author: CAF
Published: 17/08/2021

​Since the national lockdown due to the COVID-19 pandemic started in March 2020 rapid changes and challenges to the status quo in the work environment became a reality. Some industries were quick to adapt, while others had to implement a complete overhaul of how they conducted business. Although many businesses could shift their day-to-day operations to a virtual platform, this was not the case for many researchers across the world who had to keep their experiments going in a time of severe restrictions. In this context, it became evident what crucial role core facilities support staff played in upholding research output and providing researchers or students with the critical data required for publication and completion of degrees.

The use of digital technologies and social media applications became the Scanning Electron Microscopy (SEM) Unit team's primary mode of communication and collaboration. Some of the interesting international projects that were accomplished virtually by the SEM Unit are showcased in Figures 1–6. 


Figure 1. Montage images on geological rock samples, indicating elemental phase maps.


Figure 2. Perovskite morphological differences and elemental phase differences.


During the strict lockdown period, no clients were allowed into the building housing the SEM Unit. A protocol was established whereby the samples were dropped in front of the building and decontaminated. In normal situations, students were able to receive training and complete the bulk of their work on their own but during this time a substantial number of samples and SEM analysis needed to be handled, prioritised and completed in a limited amount of time by the SEM team. This required multitasking, compartmentalisation, efficient time management and excellent communication skills. 

A sample submission form system was created with online webcam communication to establish the specifics of the SEM analysis required, which varied significantly among the diverse types of samples that arrived at the EM Unit. 

The images below give a glimpse of the micro- and nano-scale universe where an electron microscopist spends most of his or her time. It is not common knowledge that a snail possesses a tongue and that said tongue is covered in teeth (radula). It is also not typical that a human meets the gaze of a fruit fly. 


Figure 3. Image of the radula of snail in native state and mounted onto SEM stub using a light microscope. Imaged using SEM MERLIN with an SE2 detector. Scale bar: 10 µM.


Figure 4. Micrographs of fruit fly structures were observed with the MERLIN SEM, using the SE2 and InLENS detector. Scale bar: 200 µM.


Figure 5. Analysis of seaworms, with the focus being specifically on the male’s sperm cells to help establish the reproduction cycle of these underwater sea creatures. ​Prepared with a fixation protocol using 2.5% GLA and 1M Cacodylate in the CAF EM lab, followed by a dehydration series in a range of ethanol concentrations from 30% to 100% and dried using 100% HMDS. Scale bar: 1 µM. 

Dr. Jurgen Kriel volunteered to conduct critical SEM analysis for the Stellenbosch Nanofiber Company who produced the necessary filter layers for medical-grade face masks. This allowed him to explore the conventional SEM capabilities of the Apreo and he had to master the art of SBF-SEM through virtual training sessions. Cloud technology and familiarity with several types of software played a key role. Kriel became the first certified SBF-SEM specialist in South Africa and the African continent in October 2020.


Figure 6. SBF-SEM 3D rendering of melanin-containing cells in lizard skin samples obtained using the Apreo Volumescope SEM. Serial sections of samples prepared following an adapted mega-metal protocol were acquired at a Z-width of 50 nm and aligned to generate a 3D image stack. 3D rendering of melanin-containing ramifications is indicated in purple, cell nuclei are indicated in white and translucent colors indicate individual cells within the tissue samples. Scale bar: 5 µm. 


Figure 7. SBF-SEM of neurons in mouse cerebral cortex. Samples were prepared using a standard mega-metal and resin-embedding protocol for tissue and acquired using the Apreo Volumescope SEM. A) Individual high-resolution image of single SBF. B) Orthogonal view of SBF dataset consisting of 200 z-slices at 50 nm z-width. C) 3D rendering of individual neurons in the region of interest outlined in red.