Or, how to explain a large digital skeletal repository to your grandmother
As we return to the university after the summer holidays, we meet in our small clusters of frazzled postgraduate students to lament the fact that none of our extended family can fully understand what our work entails on daily basis. So, we decided it would be a good idea to give detailed information on what we do at the University of Pretoria chapter of Bakeng se Afrika, down to the minutia of labelling external hard drives. How are we going about creating a large digital skeletal repository?
Note: We write this from the perspective of the University of Pretoria. We do have two more skeletal collections as part of the consortium (at Sefako Makgatho Health Sciences University and Stellenbosch University), but because our contexts are a little different, we decided to each write a blog post from our own perspective. Keep an eye out for the trials and tribulations of transporting skeletal material across the country from Stellenbosch University and building a skeletal repository from scratch from Sefako Makgatho Health Sciences University.
Step 1: Write a research protocol
All South African health research needs to be approved by an accredited Health Sciences Research Ethics Committee (HSREC), and the University of Pretoria (UP) is no different. The repository is housed at UP, therefore all researchers wanting to access the data from the Bakeng se Afrika skeletal repository need to gain approval from our HSREC. In order to facilitate this process, we recommend that anyone wanting to use the repository contact us beforehand, so that we may provide some advice with regards to research protocols and submitting to research ethics committee.
If you would like to perform new computed tomography scans on bones – instead of using those already on the database – you will also need approval from the curator of the Pretoria Bone Collection; the approval will form part of your application to the HSREC. Then, you will need to apply for experimental scanning time at the South African Nuclear Energy Corporation (Necsa). Necsa sends out calls for research proposals three times a year. You will be required to complete a research proposal template and submit it on time. If your research proposal is approved, they will grant you experimental time according to your needs.
Step 2: Select the bones to be scanned
The Pretoria Bone Collection (PBC) at the University of Pretoria consists of just over 1000 individuals with known demographics and mostly complete skeletons. The skulls and post-crania are housed in boxes, specifically designed and built for skeletal curation purposes. The boxes are organised according to number in large temperature controlled storage rooms. The PBC can only be accessed by selected staff and students at the university and by individuals with a valid research proposal.
Gabriele Krüger, the curator of the PBC, uses her database to select sets of bones to be scanned. The bones chosen relate to the type of research being conducted concurrently or bones that are listed as a priority to be scanned for the repository as part of our Standard Operating Procedures (SOPs).
Gabriele is assisted by postgraduate students to help carry the boxes of bones (usually 30 – 40 bones at a time) from the storage rooms to the laboratory of the biological anthropology section. The bones, properly packed in boxes and protected by bubble wrap, are then loaded into the car that will be transporting them to the South African Nuclear Energy Corporation (Necsa), usually Samantha Muller or myself. The bones are accompanied by a letter, written by the curator, giving permission for them to be transported and scanned.
Step 3: Transporting the bones to Necsa
With the bones securely bubble-wrapped in boxes, stacked in your vehicle, you will take on the 45 min drive to Necsa, located near Broederstroom in the North West Province. It is vital to always ensure that you have the transporting letter, in case you are stopped by the police. You will also need about R30 in cash (or a credit card – debit cards do not work), for the toll gates on the way and back. Once at Necsa, aim for entrance at Gate 1 or Gate 3 – Gate 2 is currently not in use.
Step 4 (linked to Step 1): Gain access to Necsa
Necsa is a National Key Point and getting into Necsa is no easy feat. In order to gain access, researchers have to register their intent to visit the Radiography and Tomography (RADTOM) facility well before the visit. The Necsa team requests a copy of your ID and the specific dates of your visit. When you arrive at the gate, you report to reception, where your picture is taken and you are issued with a temporary day pass. You also have to declare your laptop in their declaration book – and they give you a pass for that as well. If you are not accompanied by a contract worker or Necsa staff, they will phone someone from the lab you are visiting to escort you to the facility. As we planned to visit the facility often, many of our BsA researchers have acquired contractor’s access. For that, you must complete Necsa’s safety training exercise, after which you get to register your fingerprint for biometric access and are issued a contractor’s card.
Once you are inside Necsa, it is a good idea to memorise the road to the RADTOM facility.
The first time I went, I got lost and drove around for 45 minutes. Necsa is a vast compound made up of incredible technology surrounded by true South African bushveld. Towers and chimneys extend from mysterious buildings, and the zebra and warthogs graze in the open veld that swallows every available
space.
Step 5: Scan the bones
The Necsa RADTOM facility is accessed via the back door of Building P1500 (Physics building). You enter through a wooden door, reinforced by a steel gate, which is locked by a pin code. You sign in at the door as you walk into the analysis room. Four incredibly powerful analysis workstations, all loaded with various analytical softwares (such as VGStudioMax, Volume Graphics) are available for researchers to work on. We have spent many hours with these computers, under the tutelage of Necsa’s instrument scientists, Dr Lunga Bam and Mr Jakobus Hoffman.
If you still have the bones with you, Kobus and Lunga will help you carry them to the scanner – which is situated at the back of the facility. The bones are packed away on shelves, ready to be scanned.
The scanner used is called a Nikon XT H 225L industrial Computed-Tomography system (Nikon Metrology, Belgium), and looks like a large white box (also called a cabinet), with a sliding door into which our samples are placed. The bone selected to be scanned will be secured and stabilised by the instrument scientist using a combination of Styrofoam, florist foam and tape, to manoeuvre the bone into the right position as well as avoid any movement or vibration during the scanning process. The stabilised specimen is placed inside the scanner on a turntable and the sliding door is closed. The operator sets the optimum scanning parameters – a process that is complicated in itself and requires specific training. The MicroXCT starts the acquisition by taking two-dimensional radiographic projections at a very high resolution. The specimen rotates over 360 degrees and is scanned from all sides. As many as 1000 individual projections are created and directly saved on to the acquisition computer, each with a unique name related to the bone being scanned. This scanning process takes approximately 35 minutes.
Once the scan is complete, the projections are transferred to a dedicated computer, the reconstruction PC, at which the researcher uses the Nikon CT-Pro 3D software (Nikon Metrology, Belgium) to reconstruct the 2D projections into a three-dimensional (3D) volume. The process takes only approximately 2-3 minutes. The final volumes are then exported in a .vgl format or in 16-bits .tif images, according to the reconstruction guidelines of the particular project or institution.
In order to provide the best resolution possible for each type of bone, some bones (specifically long bones, such as the femur) are scanned in two parts – usually proximal and distal ends. These two digital bone-halves need to have overlapping parts in the separate scans in order to stitch them together. The stitching, and any other segmentation or analysis can happen on the VGStudioMAX software at one of the RADTOM facility workstations.
Step 6: Store and backup the scans
Currently, the reconstructed data is copied onto an external hard drive and marked off on the scanning checklist as completed. The scan is then backed up onto a second external hard drive. Each hard drive is marked with a unique name, which includes a number, the institution it is from and the investigator using it. The name of the primary and secondary hard drives are also noted on the database. Once our main server system, to be located at the University of Pretoria, is up and running, the scan will be saved onto the system, with the associated metadata – a selection of which will be available online via a Figshare system. Figshare is an open access data repository system used by researchers to store and preserve their data. The scans will be renamed before they go onto the system, so each individual is de-identified. Each scan will also be awarded a Digital Object Identifier (DOI) number, such as the DOI’s books get.
At the moment, we are still at the stage where we are scanning bones and storing them onto an external hard drive, but on the 28th of January 2020, Prof L’Abbé approved the purchase of our Bakeng se Afrika server. We are excited for the progress we will make in populating the repository for the next two years. The Bakeng se Afrika digital skeletal repository will be available to external researchers from the beginning of 2022.
Bakeng se Afrika UP and Necsa teams: Clarisa van der Merwe, Charlotte Theye, Gabriele Krüger, Ericka L’Abbé, Frikkie de Beer