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3D Scanning: Moving our Study of Fossils in a New Direction 


By Romala Govender

Traditionally we have used photographs to depict the specimens that are being studied. There have been changes to this technique that have led to the improvement of the quality of the photographs (Figure 1).

Figure 1. Fossil sperm whale tooth root from Hondeklip Bay, Northern Cape, South Africa (Govender 2019, 2021).

As technology improved, we moved from cameras using film requiring development in a dark room to the use of digital cameras. With film you only knew once it was developed if you had a useable print, while a digital camera allows the checking of a photo immediately after taking it. Software used to manipulate digital photographs means that images can be stacked to give a sharper, clearer image (Figure 2) and preparing figures for a publication is easier.

Figure 2. Fossil baleen whale ear bone from Saldanha Steel on South Africa’s west coast (Govender and Marx 2023).

The study of a specimen is not always simple and this is where new technology, like CT and micro-CT scanning, has improved our ability to study fossils that in some instances were previously inaccessible. Photogrammetry is another technique where hundreds of photographs of a specimen are taken from different angles which are then stitched together to create a 3D model.

With 3D scanning (the method of capturing an object in the real world to produce a digital 3D model), the scanner takes multiple photos of a specimen that are knitted together to produce a precise 3D model. These models can then be manipulated on a computer allowing you to view the object from various angles.

We have been fortunate through NRF/AOP funding to acquire a 3D scanner. This will allow us to be able to make specimens more accessible. In cases where researchers are not able to travel to visit the collection but need to study specimens, we will be able to provide them with scans. This will allow fragile specimens that could be damaged if handled too often available for study. Rarely are holotypes sent out on loan or put on display in an exhibition as it is continually removed for study leaving display cases empty. Some specimens need to be sampled for destructive analysis (e.g. isotope analyses, histology, DNA etc.). This is where 3D scanning has an important role as scans can be made available for study and to print so that these specimens can be put on display, become available for teaching, and have a record of specimens that will be sampled.

The scanner we are using is a Wiiboox Reeyee Pro. This a handheld scanner that can be used with a turntable as well. It consists of two cameras on either end, white light in the middle and a ring light around the cameras. The object being scanned is covered by white light patterns projected by the LED lights. The two cameras capture the white light pattern distortion on the object being scanned. The geometric information is acquired by the scanning software, which is used to construct a real-time 3D model of the objects scanned surface (scanner manual).

Figure 3. Wiiboox Reeyee Pro 3D scanner (

The scanner is calibrated before the first use and will only need to be re-calibrated if something goes wrong and the scanning data is not coming in from the scanner. We can currently scan specimens that are smaller than 10cm and but larger than 3cm and very large specimens up to 3m.

The scan is started in preview mode so you can gauge if the specimen is being tracked by the scanner once you have confirmed you can start the scan. Markers are stuck onto the turntable to allow the scanner to see the object. For a fixed scan, these markers are imported into the scanning program before you scan for the first time. The turntable rotates 30° a turn; more points are scanned providing more points for stitching the model. To get a full scan of the specimen you must turn the specimen and scan the opposite side. Below is a clip of a fixed scan.

Handheld scanning is a little more difficult, when the tracking is green the object is being scanned and a model is being created in real time. The scan starts in preview mode (Figure 4).

Figure 4. Handheld scanning preview mode (3D scanning manual)

If there is too little data and the scanned area cannot be stitched, then it appears in purple (Figure 5). The purple area must be realigned with the green to recognise the lost frame. Once the scan is complete, fixed or handheld, you can add texture to the scan which, collected during the scan, is optimised to improve the appearance. To retain the texture during export of the scan you export it as an obj format and as a stl file for printing. In some cases when the curvature of the specimen creates difficulties in scanning, the object markers can be used to make the curvature visible.

Figure 5. Lost tracking during handheld scanning.

Once the system is mastered, scanning takes less time than photography as in most cases you use the fixed scan. Large objects using handheld will take a bit longer as you must ensure tracking is not lost and if it is, that it is correctly reacquired. We have started a scanning program where we are scanning types, fragile specimens, specimens identified for destructive analysis, and study material. The largest fixed scan so far is a seal skull about 38cm long. Below is an example of a fixed scan of a baleen whale ear bone (Figure 6). This is the same specimen in figure 2.

Figure 6. 3D scan of baleen whale ear bone from Saldanha Steel described in Govender and Marx 2023.

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