A computer processing a model of a whale skull from a 3D scan

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Helping scientists study the biggest animals on Earth

Whales can tell us a lot about the ocean's health, but their vast size makes them hard to study.

By scanning whale specimens, the Museum is making data easier to handle and accessible to researchers around the world.

Whales live physically extreme lives. Living in the open ocean, they often travel vast distances or dive to amazing depths. There is great variety of behaviour and adaptions between species and they range in size from the dwarf sperm whale at 2.6 metres long to the 30-metre-long blue whale.

Whales are classed as cetaceans, a group of animals that also includes dolphins and porpoises.

Museum researcher Dr Natalie Cooper studies cetaceans because she finds them fascinating: 'They evolved from land animals, they’re the biggest animals to ever have lived on earth and they have complex communication and behaviours.'

Mysticeti whales have evolved baleen filter-feeding systems as well as the largest body sizes of any animals ever to live on Earth, while toothed whales have evolved the ability to echolocate.

Cetaceans are also great indicators of wider ocean health. If there’s a problem lower in the food chain, for example plastic pollution, it concentrates in cetaceans. So if cetacean populations are healthy, so are our oceans.

These factors make whales a valuable group for scientists to investigate. But how do you go about studying some of the largest animals on Earth?

Setting data free

'As cetaceans are rare and underwater it’s difficult for scientists to study even the smaller species and the larger species present an even bigger challenge,' explains Dr Cooper.

3D modelling can help researchers gain an understanding of large animals like whales, which are both difficult to observe in the wild and to handle as specimens. Imaging experts at the Museum are using 3D handheld surface scanners to map the surface of selected cetacean skull specimens and produce a digital version of each.

'Creating 3D scans of these specimens is democratising science', says Dr Cooper. 'People all over the world are already using the data without having to come here and physically look at the specimens.'

How to scan a skull

Prior to scanning the specimens, a conservation check was carried out. Each whale skull was assessed to determine whether contact and handling of it during the scanning process could cause any damage or deterioration.

Once the conservators had determined a specimen was stable, they prepared a full report on its conservation status, gave it a light clean and approved it for scanning,

The specimens are quite large and had to be moved by trained museum professionals. The majority of the skulls were scanned on one side and then placed on custom built frames to scan the other. This ensured minimal movement of the specimens.

Most of the whales took two scanning sessions – one for the front and one for the back. But a few took multiple rounds to catch difficult to reach areas.

Kate Burton scanning the bottlenose whale cranium. Note the target dots on the specimen.

3D surface scanning lends itself well to large, static structures like skeletons. More information on complex anatomical structures, like skulls, can be collected in 3D compared to 2D imaging. The output of these scans are dense polygon mesh models. These can be analysed to reconstruct in great detail how and why the skull evolved the way it did.

The data was captured with a Creaform Go!Scan 50 structured light scanner and assisted by the use of low adhesive target stickers. When three or more of these stickers are in the scanning range, it creates a triangulation point.  This helps the scanner to realise where it is, alongside any natural features it may pick up.

Processing the data may sound simple, but it took a while for the computer to handle the large amount of data - about 2 GB per specimen. Additionally, it takes a bit of practice to find the best points for manually aligning the two halves of the skulls and then doing any clean-up of extraneous data such as metal rods.

At the end, the two halves are connected, finely aligned, patched of any holes in data, and exported into files that can be then used in 3D graphics applications.

A southern right whale cranium from the Museum's collection, ready for scanning

Plans for research

Using the 3D models, scientists can reconstruct the complex anatomical structures of the skull. Lots of different lines of research are then opened up, such as using the data to analyse how skull shape has evolved.

Dr Cooper and two other Museum researchers, Prof Anjali Goswami and Ellen Coombs, plan to use the finished 3D datasets to perform comparative analysis between the cetacean skulls. This will help them gain further understanding into how these animals developed and adapted to life in the ocean.

Datasets from this project will be shared on Phenome10K, a free online repository for 3D scans of biological and palaeontological specimens created by Prof Goswami, to enable comparison with other vertebrates.

Ellen Coombs will be using the data to compare living and extinct species of cetaceans. '3D models are great for looking at how the shape of the skull has changed and evolved,' she says.

'By looking at extinct and living cetaceans, we want to understand how organisms responded to past climate, and to extrapolate the effects of recent, rapid climate changes.'

Prof Goswami has recently published a paper published in the journal Evolution that uses 3D scans to study how the telescoping of the skull happened in whales and when this major anatomical change occurred in their fossil record.

She says, 'We can look at why certain forms evolved and test how these differences between species reflect differences in diet and other factors.'

Data from this project is freely and openly available to researchers around the world via the Museum’s Data Portal.

Explore the features of these 3D models online, or click the links below to find out more about the Museum’s Data Portal and other ways we are using new technology to understand our collections.

Explore cetateans data

  All our scientific data is available openly on the Data Portal for global research.