Critical data from millions of insect specimens to be unlocked through cutting-edge 3D imaging technology

Over 1.6 million of the Museum’s 35 million insects have already been digitised using 2D photography. These specimens have had their images and collections data (information about where in time and space they were collected and what species they are) made available to the public via the Museum’s Data Portal. However, this landmark project is expected to provide valuable new insights and information by providing the beginnings of a high-resolution 3D dataset for all living and fossil insects and their close relatives.

The Natural History Museum and Diamond are developing an innovative new method to automatically scan and analyse all the information in a 3D image which completely describes the complex shape of organisms. Unlike existing approaches, this new method will not require any manual measurements and therefore allows extremely rapid analysis of any 3D images. 

Research Leader in Life Sciences at the Natural History Museum Professor Anjali Goswami says: “This work will bring unparalleled detail and understanding to the evolution of a group that encompasses more than half of known species. In doing so, we will launch a new field, Biodiversity Phenomics, which will lay the foundation for mapping phenotypic diversity on a global scale and provide a new perspective on the evolution and preservation of life on Earth.” 

“This detailed big data on species biology is vital in enabling targeted conservation efforts to halt the devasting decline in numbers and extinction of insect species. Most efforts to date have focused on mapping where species live in order to predict how they will be affected by environmental change, with datasets now representing tens of thousands of species. However, all organisms do not respond uniformly to changes in their environment. Whether species are large or small, specialists or generalists, carnivores or herbivores will shape their future trajectories.”

Currently, collecting data on phenotype (an organism's phenotype is how they interact with their environment and with other individuals, and encompasses their anatomy, behaviour, and more) is largely manual and time-consuming, making it difficult to scale up to thousands of specimens. Because of this, large-scale studies typically simplify complex phenotypes to just a few measurements.  But capturing phenotype is not just an issue of species numbers and the incredible variation in the anatomy of organisms effectively prevents the use of existing approaches to compare very diverse organisms. Until now, despite advanced technologies allowing 3D imaging of organisms down to individual cells, there was no method to convert those images into similarly detailed data to capture the phenotypic diversity of life on Earth. 

Professor Goswami explains: “To study the variety and volume of specimens we have will be extremely demanding - the amount of data produced, and the data analysis is daunting. But, to develop the best possible strategies to preserve biodiversity, we must know how species interact with their environment.  To achieve this, information on phenotype is critical to understanding how species evolve and respond to change.” 

The project started with an intensive two days of beamtime doing some high through-put X-ray scanning of insects and other arthropods using a new and specially designed robot arm system on the I13 beamline at Diamond, the UK’s Synchrotron.  The new robot arm system already allows the Museum to capture many more specimens than previously possible. Today it can scan around 300 insect specimens a day, but this is expected to soon increase to around a 1000 a day. Data storage and automated analyses will be the next big challenge. 

“This work is an example of the new possibilities open to users with the new high throughput robot arm system alongside Diamond’s I13 beamline. It provides a powerful new tool for studying past, present, and future biodiversity at an unprecedented scale.  It is particularly valuable for high-throughput X-ray scanning of insects and other arthropods because it can image biological structures such as muscles where a property called coherence is needed. For example, with coherent light you can see soft matter, such as muscles, which you can’t see normally with medical CT scan.  So, the addition of the robot arm – puts us in the unique position of getting high throughput and minute detail on what can be very challenging specimens,” comments Professor Christoph Rau, Principal Beamline Scientist at Diamond.

The Natural History Museum announced last year that it will be creating a new state of the art collections, research and digitisation centre on the Harwell Science and Innovation Campus in 2026. It will unite two world-class science and innovation networks – building on the existing strong links the Museum has with Diamond Light Source as well as the European Space Agency, UKRI facilities and Oxford Nanopore Technologies amongst others.

“Although we have worked with Diamond for many years, we are very excited about all the possible synergies and new collaborations going forward with them and other facilities on the Campus.  A key aim of the new centre will be to harness novel technologies and analysis techniques to gain new insights into the natural world and this current project is a prime example of that. We hope that the centre will open up the collections to even more researchers and partners to tackle some of the planet’s key challenges such as biodiversity loss and climate change,” concludes Professor Goswami.

ENDS

For further information please contact Diamond Communications:                                    Lorna Campbell +44 7836 625999 or Isabelle Boscaro-Clarke +44 1235 778130

Editors Notes: 

The I13 Imaging and Coherence beamline also known as the Diamond Manchester Imaging branchline is for multi-scale imaging in the energy range of 6 - 30 keV. The achievable resolution ranges from several microns to some tens of nanometers with two branchlines operating independently for this purpose.”

The Diamond Manchester Imaging branchline performs mainly in-line phase contrast tomography with a strong emphasis on dedicated sample environments. A new full-field microscope using Zernike phase contrast imaging over a field of view of 50-100 μm and a resolution of 50 - 100 nm is now in operation, with a growing user community, allowing Diamond to identify nano-sized structures under dynamic conditions. The new robot arm enables high-throughput and remote studies with measurements of up to 300 samples per day demonstrated in early testing. This will allow for large sampling and parametric studies in a range of science areas and the possibility of sample mail-in services. The highest spatial resolution, of 30 nm, is achieved on the coherence branch with ptychographic imaging. Continuous improvements have reduced ptycho-tomography scans from days to a few hours, and ongoing fly-scanning developments aim to reduce this even further. Ptychography has become now a standard user-friendly experiment. Instrumental upgrades for Bragg-CDI (new detector robot software) expands the experimental capabilities for studying nano-crystalline structures and has been applied successfully in combination with ptychography. 

Natural History Museum

The Natural History Museum is both a world-leading science research centre and the most-visited natural history museum in Europe. With a vision of a future in which both people and the planet thrive, it is uniquely positioned to be a powerful champion for balancing humanity’s needs with those of the natural world.

It is custodian of one of the world’s most important scientific collections comprising over 80 million specimens. The scale of this collection enables researchers from all over the world to document how species have and continue to respond to environmental changes - which is vital in helping predict what might happen in the future and informing future policies and plans to help the planet.

The Museum’s 300 scientists continue to represent one of the largest groups in the world studying and enabling research into every aspect of the natural world. Their science is contributing critical data to help the global fight to save the future of the planet from the major threats of climate change and biodiversity loss through to finding solutions such as the sustainable extraction of natural resources.

The Museum uses its enormous global reach and influence to meet its mission to create advocates for the planet - to inform, inspire and empower everyone to make a difference for nature. We welcome over five million visitors each year; our digital output reaches hundreds of thousands of people in over 200 countries each month and our touring exhibitions have been seen by around 30 million people in the last 10 years.

Diamond Light Source: www.diamond.ac.uk  Twitter: @DiamondLightSou

Diamond Light Source provides industrial and academic user communities with access to state-of-the-art analytical tools to enable world-changing science. Shaped like a huge ring, it works like a giant microscope, accelerating electrons to near light speeds, to produce a light 10 billion times brighter than the Sun, which is then directed off into 33 laboratories known as ‘beamlines’. In addition to these, Diamond offers access to several integrated laboratories including the world-class Electron Bio-imaging Centre (eBIC) and the Electron Physical Science Imaging Centre (ePSIC).

Diamond serves as an agent of change, addressing 21st century challenges such as disease, clean energy, food security and more. Since operations started, more than 14,000 researchers from both academia and industry have used Diamond to conduct experiments, with the support of approximately 760 world-class staff. More than 10,000 scientific articles have been published by our users and scientists.

Funded by the UK Government through the Science and Technology Facilities Council (STFC), and by the Wellcome Trust, Diamond is one of the most advanced scientific facilities in the world, and its pioneering capabilities are helping to keep the UK at the forefront of scientific research.