Reconstructing the world’s ant diversity in 3D

(Press-News.org) The shape of an organism is the first way we experience most species and the subject of one of the oldest pursuits in biology. However, the application of big data and computational methods for studying organismal shape has been held back by key technical bottlenecks, making it difficult to capture and share accurate 3D morphological data on large scales.

Now, researchers have broken this bottleneck with a project on ants, small but critical organisms in many ecosystems around the world. Using modern technology, researchers have generated and released a giant and freely available database of over 2000 3D ant models. The project, Antscan, used high-throughput X-ray micro-CT scanning (similar to medical CT scans but in much higher magnification) powered by a synchrotron particle accelerator to rapidly scan a huge number of specimens. These 3D images don’t merely show the exterior exoskeleton of the ants, but also reveal their internal structures like muscles, nervous system, digestive system, and stingers at micrometer resolution. The interdisciplinary work is the culmination of a long project co-led by researchers at the Okinawa Institute of Science and Technology (OIST) in Japan and the Karlsruhe Institute of Technology (KIT) in Germany and involving numerous collaborators from around the world. A new paper in Nature Methods presents both the data and the workflow used to acquire it, providing a blueprint for future large-scale quantification projects.

“This work moves us further into the big data era of capturing, analyzing, and sharing organismal shape and form,” says Professor Evan Economo of the Biodiversity and Biocomplexity Unit at OIST. Antscan adds to the growing collection of major resources on ants tied to OIST, including comprehensive data on the spread of all ant species published in 2022 and high-quality genomes covering most ant genera published last year. And in a recent Science Advances study, the researchers used Antscan data to investigate the fundamental balance of quantity versus quality in organizing ant colonies, finding strong proof that prioritizing the nutritionally cheap ants over more heavily armored and ‘expensive’ ants facilitates the development of larger, more sophisticated, and more resilient ant societies. “The potential for integrating this data is immense and very exciting,” says Economo.

An open library of life The computational study of morphology, especially in small-sized, diverse groups like ants, has been hindered by the very complexity it aims to capture. Ant specimens are typically collected by hand, but while the traditional method of drying and mounting them preserves their rigid, external exoskeletons, their internal organs deteriorate over time. Another major challenge is size. Many species are barely visible to the naked eye, and accurately quantifying their morphology in 3D requires sophisticated microscopy like micro-CT scans. But because CT scans are both time-consuming and expensive, many species have been excluded from detailed analysis. “If we were to carry out this project with a lab-based CT scanner, it would take around six years of continuous operation. With our setup, we scanned 2000 specimens in a single week,” says first author and OIST graduate Dr. Julian Katzke.

Antscan is the product of close collaboration between OIST, KIT, and the global community of ant researchers. “At times, this work involved our entire lab — we sat for two weeks straight sorting each ant by hand after a full month of cataloging,” recalls Katzke. OIST facilitated the collection of ethanol-preserved ants from countless partner institutions, museum collections, and experts around the world, sorted them all by species and caste, and standardized the metadata, ensuring accurate and fair labelling of each specimen, including who collected the ant, where, and when. Standardized trays of vials with individual ants were then transported to KIT for imaging in their high-throughput synchrotron micro-CT facility. Here, a particle accelerator producing a high-intensity X-ray beam combined with a robot arm for automatically swapping vials produced 3000 negative 2D images of each individual ant, which were then reconstructed into a 3D model, or tomogram.

A key feature of Antscan is its accessibility. All raw files are freely available for anyone to download, and the portal features a built-in viewer for each ant, enabling easy online access to the 3D models. “One of our goals was to democratize access to high-resolution micro-CT scans, which can be prohibitively expensive, especially for smaller institutions or non-institutional experts like citizen scientists, local collectors, or artists and educators,” says Katzke. With the ants’ exoskeleton and musculature captured in high resolution, scientists and artists alike can better model ant movement, both to study locomotion and to create more realistic depictions in multimedia. Katzke concludes: “To me, that’s the most exciting part of the project: opening up the database to a potentially infinite variety of perspectives. I’m thrilled to see how other people will use this data in ways that I couldn’t have imagined.”

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