Background

With well over a million described species, insects are by far the largest group of organisms on Earth. They perform key functions in our ecosystems and serve as models for biomimetic design. The ongoing dramatic decline in biodiversity, and in particular the loss of insect diversity, has brought the importance of insects into the public eye. Scientific collections of insects are of fundamental value not only for documenting and describing populations, species and biodiversity, but also for understanding the interplay between morphology, physiology and genetics, and for monitoring the effects of environmental and climatic influences.

The digital transformation of our society can greatly enhance the value of scientific insect collections, as data from any digital specimen could be analyzed and made available online worldwide without the need for physical handling, shipping, or processing. But despite impressive advances in imaging techniques, the 3D digitization of whole insects (including internal soft tissues) has so far lagged behind the rapid advances in genetic sequencing.

Initiated by scientists from Okinawa Institute of Science and Technology (OIST, Japan) and Karlsruhe Institute of Technology (KIT, Germany) and based on a global collaboration of biodiversity stakeholders, the Antscan initiative has the ambitious goal of generating 3D images of thousands of insects in a short period of time. Conceived as a pilot project for the digitization of a diverse group of small invertebrates, the initiative focuses on ants as a globally distributed, ecologically dominant group of insects, but offers a project design adaptable to other small organisms. By combining state-of-the-art 3D imaging technology, optimized data processing pipelines, and artificial intelligence, we have established a powerful workflow suitable for large-scale digitization of scientific collections. The resulting data repository serves as a vast resource for the study of ant morphology, anatomy and evolution.

The ants of Antscan

In Antscan we have the ambition to adequately digitize the morphological side of ant biodiversity. Since there are more than 15,000 described species and ants are distributed worldwide, the Antscan project must reflect this diversity. Antscan brought together museum curators and ant researchers from around the world to provide a diverse set of ants.

A lot of data

The unprocessed data of a single scan is about 92.5 GB. If you consider that we performed more than 4,000 scans in total, you can get an idea of the total amount of data we generated during the course of this project. And when you consider that all this data needs to be backed up and archived, you can imagine that proper data management is essential for a project like Antscan. Fortunately, the Scientific Computing Center of KIT offers long-term archiving of scientific data and with RADAR4KIT provides a service to make scientific datasets available to the public. In order to facilitate data handling, we have processed all Antscan datasets to make them more user-friendly, i.e. by background removal or merging of datasets that were composed of several scans.

What can we do with such data?

The vast amount of 3D morphological data from many different ant species is helping us understand their enormous diversity and evolutionary patterns. By digitizing and analyzing large sample sets, scientists can link physical traits with genetic and environmental information. This allows them to study how ants adapt to changing environments and identify key traits that promote biodiversity. In addition, our 3D data can enhance research in areas such as functional morphology and biomimetics, leading to new discoveries and innovations.

But Antscan goes far beyond scientific research. Our data also provide valuable resources for education, allowing students and the public to virtually "dissect" ants and explore their diversity in an interactive and engaging way. For example, processed tomographic data can be integrated into virtual reality or augmented reality environments. Outreach programs can use digital or printed 3D models to raise awareness of biodiversity and conservation efforts.

Alcohol-preserved specimens at the Australian National Insect Collection in Canberra.

The two main ways of storing and preserving insects in science are either pinning them or preserving them in alcohol. Pinning ants to a fine piece of paper and placing the paper on a metal makes them very easy to observe under a microscope and is therefore invaluable for measuring ants and describing new species. This works because the ant's exoskeleton can remain intact even when the ant is completely desiccated. Dried ants, however, were not suitable for Antscan, as our aim was to digitize the internal soft tissues as well. Conveniently, nowadays many specimens within scientific insect collections are stored in alcohol (e.g. to facilitate DNA analyses), thus preserving the anatomy. Therefore, all Antscan samples originate from such alcohol collections.

Digitizing thousands of ants at a particle accelerator

X-ray computed tomography (CT) is a well-established technique for creating 3D volumetric images from a series of 2D projections. Today, clinical CT systems are important diagnostic tools. An X-ray tube rotates around the patient and acquires the necessary projections to create a 3D image. Micro-computed tomography (micro-CT) is routinely used to examine samples ranging in size from millimeters to centimeters for various fields such as materials science, biology, paleontology, geology, and archaeology. Unlike clinical CT, the X-ray source is stationary and the samples rotate during data acquisition. Because micro-CT samples are typically dose insensitive, the amount of radiation deposited on the samples can be much higher than in clinical systems. As a result, micro-CT setups can achieve high resolution and good contrast.

Synchrotron micro-CT is a special type of this technique in which the source of X-rays is not a conventional X-ray tube but a synchrotron, a type of particle accelerator. Dedicated experimental station (beamlines) at synchrotrons provide X-rays that are much more intense and brilliant than those from tubes. As a result, samples can be processed much faster and with better contrast than in desktop micro-CT systems. The KIT Light Source, the synchrotron at Karlsruhe Institute of Technology (KIT), has a dedicated high-throughput setup that uses fast robotics and high-speed cameras. Taking advantage of these unique possibilities, the Antscan team was able to collect the raw data of all specimens in just a few days. After the experiment at the beamline, the 3D images (tomograms) were automatically reconstructed from the acquired projections.

The open repository

To make the project data available to the public, Antscan provides an open repository of 3D datasets and detailed metadata for each ant specimen scanned in the project. Built on the popular Biomedisa platform, the repository allows users to search the database by keyword and view 3D surface previews and interactive models. Each entry includes taxonomic rank, ecological information, and specimen identifiers, as well as geographic and habitat details and genome sequencing status. Registered users can apply image segmentation methods and share datasets via the Biomedisa app.