High-throughput phenomics of global ant biodiversity
Julian KatzkeiD, Francisco Hita GarciaiD, Philipp D. LöseliD, Fumika Azuma, Tomáš FaragóiD, Lazzat AibekovaiD, Alexandre Casadei‐FerreiraiD, Shubham GautamiD, Adrian RichteriD, Evropi ToulkeridouiD, Sabine Bremer, Elias HamanniD, Jenny Hein, Janes OdariD, Chandan SarkariD, M. S. ZubériD, Jacobus J. BoomsmaiD, Rodrigo Machado Feitosa, Lukas SchraderiD, Guojie ZhangiD, Sándor CsősziD, Minsoo DongiD, Olívia EvangelistaiD, Georg Fischer, Brian Lee FisheriD, , Thomas van de KampiD
Abstract
The big data era in biology is underway, but the study of organismal form has been slow to capitalize on advances in imaging and computation. Modern imaging can digitize whole organisms, but low throughput has limited the effort to document morphological diversity. Within the open science initiative Antscan, we applied high-throughput synchrotron X-ray microtomography to capture phenotypes across a diverse and ecologically dominant insect group -- ants. We provide 2193 whole-body 3D ant datasets from 792 species to broadly cover the ant phylogeny with a global scope, also pairing phenomic data with genome sequencing projects. Scans acquired with standardized parameters facilitate automated analysis and free access to data can broaden the audience and incentivize methods development. Antscan presents a scalable approach to create libraries of diverse anatomies, heralding a new era of studies on the evolution, structure, and function of organismal phenotypes.
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In-depth summary
Claude Opus 5.5 · xhigh effort · 5 Nov 2026 · from the full text of version 1 (29 Nov 2025) · CC BY 4.0
Antscan provides 2,193 standardized whole-body 3D synchrotron micro-CT datasets across 792 ant species (212 genera), pairing morphological volumes with automated deep-learning segmentation and genome sequencing projects.
Three-dimensional digitization of insect biodiversity using conventional laboratory micro-CT has been bottlenecked by multi-hour scan times, tissue-altering chemical staining, and non-standardized image contrast that impedes automated analysis. High-throughput synchrotron phase-contrast microtomography with robotic sample exchange overcomes these barriers to capture soft and hard internal anatomy non-destructively in ethanol-preserved specimens.
Key results
ShownAntscan digitized 2,193 ant specimens and 32 outgroup wasps spanning global ant phylogenetic and caste diversity, with a subset linked to genome sequencing projects.
The collection covers 14 of 16 extant ant subfamilies, 212 of ~345 recognized genera (>90% of described ant species), and at least 792 species (659 identified species plus 133 morphospecies across 1,671 workers, 291 queens, and 220 males), with 585 specimens (186 species, 157 from the same nest series) paired with genome projects. · Abstract; Phylogenetic coverage; Tomographic data
ShownRobotic synchrotron phase-contrast micro-CT accelerated whole-body 3D imaging by orders of magnitude compared with conventional laboratory micro-CT.
Across 4,010 individual scans at effective pixel sizes of 1.22, 2.44, or 6.11 µm (scan durations of 21 to 85 seconds), Antscan operated at ~25 scans per hour including file transfer, whereas equivalent scans taking ~12 hours each on a single laboratory micro-CT scanner would require more than six years of continuous operation. · Discussion; High-throughput synchrotron X-ray…
ShownAutomated neural network segmentation in Biomedisa generated whole-body 3D surface meshes and cropped background volumes to substantially compress repository size.
A deep neural network trained on 12 scans (and retrained on 34 whole-body segmentations: 27 training, 7 validation) automatically segmented and cropped all volumetric datasets, reducing online database storage size by about 70%. · Tomographic data; Post-processing of tomographic data
ShownComparative screening of Antscan tomograms revealed that cuticular biomineral armor is widespread across fungus-growing attine ants rather than restricted to a single species.
A high-absorption cuticular layer (threshold 200-255 vs cuticle 105-255), previously known only in Acromyrmex echinatior, was detected across fungus-growing ants (Myrmicinae: Attini) except in the genera Atta, Kalathomyrmex, and Mycocepurus, and was absent in all screened species outside Attini. · Exemplary use cases; Further post-processing of exemplary data sets
Methods, data and reproducibility
Sorted ethanol-preserved ants into 48-vial trays and scanned them in toto at two KIT Light Source beamlines using a robotic sample exchanger, high-speed camera, and blended phase-retrieval/absorption 3D reconstruction (plus 6 oversized iodine-stained ants by lab micro-CT). Stitched multi-height scans via Simple-ITK, segmented/cropped volumes with a deep neural network in Biomedisa, and hosted data on RADAR4KIT.
- Whole-body 3D synchrotron and laboratory X-ray micro-CT tomograms, surface meshes, and specimen metadata of ants and outgroup wasps · ants (Formicidae) and outgroup Hymenoptera · n = 2193 ants (792 species, 212 genera) and 32 outgroup wasps from 4010 scans
- Methods & tools
- Biomedisa, concert, syris, UFO framework, tofu, Simple-ITK, Paraview, Fiji, Amira, Slicer 3D, CINEMA 4D R20
- Data & accessions
- https://www.antscan.info/https://biomedisa.info/antscan/https://radar.kit.edu/radar/en/search?query=antscan
- Software & environment
- Biomedisa deep learning framework, concert, syris, UFO framework, tofu, Simple-ITK, Paraview, Fiji, Amira, Slicer 3D, CINEMA 4D R20, MySQL
- Assay conditions & compute
- GPU-based tomographic reconstruction at KIT Scientific Computing Center; total storage for processed and raw datasets exceeds 100 Terabytes
- Reproducibility gaps
- Raw X-ray projections and intermediate image files are archived at KIT and only provided upon reasonable request.
Limitations (3)
- Some specimens drawn from standing collections exhibited soft tissue shrinkage and decay from prior DNA extraction, air exposure, or storage, restricting those scans to exoskeletal analyses. · stated by the authors
- Manual specimen positioning prior to automated scanning resulted in partial truncation of protruding legs and antennae in some larger specimens within a magnification tier. · stated by the authors
- Six of the largest ant specimens exceeded the synchrotron field of view and required iodine staining and laboratory micro-CT, and 132 previously iodine-stained specimens could not undergo phase retrieval. · stated by the authors
Who should read:Read this if you study insect morphology, comparative phenomics, or bioimage informatics and want open 3D micro-CT volumes or high-throughput synchrotron scanning workflows.
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