High-throughput phenomics of global ant biodiversity

Julian Katzke; Francisco Hita Garcia; Philipp D. Losel; Fumika Azuma; Tomas Farago; Lazzat Aibekova; Alexandre Casadei-Ferreira; Shubham Gautam; Adrian Richter; Evropi Toulkeridou; Sabine Bremer; Elias Hamann; Jenny Hein; Janes Odar; Chandan Sarkar; Marcus Zuber; Jacobus J. Boomsma; Rodrigo M. Feitosa; Lukas Schrader; Guojie Zhang; Sandor Csosz; Minsoo Dong; Olivia Evangelista; Georg Fischer; Brian L. Fisher; Jaime A. Florez-Fernandez; GAGA Consortium; Jurgen Gadau; Daniele Giannetti; David Nash; Jes Soe Pedersen; Morten Schiott; Andras Tartally; Donato A. Grasso; Benoit Guenard; Peter G. Hawkes; Robert A. Johnson; Roberto A. Keller; Rasmus S. Larsen; Timothy A. Linksvayer; Cong Liu; Arthur Matte; Masako Ogasawara; Hao Ran; Juanita Rodriguez; Enrico Schifani; Ted R. Schultz; Jonathan Z. Shik; Jeffrey Sosa-Calvo; Chao Tong; Leonardo Tozetto; Seonwoo Yoon; Masashi Yoshimura; Jie Zhao; Tilo Baumbach; Evan P. Economo; Thomas van de Kamp; Stephane de Greef

doi:10.1038/s41592-026-03005-0

High-throughput phenomics of global ant biodiversity

Julian Katzke^*, Francisco Hita Garcia, Philipp D. Losel, Fumika Azuma, Tomas Farago, Lazzat Aibekova, Alexandre Casadei-Ferreira, Shubham Gautam, Adrian Richter, Evropi Toulkeridou, Sabine Bremer, Elias Hamann, Jenny Hein, Janes Odar, Chandan Sarkar, Marcus Zuber, Jacobus J. Boomsma, Rodrigo M. Feitosa, Lukas Schrader, Guojie ZhangSandor Csosz, Minsoo Dong, Olivia Evangelista, Georg Fischer, Brian L. Fisher, Jaime A. Florez-Fernandez, GAGA Consortium, Jurgen Gadau, Daniele Giannetti, David Nash, Jes Soe Pedersen, Morten Schiott, Andras Tartally, Donato A. Grasso, Benoit Guenard, Peter G. Hawkes, Robert A. Johnson, Roberto A. Keller, Rasmus S. Larsen, Timothy A. Linksvayer, Cong Liu, Arthur Matte, Masako Ogasawara, Hao Ran, Juanita Rodriguez, Enrico Schifani, Ted R. Schultz, Jonathan Z. Shik, Jeffrey Sosa-Calvo, Chao Tong, Leonardo Tozetto, Seonwoo Yoon, Masashi Yoshimura, Jie Zhao, Tilo Baumbach, Evan P. Economo^*, Thomas van de Kamp, Stephane de Greef

^*Corresponding author for this work

Research output: Contribution to journal › Journal article › Research › peer-review

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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. Imaging approaches can digitize whole organisms, but low throughput has limited the effort to document morphological diversity. Here, 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. At https://www.antscan.info, we provide 2,193 whole-body three-dimensional ant datasets from 212 genera and 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 an era of studies on the evolution, structure and function of organismal phenotypes.

Original language	English
Journal	Nature Methods
Volume	23
Issue number	3
Pages (from-to)	663-672
Number of pages	16
ISSN	1548-7091
DOIs	https://doi.org/10.1038/s41592-026-03005-0
Publication status	Published - 2026

Keywords

Computed-tomography
Hymenoptera-formicidae
High-resolution
Image
Classification
Visualization
Digitization
Morphology
Framework
Tool

Access to Document

10.1038/s41592-026-03005-0Licence: CC BY

Full textFinal published version, 3.9 MBLicence: CC BY

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Cite this

Katzke, J., Hita Garcia, F., Losel, P. D., Azuma, F., Farago, T., Aibekova, L., Casadei-Ferreira, A., Gautam, S., Richter, A., Toulkeridou, E., Bremer, S., Hamann, E., Hein, J., Odar, J., Sarkar, C., Zuber, M., Boomsma, J. J., Feitosa, R. M., Schrader, L., ... de Greef, S. (2026). High-throughput phenomics of global ant biodiversity. Nature Methods, 23(3), 663-672. https://doi.org/10.1038/s41592-026-03005-0

Katzke, J, Hita Garcia, F, Losel, PD, Azuma, F, Farago, T, Aibekova, L, Casadei-Ferreira, A, Gautam, S, Richter, A, Toulkeridou, E, Bremer, S, Hamann, E, Hein, J, Odar, J, Sarkar, C, Zuber, M, Boomsma, JJ, Feitosa, RM, Schrader, L , Zhang, G, Csosz, S, Dong, M, Evangelista, O, Fischer, G, Fisher, BL, Florez-Fernandez, JA, GAGA Consortium, Gadau, J, Giannetti, D, Nash, D , Pedersen, JS, Schiott, M, Tartally, A, Grasso, DA, Guenard, B, Hawkes, PG, Johnson, RA, Keller, RA, Larsen, RS, Linksvayer, TA, Liu, C, Matte, A, Ogasawara, M, Ran, H, Rodriguez, J, Schifani, E, Schultz, TR, Shik, JZ, Sosa-Calvo, J, Tong, C, Tozetto, L, Yoon, S, Yoshimura, M, Zhao, J, Baumbach, T, Economo, EP, van de Kamp, T & de Greef, S 2026, 'High-throughput phenomics of global ant biodiversity', Nature Methods, vol. 23, no. 3, pp. 663-672. https://doi.org/10.1038/s41592-026-03005-0

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title = "High-throughput phenomics of global ant biodiversity",

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. Imaging approaches can digitize whole organisms, but low throughput has limited the effort to document morphological diversity. Here, 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. At https://www.antscan.info, we provide 2,193 whole-body three-dimensional ant datasets from 212 genera and 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 an era of studies on the evolution, structure and function of organismal phenotypes.",

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author = "Julian Katzke and {Hita Garcia}, Francisco and Losel, {Philipp D.} and Fumika Azuma and Tomas Farago and Lazzat Aibekova and Alexandre Casadei-Ferreira and Shubham Gautam and Adrian Richter and Evropi Toulkeridou and Sabine Bremer and Elias Hamann and Jenny Hein and Janes Odar and Chandan Sarkar and Marcus Zuber and Boomsma, {Jacobus J.} and Feitosa, {Rodrigo M.} and Lukas Schrader and Guojie Zhang and Sandor Csosz and Minsoo Dong and Olivia Evangelista and Georg Fischer and Fisher, {Brian L.} and Florez-Fernandez, {Jaime A.} and {GAGA Consortium} and Jurgen Gadau and Daniele Giannetti and David Nash and Pedersen, {Jes Soe} and Morten Schiott and Andras Tartally and Grasso, {Donato A.} and Benoit Guenard and Hawkes, {Peter G.} and Johnson, {Robert A.} and Keller, {Roberto A.} and Larsen, {Rasmus S.} and Linksvayer, {Timothy A.} and Cong Liu and Arthur Matte and Masako Ogasawara and Hao Ran and Juanita Rodriguez and Enrico Schifani and Schultz, {Ted R.} and Shik, {Jonathan Z.} and Jeffrey Sosa-Calvo and Chao Tong and Leonardo Tozetto and Seonwoo Yoon and Masashi Yoshimura and Jie Zhao and Tilo Baumbach and Economo, {Evan P.} and {van de Kamp}, Thomas and {de Greef}, Stephane",

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AU - Katzke, Julian

AU - Hita Garcia, Francisco

AU - Losel, Philipp D.

AU - Azuma, Fumika

AU - Farago, Tomas

AU - Aibekova, Lazzat

AU - Casadei-Ferreira, Alexandre

AU - Gautam, Shubham

AU - Richter, Adrian

AU - Toulkeridou, Evropi

AU - Bremer, Sabine

AU - Hamann, Elias

AU - Hein, Jenny

AU - Odar, Janes

AU - Sarkar, Chandan

AU - Zuber, Marcus

AU - Boomsma, Jacobus J.

AU - Feitosa, Rodrigo M.

AU - Schrader, Lukas

AU - Zhang, Guojie

AU - Csosz, Sandor

AU - Dong, Minsoo

AU - Evangelista, Olivia

AU - Fischer, Georg

AU - Fisher, Brian L.

AU - Florez-Fernandez, Jaime A.

AU - GAGA Consortium

AU - Gadau, Jurgen

AU - Giannetti, Daniele

AU - Nash, David

AU - Pedersen, Jes Soe

AU - Schiott, Morten

AU - Tartally, Andras

AU - Grasso, Donato A.

AU - Guenard, Benoit

AU - Hawkes, Peter G.

AU - Johnson, Robert A.

AU - Keller, Roberto A.

AU - Larsen, Rasmus S.

AU - Linksvayer, Timothy A.

AU - Liu, Cong

AU - Matte, Arthur

AU - Ogasawara, Masako

AU - Ran, Hao

AU - Rodriguez, Juanita

AU - Schifani, Enrico

AU - Schultz, Ted R.

AU - Shik, Jonathan Z.

AU - Sosa-Calvo, Jeffrey

AU - Tong, Chao

AU - Tozetto, Leonardo

AU - Yoon, Seonwoo

AU - Yoshimura, Masashi

AU - Zhao, Jie

AU - Baumbach, Tilo

AU - Economo, Evan P.

AU - van de Kamp, Thomas

AU - de Greef, Stephane

PY - 2026

Y1 - 2026

N2 - 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. Imaging approaches can digitize whole organisms, but low throughput has limited the effort to document morphological diversity. Here, 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. At https://www.antscan.info, we provide 2,193 whole-body three-dimensional ant datasets from 212 genera and 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 an era of studies on the evolution, structure and function of organismal phenotypes.

AB - 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. Imaging approaches can digitize whole organisms, but low throughput has limited the effort to document morphological diversity. Here, 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. At https://www.antscan.info, we provide 2,193 whole-body three-dimensional ant datasets from 212 genera and 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 an era of studies on the evolution, structure and function of organismal phenotypes.

KW - Computed-tomography

KW - Hymenoptera-formicidae

KW - High-resolution

KW - Image

KW - Classification

KW - Visualization

KW - Digitization

KW - Morphology

KW - Framework

KW - Tool

U2 - 10.1038/s41592-026-03005-0

DO - 10.1038/s41592-026-03005-0

M3 - Journal article

C2 - 41787133

SN - 1548-7091

VL - 23

SP - 663

EP - 672

JO - Nature Methods

JF - Nature Methods

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