The IBEX Knowledge-Base: A central resource for multiplexed imaging techniques

Andrea J Radtke¹, Ifeanyichukwu U Anidi², Leanne Arakkal³, Armando J Arroyo-Mejias³, Rebecca T Beuschel³, Katy Börner⁴, Colin J Chu⁵, Beatrice Clark³, Menna R Clatworthy⁶, Jake Colautti⁷, Fabian Coscia⁸, Joshua Croteau⁹, Saven Denha⁷, Rose Dever¹⁰, Walderez O Dutra¹¹, Sonja Fritzsche⁸, Spencer Fullam¹², Michael Y Gerner¹³, Anita Gola¹⁴, Kenneth J Gollob¹⁵, Jonathan M Hernandez¹⁶, Jyh Liang Hor³, Hiroshi Ichise³, Zhixin Jing³, Danny Jonigk^{17

18}, Evelyn Kandov³, Wolfgang Kastenmüller¹⁹, Joshua F E Koenig⁷, Rosa K Kortekaas²⁰, Aanandita Kothurkar⁵, Alexandra Y Kreins^{21

22}, Ian T Lamborn³, Yuri Lin¹⁶, Katia Luciano Pereira Morais¹⁵, Aleksandra Lunich², Jean C S Luz²³, Ryan B MacDonald⁵, Chen Makranz²⁴, Vivien I Maltez²⁵, John E McDonough²⁰, Ryan V Moriarty²⁶, Juan M Ocampo-Godinez^{21

27

28}, Vitoria M Olyntho⁷, Annette Oxenius²⁹, Kartika Padhan¹, Kirsten Remmert¹⁶, Nathan Richoz⁶, Edward C Schrom³, Wanjing Shang³, Lihong Shi³⁰, Rochelle M Shih³, Emily Speranza³¹, Salome Stierli³², Sarah A Teichmann^{33

34}, Tibor Z Veres³, Megan Vierhout⁷, Brianna T Wachter³⁵, Adam K Wade-Vallance³, Margaret Williams², Nathan Zangger²⁹, Ronald N Germain^{1

3}, Ziv Yaniv³⁶

Affiliations

¹ Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
² Critical Care Medicine and Pulmonary Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
³ Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
⁴ Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America.
⁵ UCL Institute of Ophthalmology and NIHR Moorfields Biomedical Research Centre, London, United Kingdom.
⁶ Molecular Immunity Unit, Laboratory of Molecular Biology, Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge Department of Medicine, Cambridge, United Kingdom.
⁷ Department of Medicine, McMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Faculty of Health Sciences, McMaster University, Hamilton, Canada.
⁸ Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany.
⁹ Department of Business Development, BioLegend Inc., San Diego, California, United States of America.
¹⁰ Functional Immunogenomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
¹¹ Laboratory of Cell-Cell Interactions, Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
¹² Division of Rheumatology, Rush University Medical Center, Chicago, Illinois, United States of America.
¹³ Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America.
¹⁴ Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, New York, United States of America.
¹⁵ Center for Research in Immuno-oncology (CRIO), Hospital Israelita Albert Einstein, São Paulo, Brazil.
¹⁶ Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
¹⁷ Institute of Pathology, Aachen Medical University, RWTH Aachen, Aachen, Germany.
¹⁸ German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.
¹⁹ Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
²⁰ Department of Medicine, McMaster University, Firestone Institute for Respiratory Health, St Joseph's Healthcare, Hamilton, Canada.
²¹ Infection Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom.
²² Department of Immunology and Gene Therapy, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.
²³ Viral Vector Laboratory, Cancer Institute of São Paulo, University of São Paulo, São Paulo, Brazil.
²⁴ Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
²⁵ Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America.
²⁶ Department of Cellular and Developmental Biology, Northwestern University, Chicago, Illinois, United States of America.
²⁷ Laboratorio de Bioingeniería de Tejidos, Departamento de Estudios de Posgrado e Investigación, Universidad Nacional Autónoma de México, Mexico City, Mexico.
²⁸ Laboratorio de Inmunoquímica I, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico.
²⁹ Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
³⁰ Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
³¹ Florida Research and Innovation Center, Cleveland Clinic Lerner Research Institute, Port Saint Lucie, Florida, United States of America.
³² Institute of Anatomy, University of Zurich, Zurich, Switzerland.
³³ Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, United Kingdom.
³⁴ Department of Medicine, University of Cambridge, Cambridge, United Kingdom.
³⁵ Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
³⁶ Bioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.

PMID: 40106489
PMCID: PMC12135934
DOI: 10.1371/journal.pbio.3003070

The IBEX Knowledge-Base: A central resource for multiplexed imaging techniques

Andrea J Radtke et al. PLoS Biol. 2025.

. 2025 Mar 19;23(3):e3003070.

doi: 10.1371/journal.pbio.3003070. eCollection 2025 Mar.

Authors

Affiliations

¹ Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
² Critical Care Medicine and Pulmonary Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
³ Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
⁴ Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America.
⁵ UCL Institute of Ophthalmology and NIHR Moorfields Biomedical Research Centre, London, United Kingdom.
⁶ Molecular Immunity Unit, Laboratory of Molecular Biology, Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge Department of Medicine, Cambridge, United Kingdom.
⁷ Department of Medicine, McMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Faculty of Health Sciences, McMaster University, Hamilton, Canada.
⁸ Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany.
⁹ Department of Business Development, BioLegend Inc., San Diego, California, United States of America.
¹⁰ Functional Immunogenomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
¹¹ Laboratory of Cell-Cell Interactions, Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
¹² Division of Rheumatology, Rush University Medical Center, Chicago, Illinois, United States of America.
¹³ Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America.
¹⁴ Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, New York, United States of America.
¹⁵ Center for Research in Immuno-oncology (CRIO), Hospital Israelita Albert Einstein, São Paulo, Brazil.
¹⁶ Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
¹⁷ Institute of Pathology, Aachen Medical University, RWTH Aachen, Aachen, Germany.
¹⁸ German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.
¹⁹ Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
²⁰ Department of Medicine, McMaster University, Firestone Institute for Respiratory Health, St Joseph's Healthcare, Hamilton, Canada.
²¹ Infection Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom.
²² Department of Immunology and Gene Therapy, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.
²³ Viral Vector Laboratory, Cancer Institute of São Paulo, University of São Paulo, São Paulo, Brazil.
²⁴ Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
²⁵ Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America.
²⁶ Department of Cellular and Developmental Biology, Northwestern University, Chicago, Illinois, United States of America.
²⁷ Laboratorio de Bioingeniería de Tejidos, Departamento de Estudios de Posgrado e Investigación, Universidad Nacional Autónoma de México, Mexico City, Mexico.
²⁸ Laboratorio de Inmunoquímica I, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico.
²⁹ Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
³⁰ Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
³¹ Florida Research and Innovation Center, Cleveland Clinic Lerner Research Institute, Port Saint Lucie, Florida, United States of America.
³² Institute of Anatomy, University of Zurich, Zurich, Switzerland.
³³ Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, United Kingdom.
³⁴ Department of Medicine, University of Cambridge, Cambridge, United Kingdom.
³⁵ Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
³⁶ Bioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.

PMID: 40106489
PMCID: PMC12135934
DOI: 10.1371/journal.pbio.3003070

Abstract

Multiplexed imaging is a powerful approach in spatial biology, although it is complex, expensive and labor-intensive. Here, we present the IBEX Knowledge-Base, a central resource for reagents, protocols and more, to enhance knowledge sharing, optimization and innovation of spatial proteomics techniques.

Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

PubMed Disclaimer

Conflict of interest statement

I have read the journal's policy and the authors of this manuscript have the following competing interests: SAT is a remunerated Scientific Advisory Board member of Qiagen, Foresite Labs, OMass Therapeutics, and a consultant and equity holder of TransitionBio and EnsoCell, and a non-executive board director of 10x Genomics, as well as part-time employee of GlaxoSmithKline. JC is an employee and stakeholder of BioLegend (revvity inc.). AJR is now an employee of Leica Microsystems. All other authors declare no competing interests.

Figures

**Fig 1. The IBEX Knowledge-Base is a central portal for IBEX and related multiplexed tissue imaging techniques.**
The IBEX Knowledge-Base is an open, global repository providing information related to IBEX and other spatial biology methods. The evolving state of knowledge is reflected by the plus signs associated with the information found here. The 50+ unique tissue combinations are calculated using details related to the target species, tissue preservation method, target tissue, and tissue state, e.g., infected with a particular pathogen. The crown denotes contributions leading to authorship on the Zenodo release (some restrictions apply). The ibex (goat) climbing the mountain is symbolic of the method’s namesake. To date, more than 25 contributors from Brazil, Canada, Germany, Mexico, Switzerland, the United Kingdom, and the United States have shared their expertise with the community.

See this image and copyright information in PMC

References

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The IBEX Knowledge-Base: A central resource for multiplexed imaging techniques

Affiliations

The IBEX Knowledge-Base: A central resource for multiplexed imaging techniques

Authors

Affiliations

Abstract

Conflict of interest statement

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