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[Preprint]. 2024 Jul 26:arXiv:2407.19059v1.

The IBEX Knowledge-Base: Achieving more together with open science

Andrea J Radtke¹, Ifeanyichukwu Anidi², Leanne Arakkal³, Armando Arroyo-Mejias³, Rebecca T Beuschel^{3

4}, Katy Börner⁵, Colin J Chu⁶, Beatrice Clark³, Menna R Clatworthy⁷, Jake Colautti⁸, Joshua Croteau⁹, Saven Denha⁸, Rose Dever¹⁰, Walderez O Dutra¹¹, Sonja Fritzsche¹², Spencer Fullam¹³, Michael Y Gerner¹⁴, Anita Gola¹⁵, Kenneth J Gollob¹⁶, Jonathan M Hernandez¹⁷, Jyh Liang Hor³, Hiroshi Ichise³, Zhixin Jing³, Danny Jonigk^{18

19}, Evelyn Kandov^{3

20}, Wolfgang Kastenmüller²¹, Joshua F E Koenig⁸, Aanandita Kothurkar⁶, Alexandra Y Kreins^{22

23}, Ian Lamborn³, Yuri Lin¹⁷, Katia Luciano Pereira Morais¹⁶, Aleksandra Lunich², Jean C S Luz²⁴, Ryan B MacDonald⁶, Chen Makranz²⁵, Vivien I Maltez²⁶, Ryan V Moriaty²⁷, Juan M Ocampo-Godinez^{22

28

29}, Vitoria M Olyntho⁸, Kartika Padhan¹, Kirsten Remmert¹⁷, Nathan Richoz⁷, Edward C Schrom³, Wanjing Shang³, Lihong Shi³⁰, Rochelle M Shih³, Emily Speranza³¹, Salome Stierli³², Sarah A Teichmann^{33

34}, Tibor Z Veres³, Megan Vierhout⁸, Brianna T Wachter³⁵, Adam K Wade-Vallance³, Margaret Williams², Nathan Zangger³⁶, Ronald N Germain^{1

3}, Ziv Yaniv³⁷

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, MD, USA.
² Critical Care Medicine and Pulmonary Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
³ Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
⁴ Current address for Rebecca T. Beuschel: Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
⁵ Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
⁶ UCL Institute of Ophthalmology and NIHR Moorfields Biomedical Research Centre, London, UK.
⁷ Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge Department of Medicine, Molecular Immunity Unit, Laboratory of Molecular Biology, Cambridge, UK.
⁸ McMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada.
⁹ Department of Business Development, BioLegend Inc., San Diego, CA, USA.
¹⁰ Functional Immunogenomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
¹¹ Laboratory of Cell-Cell Interactions, Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
¹² Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany.
¹³ Division of Rheumatology, Rush University Medical Center, Chicago, IL, USA.
¹⁴ Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA.
¹⁵ Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.
¹⁶ Center for Research in Immuno-oncology (CRIO), Hospital Israelita Albert Einstein, Sao Paulo, SP, Brazil.
¹⁷ Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
¹⁸ Institute of Pathology, Aachen Medical University, RWTH Aachen, Aachen, Germany.
¹⁹ German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.
²⁰ Current address for Evelyn Kandov: Department of Pharmacology, Vanderbilt Brain Institute, Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN, USA.
²¹ Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg; Würzburg, Germany.
²² Infection Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, UK.
²³ Great Ormond Street Hospital for Children NHS Foundation Trust, Department of Immunology and Gene Therapy, London, UK.
²⁴ Viral Vector Laboratory, Cancer Institute of São Paulo, University of São Paulo, SP, Brazil.
²⁵ Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
²⁶ Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
²⁷ Department of Cellular and Developmental Biology, Northwestern University, Chicago, IL, USA.
²⁸ Laboratorio de Bioingeniería de Tejidos, Departamento de Estudios de Posgrado e Investigación, Universidad Nacional Autónoma de México, Mexico City, Mexico.
²⁹ Laboratorio de Inmunoquímica I, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico.
³⁰ Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
³¹ Florida Research and Innovation Center, Cleveland Clinic Lerner Research Institute, Port Saint Lucie, FL, USA.
³² Institute of Anatomy, University of Zurich, Zurich, Switzerland.
³³ Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, UK.
³⁴ Department of Medicine, University of Cambridge, Cambridge, UK.
³⁵ Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
³⁶ Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
³⁷ Bioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.

PMID: 39398203
PMCID: PMC11468668

The IBEX Knowledge-Base: Achieving more together with open science

Andrea J Radtke et al. ArXiv. 2024.

[Preprint]. 2024 Jul 26:arXiv:2407.19059v1.

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, MD, USA.
² Critical Care Medicine and Pulmonary Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
³ Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
⁴ Current address for Rebecca T. Beuschel: Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
⁵ Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
⁶ UCL Institute of Ophthalmology and NIHR Moorfields Biomedical Research Centre, London, UK.
⁷ Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge Department of Medicine, Molecular Immunity Unit, Laboratory of Molecular Biology, Cambridge, UK.
⁸ McMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada.
⁹ Department of Business Development, BioLegend Inc., San Diego, CA, USA.
¹⁰ Functional Immunogenomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
¹¹ Laboratory of Cell-Cell Interactions, Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
¹² Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany.
¹³ Division of Rheumatology, Rush University Medical Center, Chicago, IL, USA.
¹⁴ Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA.
¹⁵ Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.
¹⁶ Center for Research in Immuno-oncology (CRIO), Hospital Israelita Albert Einstein, Sao Paulo, SP, Brazil.
¹⁷ Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
¹⁸ Institute of Pathology, Aachen Medical University, RWTH Aachen, Aachen, Germany.
¹⁹ German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.
²⁰ Current address for Evelyn Kandov: Department of Pharmacology, Vanderbilt Brain Institute, Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN, USA.
²¹ Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg; Würzburg, Germany.
²² Infection Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, UK.
²³ Great Ormond Street Hospital for Children NHS Foundation Trust, Department of Immunology and Gene Therapy, London, UK.
²⁴ Viral Vector Laboratory, Cancer Institute of São Paulo, University of São Paulo, SP, Brazil.
²⁵ Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
²⁶ Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
²⁷ Department of Cellular and Developmental Biology, Northwestern University, Chicago, IL, USA.
²⁸ Laboratorio de Bioingeniería de Tejidos, Departamento de Estudios de Posgrado e Investigación, Universidad Nacional Autónoma de México, Mexico City, Mexico.
²⁹ Laboratorio de Inmunoquímica I, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico.
³⁰ Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
³¹ Florida Research and Innovation Center, Cleveland Clinic Lerner Research Institute, Port Saint Lucie, FL, USA.
³² Institute of Anatomy, University of Zurich, Zurich, Switzerland.
³³ Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, UK.
³⁴ Department of Medicine, University of Cambridge, Cambridge, UK.
³⁵ Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
³⁶ Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
³⁷ Bioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.

PMID: 39398203
PMCID: PMC11468668

Abstract

Iterative Bleaching Extends multipleXity (IBEX) is a versatile method for highly multiplexed imaging of diverse tissues. Based on open science principles, we created the IBEX Knowledge-Base, a resource for reagents, protocols and more, to empower innovation.

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Conflict of interest statement

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.). All other authors declare no competing interests.

Figures

**Figure 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.

See this image and copyright information in PMC

References

1. Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, et al. Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. Nature Methods. 2022;19(3):284–95. doi: 10.1038/s41592-021-01316-y. - DOI - PMC - PubMed
1. Radtke AJ, Roschewski M. The follicular lymphoma tumor microenvironment at single-cell and spatial resolution. Blood. 2024;143(12):1069–79. doi: 10.1182/blood.2023020999. - DOI - PMC - PubMed
1. Radtke AJ, Kandov E, Lowekamp B, Speranza E, Chu CJ, Gola A, et al. IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues. Proc Natl Acad Sci USA. 2020;117(52):33455–65. doi: 10.1073/pnas.2018488117. - DOI - PMC - PubMed
1. Radtke AJ, Chu CJ, Yaniv Z, Yao L, Marr J, Beuschel RT, et al. IBEX: an iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues. Nat Protoc. 2022;17(2):378–401. doi: 10.1038/s41596-021-00644-9. - DOI - PubMed
1. Yaniv Z. Lowekamp B. SimpleITK Imaris Extensions. Zenodo. 2023. doi: 10.5281/zenodo.7854019. - DOI

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This is a preprint.

The IBEX Knowledge-Base: Achieving more together with open science

Affiliations

The IBEX Knowledge-Base: Achieving more together with open science

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

Grants and funding