The IBEX knowledge-base a community resource enabling adoption and development of immunofluorescence imaging methods

Ziv Yaniv¹, Ifeanyichukwu U Anidi², Leanne Arakkal³, Armando J Arroyo-Mejías³, Rebecca T Beuschel³, Katy Börner⁴, Colin J Chu⁵, Beatrice H Clark³, Menna R Clatworthy⁶, Jake Colautti⁷, Fabian Coscia⁸, Joshua Croteau⁹, Saven Denha⁷, Rose Dever¹⁰, Walderez O Dutra¹¹, Sonja Fritzsche^{8

12}, 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 Kandov³, Wolfgang Kastenmüller²⁰, Joshua F E Koenig⁷, Aanandita Kothurkar⁵, Rosa K Kortekaas²¹, Alexandra Y Kreins²², Ian T Lamborn³, Yuri Lin¹⁷, Katia Luciano Pereira Morais¹⁶, Aleksandra Lunich², Jean C S Luz²³, Ryan B MacDonald⁵, Chen Makranz²⁴, Vivien I Maltez²⁵, John E McDonough²¹, Ryan V Moriarty²⁶, Juan M Ocampo-Godinez^{22

27}, Vitoria Murakami Olyntho⁷, Annette Oxenius²⁸, Kartika Padhan^{3

29}, Kirsten Remmert¹⁷, Nathan Richoz⁶, Edward C Schrom³, Wanjing Shang³, Lihong Shi³⁰, Rochelle M Shih³, Emily Speranza³¹, Salome Stierli³², Sarah A Teichmann³³, Tibor Z Verse³, Megan Vierhout^{7

21}, Brianna T Wachter³⁴, Adam K Wade-Vallance³, Margaret Williams², Nathan Zangger²⁸, Ronald N Germain^{3

29}, Andrea J Radtke^{3

29

35}

Affiliations

¹ Bioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States.
² Critical Care Medicine and Pulmonary Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States.
³ Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.
⁴ Department of Intelligent Systems Engineering, Indiana University, Bloomington, United States.
⁵ UCL Institute of Ophthalmology and NIHR Moorfields Biomedical Research Centre, London, United Kingdom.
⁶ Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge Department of Medicine, Molecular Immunity Unit, Laboratory of Molecular Biology, Cambridge, United Kingdom.
⁷ McMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, 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, United States.
¹⁰ Functional Immunogenomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, United States.
¹¹ Laboratory of Cell-Cell Interactions, Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
¹² Humboldt-Universität zu Berlin, Institute of Biology, Berlin, Germany.
¹³ Division of Rheumatology, Rush University Medical Center, Chicago, United States.
¹⁴ Department of Immunology, University of Washington School of Medicine, Seattle, United States.
¹⁵ Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, United States.
¹⁶ Center for Research in Immuno-oncology (CRIO), Hospital Israelita Albert Einstein, Sao Paulo, Brazil.
¹⁷ Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, United States.
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 Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
²¹ Department of Medicine, McMaster University, Firestone Institute for Respiratory Health, St Joseph's Healthcare, Hamilton, Canada.
²² Infection Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom.
²³ Viral Vector Laboratory, Cancer Institute of São Paulo, University of São Paulo, Sao Paulo, Brazil.
²⁴ Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, United States.
²⁵ Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, University of California San Diego, La Jolla, United States.
²⁶ Department of Cellular and Developmental Biology, Northwestern University, Chicago, United States.
²⁷ Laboratorio de Bioingeniería de Tejidos, Departamento de Estudios de Posgrado e Investigación, Universidad Nacional Autónoma de México, Mexico City, Mexico.
²⁸ Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
²⁹ Center for Advanced Tissue Imaging Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.
³⁰ Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States.
³¹ Florida Research and Innovation Center, Cleveland Clinic Foundation, Port Saint Lucie, United States.
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 Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States.
³⁵ Leica Microsystems, Wetzlar, Germany.

PMID: 41575186
PMCID: PMC12829988
DOI: 10.7554/eLife.105737

The IBEX knowledge-base a community resource enabling adoption and development of immunofluorescence imaging methods

Ziv Yaniv et al. Elife. 2026.

. 2026 Jan 23:14:RP105737.

doi: 10.7554/eLife.105737.

Authors

Affiliations

¹ Bioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States.
² Critical Care Medicine and Pulmonary Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States.
³ Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.
⁴ Department of Intelligent Systems Engineering, Indiana University, Bloomington, United States.
⁵ UCL Institute of Ophthalmology and NIHR Moorfields Biomedical Research Centre, London, United Kingdom.
⁶ Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge Department of Medicine, Molecular Immunity Unit, Laboratory of Molecular Biology, Cambridge, United Kingdom.
⁷ McMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, 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, United States.
¹⁰ Functional Immunogenomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, United States.
¹¹ Laboratory of Cell-Cell Interactions, Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
¹² Humboldt-Universität zu Berlin, Institute of Biology, Berlin, Germany.
¹³ Division of Rheumatology, Rush University Medical Center, Chicago, United States.
¹⁴ Department of Immunology, University of Washington School of Medicine, Seattle, United States.
¹⁵ Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, United States.
¹⁶ Center for Research in Immuno-oncology (CRIO), Hospital Israelita Albert Einstein, Sao Paulo, Brazil.
¹⁷ Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, United States.
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 Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
²¹ Department of Medicine, McMaster University, Firestone Institute for Respiratory Health, St Joseph's Healthcare, Hamilton, Canada.
²² Infection Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom.
²³ Viral Vector Laboratory, Cancer Institute of São Paulo, University of São Paulo, Sao Paulo, Brazil.
²⁴ Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, United States.
²⁵ Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, University of California San Diego, La Jolla, United States.
²⁶ Department of Cellular and Developmental Biology, Northwestern University, Chicago, United States.
²⁷ Laboratorio de Bioingeniería de Tejidos, Departamento de Estudios de Posgrado e Investigación, Universidad Nacional Autónoma de México, Mexico City, Mexico.
²⁸ Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
²⁹ Center for Advanced Tissue Imaging Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.
³⁰ Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States.
³¹ Florida Research and Innovation Center, Cleveland Clinic Foundation, Port Saint Lucie, United States.
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 Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States.
³⁵ Leica Microsystems, Wetzlar, Germany.

PMID: 41575186
PMCID: PMC12829988
DOI: 10.7554/eLife.105737

Abstract

The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the open-source software community and includes three facets: a development platform (GitHub), static website, and service for data archiving. The Knowledge-Base facilitates the practice of open science throughout the research life cycle by providing validation data for recommended and non-recommended reagents, such as primary and secondary antibodies. In addition to reporting negative data, the Knowledge-Base empowers method adoption and evolution by providing a venue for sharing protocols, videos, datasets, software, and publications. A dedicated discussion forum fosters a sense of community among researchers while addressing questions not covered in published manuscripts. Together, scientists from around the world are advancing scientific discovery at a faster pace, reducing wasted time and effort, and instilling greater confidence in the resulting data.

Keywords: cell biology; human; mouse; multiplexed optical imaging; open science; reagent validation; rhesus macaque; spatial biology; xenopus; zebrafish.

PubMed Disclaimer

Conflict of interest statement

ZY, IA, LA, AA, RB, KB, CC, BC, MC, JC, FC, SD, RD, WD, SF, SF, MG, AG, KG, JH, JH, HI, ZJ, DJ, EK, WK, JK, AK, RK, AK, IL, YL, KL, AL, JL, RM, CM, VM, JM, RM, JO, VM, AO, KP, KR, NR, ES, WS, LS, RS, ES, SS, TV, MV, BW, AW, MW, NZ, RG No competing interests declared, JC JC is an employee and stakeholder of BioLegend (revvity inc). The author has no other competing interests to declare, ST SAT is a remunerated Scientific Advisory Board member of BioOptimus, Foresite Labs, Xaira 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, AR AJR is an employee of Leica Microsystems. The author has no other competing interests to declare

Figures

**Figure 1.. Schematic overview of IBEX KB design and contents.**
The IBEX KB enables open exploration of reagents, protocols, datasets, and advice related to multiplexed imaging from members of the global scientific community. The overall design consists of three facets: a GitHub source repository (purple mountain), a static website (green mountain), and a Zenodo data repository hosting citable archival versions of the data (blue mountain). Every addition to the KB initiates an update to the IBEX Imaging Community Website outlined in steps 1–4. In contrast, updates to the authoritative version on Zenodo are initiated by community members when a significant update to the state of knowledge justifies a new release.

**Figure 2.. Computational workflow for static website generation.**
Data displayed on the static website is generated from human and machine-readable comma-separated value (csv), bibliography database (bib), jpg images, and markdown template (M down arrow) files. Following a new submission, custom Python scripts expand the template markdown files to include the new data. Existing data (unprocessed markdown files) remain unchanged. The website is automatically generated via Python scripts utilizing the GitHub continuous integration compute infrastructure and static website creation services (Jekyll).

**Figure 3.. The IBEX KB provides several ways to contribute and use data.**
Summary of supported data types and ways to contribute or use the KB. Crown icon indicates contributions that result in authorship on the Zenodo archival versions.

**Figure 4.. Guidelines for contributing data and flow chart detailing how to add a reagent contribution.**
(A) Details for contributing data to the IBEX KB. Files that need to be modified are highlighted in blue with data file name bolded. (B) Flow chart demonstrating how to add a reagent contribution. Files that need to be modified are highlighted in green with data file name bolded.

See this image and copyright information in PMC

Update of

The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods.
Yaniv Z, Anidi IU, Arakkal L, Arroyo-Mejías AJ, Beuschel RT, Börner K, Chu CJ, Clark B, Clatworthy MR, Colautti J, Coscia F, Croteau J, Denha S, Dever R, Dutra WO, Fritzsche S, Fullam S, Gerner MY, Gola A, Gollob KJ, Hernandez JM, Hor JL, Ichise H, Jing Z, Jonigk D, Kandov E, Kastenmüller W, Koenig JFE, Kothurkar A, Kortekaas RK, Kreins AY, Lamborn IT, Lin Y, Morais KLP, Lunich A, Luz JCS, MacDonald RB, Makranz C, Maltez VI, McDonough JE, Moriarty RV, Ocampo-Godinez JM, Olyntho VM, Oxenius A, Padhan K, Remmert K, Richoz N, Schrom EC, Shang W, Shi L, Shih RM, Speranza E, Stierli S, Teichmann SA, Veres TZ, Vierhout M, Wachter BT, Williams M, Zangger N, Germain RN, Radtke AJ. Yaniv Z, et al. ArXiv [Preprint]. 2024 Dec 17:arXiv:2412.12965v1. ArXiv. 2024. Update in: Elife. 2026 Jan 23;14:RP105737. doi: 10.7554/eLife.105737. PMID: 39764400 Free PMC article. Updated. Preprint.

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The IBEX knowledge-base a community resource enabling adoption and development of immunofluorescence imaging methods

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The IBEX knowledge-base a community resource enabling adoption and development of immunofluorescence imaging methods

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Conflict of interest statement

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