ArticleeLife2026
The IBEX knowledge-base a community resource enabling adoption and development of immunofluorescence imaging methods.
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Article in eLife, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2citing papers in PubMed
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Who cites it
2 citing papers in PubMed.
- Spatial proteomic mapping of the human and mouse retina using IBEX.JCI insight · 2026Article
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Authors and funding
62 authors.
Ziv YanivBioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States.ORCID https://orcid.org/0000-0003-0315-7727
Ifeanyichukwu U AnidiCritical Care Medicine and Pulmonary Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States.ORCID https://orcid.org/0000-0002-2692-1225
Leanne ArakkalLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.
Armando J Arroyo-MejíasLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.
Rebecca T BeuschelLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.
Katy BörnerDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, United States.
Colin J ChuUCL Institute of Ophthalmology and NIHR Moorfields Biomedical Research Centre, London, United Kingdom.ORCID https://orcid.org/0000-0003-2088-8310
Beatrice H ClarkLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.
Menna R ClatworthyCambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge Department of Medicine, Molecular Immunity Unit, Laboratory of Molecular Biology, Cambridge, United Kingdom.ORCID https://orcid.org/0000-0002-3340-9828
Jake ColauttiMcMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, Canada.
Fabian CosciaMax-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany.ORCID https://orcid.org/0000-0002-2244-5081
Joshua CroteauDepartment of Business Development, BioLegend Inc, San Diego, United States.
Saven DenhaMcMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, Canada.ORCID https://orcid.org/0009-0004-8162-409X
Rose DeverFunctional Immunogenomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, United States.
Walderez O DutraLaboratory of Cell-Cell Interactions, Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Sonja FritzscheMax-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany.ORCID https://orcid.org/0000-0003-3335-3534
Spencer FullamDivision of Rheumatology, Rush University Medical Center, Chicago, United States.ORCID https://orcid.org/0000-0001-9012-3802
Michael Y GernerDepartment of Immunology, University of Washington School of Medicine, Seattle, United States.ORCID https://orcid.org/0000-0001-5406-8308
Anita GolaRobin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, United States.
Kenneth J GollobCenter for Research in Immuno-oncology (CRIO), Hospital Israelita Albert Einstein, Sao Paulo, Brazil.
Jonathan M HernandezSurgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, United States.
Jyh Liang HorLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.ORCID https://orcid.org/0000-0001-6721-4204
Hiroshi IchiseLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.ORCID https://orcid.org/0000-0002-5187-810X
Zhixin JingLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.ORCID https://orcid.org/0000-0003-1118-7432
Danny JonigkInstitute of Pathology, Aachen Medical University, RWTH Aachen, Aachen, Germany.
Evelyn KandovLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.
Wolfgang KastenmüllerWürzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
Joshua F E KoenigMcMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, Canada.ORCID https://orcid.org/0000-0002-8909-5039
Aanandita KothurkarUCL Institute of Ophthalmology and NIHR Moorfields Biomedical Research Centre, London, United Kingdom.
Rosa K KortekaasDepartment of Medicine, McMaster University, Firestone Institute for Respiratory Health, St Joseph's Healthcare, Hamilton, Canada.ORCID https://orcid.org/0000-0002-8728-1735
Alexandra Y KreinsInfection Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom.ORCID https://orcid.org/0000-0001-8748-5837
Ian T LambornLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.
Yuri LinSurgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, United States.ORCID https://orcid.org/0009-0006-9784-2694
Katia Luciano Pereira MoraisCenter for Research in Immuno-oncology (CRIO), Hospital Israelita Albert Einstein, Sao Paulo, Brazil.
Aleksandra LunichCritical Care Medicine and Pulmonary Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States.
Jean C S LuzViral Vector Laboratory, Cancer Institute of São Paulo, University of São Paulo, Sao Paulo, Brazil.
Ryan B MacDonaldUCL Institute of Ophthalmology and NIHR Moorfields Biomedical Research Centre, London, United Kingdom.ORCID https://orcid.org/0000-0003-4194-8925
Chen MakranzNeuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, United States.
Vivien I MaltezDivision of Allergy, Immunology and Rheumatology, Department of Pediatrics, University of California San Diego, La Jolla, United States.
John E McDonoughDepartment of Medicine, McMaster University, Firestone Institute for Respiratory Health, St Joseph's Healthcare, Hamilton, Canada.ORCID https://orcid.org/0000-0003-2497-0258
Ryan V MoriartyDepartment of Cellular and Developmental Biology, Northwestern University, Chicago, United States.
Juan M Ocampo-GodinezInfection Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom.
Vitoria Murakami OlynthoMcMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, Canada.ORCID https://orcid.org/0000-0003-2634-6838
Annette OxeniusInstitute of Microbiology, ETH Zurich, Zurich, Switzerland.
Kartika PadhanLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.
Kirsten RemmertSurgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, United States.
Nathan RichozCambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge Department of Medicine, Molecular Immunity Unit, Laboratory of Molecular Biology, Cambridge, United Kingdom.
Edward C SchromLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.
Wanjing ShangLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.ORCID https://orcid.org/0009-0007-0646-7946
Lihong ShiLaboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States.
Rochelle M ShihLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.
Emily SperanzaFlorida Research and Innovation Center, Cleveland Clinic Foundation, Port Saint Lucie, United States.ORCID https://orcid.org/0000-0003-0666-4804
Salome StierliInstitute of Anatomy, University of Zurich, Zurich, Switzerland.
Sarah A TeichmannCambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way,Cambridge Biomedical Campus, Cambridge, United Kingdom.ORCID https://orcid.org/0000-0002-6294-6366
Tibor Z VerseLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.
Megan VierhoutMcMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, Canada.ORCID https://orcid.org/0000-0001-5813-2581
Brianna T WachterLaboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States.
Adam K Wade-VallanceLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.ORCID https://orcid.org/0000-0002-6863-1461
Margaret WilliamsCritical Care Medicine and Pulmonary Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States.
Nathan ZanggerInstitute of Microbiology, ETH Zurich, Zurich, Switzerland.ORCID https://orcid.org/0000-0003-1130-1899
Ronald N GermainLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.ORCID https://orcid.org/0000-0003-1495-9143
Andrea J RadtkeLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, United States.
Funding
IMMUNE MECHANISMS OF PROTECTION AGAINST MYCOBACTERIUM TUBERCULOSIS CENTER (IMPAC-TB) - SARS-CoV-2 RELATED RESEARCH75N93019C00070 · NIAID · SEATTLE CHILDREN'S HOSPITAL · PI URDAHL, KEVIN · 2019 to 2025
$86.6MSenNet Supplement - Consortium BenchmarkingU24CA268108 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Philip D. Blood, JONATHAN C. SILVERSTEIN · 2021 to 2026
$22.1MUC San Diego FIRST ProgramU54CA272220 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MARIA ELENA MARTINEZ, Joann Trejo · 2022 to 2026
$21.2MConProject-002U2CDK114886 · NIDDK · UNIVERSITY OF WASHINGTON · PI KRETZLER, MATTHIAS · 2017 to 2021
$21.0M3D Multiscale Biomolecular Human Reference Atlas Construction, Visualization and Usage [4 of 5]OT2OD033756 · OD · TRUSTEES OF INDIANA UNIVERSITY · PI BORNER, KATY · 2022 to 2025
$7.4MThe Roles of Lymphoid Tissue Microenvironments in Guiding the Immune ResponseR01AI134713 · NIAID · UNIVERSITY OF WASHINGTON · PI Michael Gerner · 2018 to 2026
$4.4MNational Institute of Diabetes and Digestive and Kidney Diseases ATLAS (D2K-ATLAS) Center as an accessible, comprehensive data portfolio for renal and genitourinary development and diseaseU24DK135157 · NIDDK · BRIGHAM AND WOMEN'S HOSPITAL · PI JAIN, SANJAY, VALERIUS, MICHAEL TODD · 2022 to 2023
$3.4MThe Role of Mechanosensation Pathways in Osteoarthritis Joint Damage and PainR01AR077019 · NIAMS · RUSH UNIVERSITY MEDICAL CENTER · PI Rachel Elizabeth Miller · 2021 to 2026
$2.7MMultiplex imaging in therapy refractory tumors: understanding the spatiotemporal facets of an immunosuppressive environmentR00GM147841 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Vivien Ileana Maltez · 2024 to 2026
$746kBiotechnology and Biological Sciences Research Council BB/S010386/1CIHR 170793CNPq, FAPEMIG, FAPESP #2021/00408-6Damon Runyon Cancer Research Foundation DRG 2409-20European Research Council 771883European Research Council 819329-STEP2National Council of Humanities, Science and Technology (Conahcyt) B210344National Council of Humanities, Science and Technology (Conahcyt) CVU: 10008National Polytechnic Institute (IPN) of Mexico DRI/DII/0445/2024NCI NIH HHS U24 CA268108NCI NIH HHS U54 CA272220NIAID NIH HHS 75N93019C00070NIAID NIH HHS R01 AI134713NIAMS NIH HHS R01 AR077019NIDDK NIH HHS U24 DK135157NIDDK NIH HHS U2C DK114886NIGMS NIH HHS R00 GM147841NIH HHS 75N93019C00070NIH HHS HHSN316201300006W/75N93022F00001NIH HHS K99/R00 4R00GM147841-02NIH HHS OT2 OD033756NIH HHS OT2OD033756NIH HHS R01AI134713NIH HHS R01AR077019NIH HHS U24CA268108NIH HHS U24DK135157NIH HHS U2CDK114886NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation NIHR203332NIHR Cambridge Biomedical Research Centre NIHR203312São Paulo Research Foundation FAPESP fellowship 2023/01697-7Wellcome TrustWellcome Trust 10.35802/220268Wellcome Trust 10.35802/224586Wellcome Trust 222096/Z/20/Z
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.
Indexed as
Fluorescent Antibody TechniqueKnowledge BasesAnimalsHumansInformation DisseminationSoftwarecell biologyhumanmousemultiplexed optical imagingopen sciencereagent validationrhesus macaquespatial biologyxenopuszebrafish
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