ArticleArXiv2024
The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods.
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61 authors.
Ziv YanivBioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Ifeanyichukwu U AnidiCritical Care Medicine and Pulmonary Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
Leanne ArakkalLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
Armando J Arroyo-MejíasLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
Rebecca T BeuschelLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
Katy BörnerDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
Colin J ChuUCL Institute of Ophthalmology and NIHR Moorfields Biomedical Research Centre, London, UK.
Beatrice ClarkLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
Menna R ClatworthyCambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge Department of Medicine, Molecular Immunity Unit, Laboratory of Molecular Biology, Cambridge, UK.
Jake ColauttiMcMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada.
Fabian CosciaMax-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany.
Joshua CroteauDepartment of Business Development, BioLegend Inc., San Diego, CA, USA.
Saven DenhaMcMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada.
Rose DeverFunctional Immunogenomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
Walderez O DutraLaboratory of Cell-Cell Interactions, Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
Sonja FritzscheMax-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany.
Spencer FullamDivision of Rheumatology, Rush University Medical Center, Chicago, IL, USA.
Michael Y GernerDepartment of Immunology, University of Washington School of Medicine, Seattle, WA, USA.
Anita GolaRobin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.
Kenneth J GollobCenter for Research in Immuno-oncology (CRIO), Hospital Israelita Albert Einstein, Sao Paulo, SP, Brazil.
Jonathan M HernandezSurgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Jyh Liang HorLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
Hiroshi IchiseLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
Zhixin JingLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
Danny JonigkInstitute of Pathology, Aachen Medical University, RWTH Aachen, Aachen, Germany.
Evelyn KandovLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
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, ON, Canada.
Aanandita KothurkarUCL Institute of Ophthalmology and NIHR Moorfields Biomedical Research Centre, London, UK.
Rosa K KortekaasDepartment of Medicine, McMaster University, Firestone Institute for Respiratory Health, St Joseph's Healthcare, Hamilton, ON, Canada.
Alexandra Y KreinsInfection Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, UK.
Ian T LambornLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
Yuri LinSurgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Katia Luciano Pereira MoraisCenter for Research in Immuno-oncology (CRIO), Hospital Israelita Albert Einstein, Sao Paulo, SP, Brazil.
Aleksandra LunichCritical Care Medicine and Pulmonary Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
Jean C S LuzViral Vector Laboratory, Cancer Institute of São Paulo, University of São Paulo, SP, Brazil.
Ryan B MacDonaldUCL Institute of Ophthalmology and NIHR Moorfields Biomedical Research Centre, London, UK.
Chen MakranzNeuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Vivien I MaltezDivision of Allergy, Immunology and Rheumatology, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
John E McDonoughDepartment of Medicine, McMaster University, Firestone Institute for Respiratory Health, St Joseph's Healthcare, Hamilton, ON, Canada.
Ryan V MoriartyDepartment of Cellular and Developmental Biology, Northwestern University, Chicago, IL, USA.
Juan M Ocampo-GodinezInfection Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, UK.
Vitoria M OlynthoMcMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada.
Annette OxeniusInstitute of Microbiology, ETH Zurich, Zurich, Switzerland.
Kartika PadhanLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
Kirsten RemmertSurgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Nathan RichozCambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge Department of Medicine, Molecular Immunity Unit, Laboratory of Molecular Biology, Cambridge, UK.
Edward C SchromLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
Wanjing ShangLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
Lihong ShiLaboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Rochelle M ShihLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
Emily SperanzaFlorida Research and Innovation Center, Cleveland Clinic Lerner Research Institute, Port Saint Lucie, FL, USA.
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, UK.
Tibor Z VeresLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
Megan VierhoutMcMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada.
Brianna T WachterLaboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Margaret WilliamsCritical Care Medicine and Pulmonary Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
Nathan ZanggerInstitute of Microbiology, ETH Zurich, Zurich, Switzerland.
Ronald N GermainLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
Andrea J RadtkeLymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
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
$22.1MConProject-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
$7.4MTRAINING PROGRAM IN IMMUNOLOGY &MOLECULAR PATHOGENESIST32AI007476 · NIAID · NORTHWESTERN UNIVERSITY AT CHICAGO · PI Edward Benjamin Thorp · 1996 to 2026
$6.6MThe 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
$746kNCI NIH HHS U24 CA268108NIAID NIH HHS 75N93019C00070NIAID NIH HHS R01 AI134713NIAID NIH HHS T32 AI007476NIAMS NIH HHS R01 AR077019NIDDK NIH HHS U24 DK135157NIDDK NIH HHS U2C DK114886NIGMS NIH HHS R00 GM147841NIH HHS OT2 OD033756Wellcome Trust
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, e.g., 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.
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39764400PMC
PMC11702815What OpenQuestion holds
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