Iterative Bleaching Extends Multiplexity (IBEX) Knowledge-Base
Zenodo (CERN European Organization for Nuclear Research)
Abstract
The Iterative Bleaching Extends Multiplexity (IBEX) imaging method is an iterative immunolabeling and chemical bleaching method that enables highly multiplexed imaging of diverse tissues. Development of the IBEX method and related software was led by Dr. Andrea Radtke and Dr. Ziv Yaniv. IBEX and related methods, Ce3D, Ce3D-IBEX, Opal-plex, were originally developed in the laboratory of Dr. Ronald N. Germain, US National Institutes of Health. The IBEX Imaging Community is an international group of scientists committed to sharing knowledge related to multiplexed imaging in a transparent and collaborative manner. This open, global repository is a central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). This dataset contains the current state of knowledge with respect to the IBEX microscopy imaging protocol. How to use the Knowledge-Base: Save a copy to your computer. To find a reagent: Open the reagent_resources.csv file found in the data directory. Use a spreadsheet application to filter the columns based on target name, target species, vendor, etc. To view a complete list of fluorescent probes tested by the IBEX imaging community: Open the fluorescent_probes.csv file. This file reports the spectral properties and inactivation conditions of each fluorescent probe. To import publications cited in the Knowledge-Base, import the publications.bib file found in the data directory to your reference manager. To view a local copy of the website: Open the index.md file found in the docs directory using a markdown editor such as the free Visual Studio Code. To view supporting information for a reagent (images, publications, notes): Open a specific target-conjugate-orcid combination under the docs-supporting_material directory structure using a markdown editor. This can also be visualized from the Reagent Resources page and filtered using a catalog number or other unique identifier in your web browser. Join the online IBEX Imaging community and contribute your knowledge. For more details on how to contribute, see these instructions. This research was supported by: The Intramural Research Program of the NIH, National Institute of Allergy and Infectious Diseases and National Cancer Institute, under grants 1ZIAAI001290-02, 1ZIAAI000545-33, 1ZIAAI000758-24, 1ZIAAI000974-16, 1ZIAAI001034-14. The Wellcome Trust, under grant 224586/Z/21/Z. The National Institute of Allergy and Infectious Diseases, NIH, under grant 1ZIAAI001343-01.
Authors 33
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Affiliation as printed
National Institutes of Health
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Affiliation as printed
National Institutes of Health
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Affiliation as printed
National Institutes of Health
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Affiliation as printed
National Institutes of Health
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Affiliation as printed
National Institutes of Health
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Affiliation as printed
Indiana University
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Affiliation as printed
University College London
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University of Cambridge · McMaster University
Affiliation as printed
University of Cambridge
McMaster University
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BioLegend (United States) · McMaster University
Affiliation as printed
McMaster University
BioLegend Inc
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Universidade Federal de Minas Gerais · BioLegend (United States)
Affiliation as printed
BioLegend Inc
Universidade Federal de Minas Gerais
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Rush University · McMaster University
Affiliation as printed
McMaster University
Rush University
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Universidade Federal de Minas Gerais · Rockefeller University
Affiliation as printed
Universidade Federal de Minas Gerais
Rockefeller University
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National Institutes of Health · Rush University
Affiliation as printed
Rush University
National Institutes of Health
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Michael Y. Gerner Aachen
University of Washington · Universitätsklinikum Aachen
Affiliation as printed
University of Washington
University Hospital Aachen
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National Institutes of Health · Rockefeller University
Affiliation as printed
Rockefeller University
National Institutes of Health
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University of Würzburg · Hospital Israelita Albert Einstein
Affiliation as printed
Hospital Israelita Albert Einstein
Julius Maximilians Universität Würzburg
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National Institutes of Health · McMaster University
Affiliation as printed
National Institutes of Health
McMaster University
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Danny David Jonigk Aachen
National Institutes of Health · Universitätsklinikum Aachen
Affiliation as printed
University Hospital Aachen
National Institutes of Health
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National Institutes of Health · University of Cambridge
Affiliation as printed
National Institutes of Health
University of Cambridge
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National Institutes of Health · University of Würzburg
Affiliation as printed
Julius Maximilians Universität Würzburg
National Institutes of Health
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Cleveland Clinic · McMaster University
Affiliation as printed
McMaster University
Cleveland Clinic Lerner Research Institute
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Affiliation as printed
McMaster University
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Affiliation as printed
National Institutes of Health
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Affiliation as printed
University of Cambridge
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Affiliation as printed
National Institutes of Health
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Affiliation as printed
Cleveland Clinic Lerner Research Institute
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Affiliation as printed
Wellcome Sanger Institute
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Affiliation as printed
National Institutes of Health
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Affiliation as printed
McMaster University
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Affiliation as printed
National Institutes of Health
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Affiliation as printed
National Institutes of Health
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Affiliation as printed
National Institutes of Health
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Affiliation as printed
National Institutes of Health
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