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.zenodo.json
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{
"description": "<p>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 <a href=\"https://doi.org/10.1038/s41596-021-00644-9\">IBEX method</a> and <a href=\"https://github.com/niaid/imaris_extensions\">related software</a> was led by Dr. Andrea Radtke and Dr. Ziv Yaniv. <a href=\"https://doi.org/10.1073/pnas.2018488117\">IBEX</a> and related methods, <a href=\"https://doi.org/10.1073/pnas.1708981114\">Ce3D</a>, <a href=\"https://doi.org/10.1111/imr.13052\">Ce3D-IBEX</a>, <a href=\"https://doi.org/10.1073/pnas.2018488117\">Opal-plex</a>, were originally developed in the laboratory of <a href=\"https://www.niaid.nih.gov/research/ronald-n-germain-md-phd\">Dr. Ronald N. Germain</a>, US National Institutes of Health.</p><p>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.</p><p>How to use the Knowledge-Base:<ol><li>Save a copy to your computer.</li><li>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.</li><li>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.</li><li>To import publications cited in the Knowledge-Base, import the publications.bib file found in the data directory to your reference manager.</li><li>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 <a href=\"https://code.visualstudio.com/\">Visual Studio Code</a>.</li><li>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 <a href=\"https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/reagent_resources.html\">Reagent Resources page</a> and filtered using a catalog number or other unique identifier in your web browser.</li></ol></p><p>Join the <a href=\"https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/\">online IBEX Imaging community</a> and contribute your knowledge. For more details on how to contribute, see <a href=\"https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/contrib.html\">these instructions</a>.</p><p>This research was supported by:<ul><li>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.</li><li> The Wellcome Trust, under grant 224586/Z/21/Z.</li><li> The National Institute of Allergy and Infectious Diseases, NIH, under grant 1ZIAAI001343-01.</li></ul></p>",
"keywords": [
"Open Science",
"Microscopy",
"Multiplexed Optical Imaging",
"Antibody",
"Spatial Biology"
],
"license": {
"id": "CC-BY-4.0"
},
"title": "Iterative Bleaching Extends Multiplexity (IBEX) Knowledge-Base",
"upload_type": "dataset",
"creators": [
{
"affiliation": "National Institutes of Health",
"name": "Yaniv, Ziv",
"orcid": "0000-0003-0315-7727"
},
{
"affiliation": "National Institutes of Health",
"name": "Anidi, Ifeanyichukwu",
"orcid": "0000-0002-2692-1225"
},
{
"affiliation": "National Institutes of Health",
"name": "Arakkal, Leanne",
"orcid": "0000-0001-9189-7172"
},
{
"affiliation": "National Institutes of Health",
"name": "Arroyo-Mejias, Armando",
"orcid": "0000-0002-0835-911X"
},
{
"affiliation": "National Institutes of Health",
"name": "Beuschel, Rebecca T.",
"orcid": "0000-0002-3882-457X"
},
{
"affiliation": "Indiana University",
"name": "Börner, Katy",
"orcid": "0000-0002-3321-6137"
},
{
"affiliation": "University College London",
"name": "Chu, Colin J.",
"orcid": "0000-0003-2088-8310"
},
{
"affiliation": "University of Cambridge",
"name": "Clatworthy, Menna",
"orcid": "0000-0002-3340-9828"
},
{
"affiliation": "McMaster University",
"name": "Colautti, Jake",
"orcid": "0000-0002-1461-0999"
},
{
"affiliation": "BioLegend Inc.",
"name": "Croteau, Joshua",
"orcid": "0000-0002-8142-0482"
},
{
"affiliation": "McMaster University",
"name": "Denha, Saven",
"orcid": "0009-0004-8162-409X"
},
{
"affiliation": "National Institutes of Health",
"name": "Dever, Rose",
"orcid": "0009-0004-2746-8743"
},
{
"affiliation": "Universidade Federal de Minas Gerais",
"name": "Dutra, Walderez",
"orcid": "0000-0002-7586-9996"
},
{
"affiliation": "Max Delbrück Center for Molecular Medicine",
"name": "Fritzsche, Sonja",
"orcid": "0000-0003-3335-3534"
},
{
"affiliation": "Rush University",
"name": "Fullam, Spencer",
"orcid": "0000-0001-9012-3802"},
{
"affiliation": "University of Washington",
"name": "Gerner, Michael",
"orcid": "0000-0001-5406-8308"
},
{
"affiliation": "Rockefeller University",
"name": "Gola, Anita",
"orcid": "0000-0003-1431-1398"
},
{
"affiliation": "Hospital Israelita Albert Einstein",
"name": "Gollob, Kenneth J.",
"orcid": "0000-0003-4184-3867"
},
{
"affiliation": "National Institutes of Health",
"name": "Ichise, Hiroshi",
"orcid": "0000-0002-5187-810X"
},
{
"affiliation": "National Institutes of Health",
"name": "Jing, Zhixin",
"orcid": "0000-0003-1118-7432"
},
{
"affiliation": "University Hospital Aachen",
"name": "Jonigk, Danny",
"orcid": "0000-0002-5251-2281"
},
{
"affiliation": "National Institutes of Health",
"name": "Kandov, Evelyn",
"orcid": "0000-0001-7071-9916"
},
{
"affiliation": "Julius Maximilians Universität Würzburg",
"name": "Kastenmüller, Wolfgang",
"orcid": "0000-0002-3835-1485"
},
{
"affiliation": "McMaster University",
"name": "Koenig, Joshua F. E.",
"orcid": "0000-0002-8909-5039"
},
{
"affiliation": "McMaster University",
"name": "Kortekaas, Rosa K.",
"orcid": "0000-0002-8728-1735"
},
{
"affiliation": "University College London",
"name": "Kothurkar, Aanandita",
"orcid": "0009-0000-2047-4228"
},
{
"affiliation": "National Institutes of Health",
"name": "Lamborn, Ian",
"orcid": "0009-0006-1490-3667"
},
{
"affiliation": "National Institutes of Health",
"name": "Lin, Yuri",
"orcid": "0009-0006-9784-2694"
},
{
"affiliation": "University of São Paulo",
"name": "Luz, Jean Carlos Dos Santos",
"orcid": "0000-0001-5088-7808"
},
{
"affiliation": "National Institutes of Health",
"name": "Makranz, Chen",
"orcid": "0000-0002-6944-6997"
},
{
"affiliation": "Northwestern",
"name": "Moriarty, Ryan V.",
"orcid": "0000-0001-7100-1906"
},
{
"affiliation": "McMaster University",
"name": "Murakami Olyntho, Vitoria",
"orcid": "0000-0003-2634-6838"
},
{
"affiliation": "National Institutes of Health",
"name": "Padhan, Kartika",
"orcid": "0000-0001-9561-4256"
},
{
"affiliation": "University of Cambridge",
"name": "Richoz, Nathan",
"orcid": "0000-0002-7422-3237"
},
{
"affiliation": "National Institutes of Health",
"name": "Shang, Wanjing",
"orcid": "0009-0007-0646-7946"
},
{
"affiliation": "National Institutes of Health",
"name": "Shi, Lihong",
"orcid": "0000-0002-6604-2065"
},
{
"affiliation": "National Institutes of Health",
"name": "Shih, Rochelle",
"orcid": "0000-0002-3218-4479"
},
{
"affiliation": "Cleveland Clinic Lerner Research Institute",
"name": "Speranza, Emily",
"orcid": "0000-0003-0666-4804"
},
{
"affiliation": "Wellcome Sanger Institute",
"name": "Teichmann, Sarah",
"orcid": "0000-0002-6294-6366"
},
{
"affiliation": "National Institutes of Health",
"name": "Veres, Tibor Z.",
"orcid": "0000-0002-6980-8900"
},
{
"affiliation": "McMaster University",
"name": "Vierhout, Megan",
"orcid": "0000-0001-5813-2581"
},
{
"affiliation": "National Institutes of Health",
"name": "Wachter, Brianna",
"orcid": "0000-0002-2950-2683"
},
{
"affiliation": "National Institutes of Health",
"name": "Williams, Margaret",
"orcid": "0000-0003-3697-5726"
},
{
"affiliation": "ETH Zurich",
"name": "Zangger, Nathan",
"orcid": "0000-0003-1130-1899"
},
{
"affiliation": "National Institutes of Health",
"name": "Germain, Ronald N.",
"orcid": "0000-0003-1495-9143"
},
{
"affiliation": "National Institutes of Health",
"name": "Radtke, Andrea J.",
"orcid": "0000-0003-4379-8967"
}
],
"grants": []
}