Iterative Bleaching Extends Multiplexity (IBEX) Knowledge-Base

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.迭代脱色扩展多重性成像法（Iterative Bleaching Extends Multiplexity, IBEX）是一种迭代免疫标记与化学脱色技术，可实现多种组织的高多重性成像。IBEX成像法及相关软件的开发由Andrea Radtke博士与Ziv Yaniv博士主导。IBEX及相关方法Ce3D、Ce3D-IBEX、Opal-plex最初由美国国立卫生研究院（US National Institutes of Health）Ronald N. Germain博士的实验室研发。 IBEX成像共同体是一个国际性科学家群体，致力于以透明协作的方式共享与多重成像相关的知识。该开放式全球资源库是试剂、实验方案、靶标组合、学术文献、软件与数据集的核心共享平台。除IBEX技术外，本资源库还支持标准单周期多重成像（Multiplexed 2D imaging）、基于透明化增强三维成像（Ce3D）的透明组织体积成像、高多重性三维成像（Ce3D-IBEX），以及将IBEX染料灭活方案拓展至徕卡Cell DIVE平台（Cell DIVE-IBEX）。本数据集涵盖了当前关于IBEX显微成像方案的全部已知研究内容。 知识库使用指南： 1. 将副本保存至本地计算机。 2. 查找试剂：打开数据目录下的reagent_resources.csv文件，使用电子表格软件根据靶标名称、靶标物种、供应商等条件对列进行筛选。 3. 查看IBEX成像共同体测试过的全部荧光探针列表：打开fluorescent_probes.csv文件，该文件记录了每种荧光探针的光谱特性与灭活条件。 4. 导入知识库引用的学术文献：将数据目录下的publications.bib文件导入至你的参考文献管理软件中。 5. 查看本地网站副本：使用markdown编辑器（如免费的Visual Studio Code）打开docs目录下的index.md文件。 6. 查看试剂的辅助信息（含图像、文献、备注）：使用markdown编辑器打开docs-supporting_material目录结构下的特定靶标-偶联物-ORCID组合。你也可以通过试剂资源页面在网页浏览器中使用货号或其他唯一标识符进行筛选查看。 加入线上IBEX成像共同体并贡献你的研究成果。如需了解贡献的详细步骤，请参阅相关指南。 本研究得到以下机构资助： 美国国立卫生研究院（National Institutes of Health, NIH）下属国家过敏和传染病研究所与国家癌症研究所的校内研究计划，资助编号为1ZIAAI001290-02、1ZIAAI000545-33、1ZIAAI000758-24、1ZIAAI000974-16、1ZIAAI001034-14； 惠康信托基金（Wellcome Trust），资助编号为224586/Z/21/Z； 美国国立卫生研究院下属国家过敏和传染病研究所，资助编号为1ZIAAI001343-01。