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:

1. Save a copy to your computer.
2. 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.
3. 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.
4. To import publications cited in the Knowledge-Base, import the publications.bib file found in the data directory to your reference manager.
5. 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.
6. 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.