The IBEX knowledge-base a community resource enabling adoption and development of immunofluorescence imaging methods

Bioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, United States
Critical Care Medicine and Pulmonary Branch, National Heart, Lung and Blood Institute, National Institutes of Health, United States
Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, United States
Department of Intelligent Systems Engineering, Indiana University, United States
UCL Institute of Ophthalmology and NIHR Moorfields Biomedical Research Centre, United Kingdom
Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge Department of Medicine, Molecular Immunity Unit, Laboratory of Molecular Biology, United Kingdom
McMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, Faculty of Health Sciences, McMaster University, Canada
Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Germany
Department of Business Development, BioLegend Inc, United States
Functional Immunogenomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, United States
Laboratory of Cell-Cell Interactions, Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Brazil
Humboldt-Universität zu Berlin, Institute of Biology, Germany
Division of Rheumatology, Rush University Medical Center, United States
Department of Immunology, University of Washington School of Medicine, United States
Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, United States
Center for Research in Immuno-oncology (CRIO), Hospital Israelita Albert Einstein, Brazil
Surgical Oncology Program, National Cancer Institute, National Institutes of Health, United States
Institute of Pathology, Aachen Medical University, RWTH Aachen, Germany
German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Germany
Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Germany
Department of Medicine, McMaster University, Firestone Institute for Respiratory Health, St Joseph’s Healthcare, Canada
Infection Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, United Kingdom
Viral Vector Laboratory, Cancer Institute of São Paulo, University of São Paulo, Brazil
Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, United States
Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, University of California San Diego, United States
Department of Cellular and Developmental Biology, Northwestern University, United States
Laboratorio de Bioingeniería de Tejidos, Departamento de Estudios de Posgrado e Investigación, Universidad Nacional Autónoma de México, Mexico
Institute of Microbiology, ETH Zurich, Switzerland
Center for Advanced Tissue Imaging Laboratory of Immune System Biology, NIAID, NIH, United States
Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, United States
Florida Research and Innovation Center, Cleveland Clinic Foundation, United States
Institute of Anatomy, University of Zurich, Switzerland
Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way,Cambridge Biomedical Campus, United Kingdom
Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, United States
Leica Microsystems, Germany

Jan 23, 2026

https://doi.org/10.7554/eLife.105737.3

Open access
Copyright information

Figures
Tables
Additional files

4 figures, 1 table and 2 additional files

Figures

Figure 1

Download asset Open asset

Schematic overview of IBEX KB design and contents.

The IBEX KB enables open exploration of reagents, protocols, datasets, and advice related to multiplexed imaging from members of the global scientific community. The overall design consists of three facets: a GitHub source repository (purple mountain), a static website (green mountain), and a Zenodo data repository hosting citable archival versions of the data (blue mountain). Every addition to the KB initiates an update to the IBEX Imaging Community Website outlined in steps 1–4. In contrast, updates to the authoritative version on Zenodo are initiated by community members when a significant update to the state of knowledge justifies a new release.

Figure 2

Download asset Open asset

Computational workflow for static website generation.

Data displayed on the static website is generated from human and machine-readable comma-separated value (csv), bibliography database (bib), jpg images, and markdown template (M down arrow) files. Following a new submission, custom Python scripts expand the template markdown files to include the new data. Existing data (unprocessed markdown files) remain unchanged. The website is automatically generated via Python scripts utilizing the GitHub continuous integration compute infrastructure and static website creation services (Jekyll).

Figure 3

Download asset Open asset

The IBEX KB provides several ways to contribute and use data.

Summary of supported data types and ways to contribute or use the KB. Crown icon indicates contributions that result in authorship on the Zenodo archival versions.

Figure 4

Download asset Open asset

Guidelines for contributing data and flow chart detailing how to add a reagent contribution.

(A) Details for contributing data to the IBEX KB. Files that need to be modified are highlighted in blue with data file name bolded. (B) Flow chart demonstrating how to add a reagent contribution. Files that need to be modified are highlighted in green with data file name bolded.

Tables

Table 1

IBEX imaging KB directory structure and contents.

Infrastructure-related files are found in the data, docs_in, and root directories. Content of interest for the general user is found in the data and docs directories. Using text-based files and a data lake approach enables easy navigation, viewing, and editing of the raw KB content without requiring dedicated software.

Directory	Content
data	Files describing the contents of the knowledge-base, data dictionaries (reagent_data_dict.csv, reagent_glossary.csv). Files referencing external information (protocols.csv, videos.csv, vendor_urls.csv, publications.bib). Files referencing internal information (image_resources.csv, reagent_resources.csv).
docs_in	Markdown template files.
docs	Markdown files with notes and images that support claims made with respect to reagents.
.github	Configuration files for GitHub actions (automated testing and markdown file generation using the contents of the data and docs_in directories).
root	License, basic testing configuration via pre-commit and Zenodo configuration file listing contributor details (affiliation etc.).