This is a preprint.

It has not yet been peer reviewed by a journal.

The National Library of Medicine is running a pilot to include preprints that result from research funded by NIH in PMC and PubMed.

[Preprint]. 2024 Dec 17:arXiv:2412.12965v1.

The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods

Ziv Yaniv¹, Ifeanyichukwu U Anidi², Leanne Arakkal³, Armando J Arroyo-Mejías³, Rebecca T Beuschel³, Katy Börner⁴, Colin J Chu⁵, Beatrice Clark³, Menna R Clatworthy⁶, Jake Colautti⁷, Fabian Coscia⁸, Joshua Croteau⁹, Saven Denha⁷, Rose Dever¹⁰, Walderez O Dutra¹¹, Sonja Fritzsche⁸, Spencer Fullam¹², Michael Y Gerner¹³, Anita Gola¹⁴, Kenneth J Gollob¹⁵, Jonathan M Hernandez¹⁶, Jyh Liang Hor³, Hiroshi Ichise³, Zhixin Jing³, Danny Jonigk^{17

18}, Evelyn Kandov³, Wolfgang Kastenmüller¹⁹, Joshua F E Koenig⁷, Aanandita Kothurkar⁵, Rosa K Kortekaas²⁰, Alexandra Y Kreins²¹, Ian T Lamborn³, Yuri Lin¹⁶, Katia Luciano Pereira Morais¹⁵, Aleksandra Lunich², Jean C S Luz²², Ryan B MacDonald⁵, Chen Makranz²³, Vivien I Maltez²⁴, John E McDonough²⁰, Ryan V Moriarty²⁵, Juan M Ocampo-Godinez^{21

26}, Vitoria M Olyntho⁷, Annette Oxenius²⁷, Kartika Padhan^{3

28}, Kirsten Remmert¹⁶, Nathan Richoz⁶, Edward C Schrom³, Wanjing Shang³, Lihong Shi²⁹, Rochelle M Shih³, Emily Speranza³⁰, Salome Stierli³¹, Sarah A Teichmann³², Tibor Z Veres³, Megan Vierhout^{7

20}, Brianna T Wachter³³, Margaret Williams², Nathan Zangger²⁷, Ronald N Germain^{3

28}, Andrea J Radtke^{3

28}

Affiliations

¹ Bioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
² Critical Care Medicine and Pulmonary Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
³ Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
⁴ Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
⁵ UCL Institute of Ophthalmology and NIHR Moorfields Biomedical Research Centre, London, UK.
⁶ Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge Department of Medicine, Molecular Immunity Unit, Laboratory of Molecular Biology, Cambridge, UK.
⁷ McMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada.
⁸ Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany.
⁹ Department of Business Development, BioLegend Inc., San Diego, CA, USA.
¹⁰ Functional Immunogenomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
¹¹ Laboratory of Cell-Cell Interactions, Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
¹² Division of Rheumatology, Rush University Medical Center, Chicago, IL, USA.
¹³ Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA.
¹⁴ Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.
¹⁵ Center for Research in Immuno-oncology (CRIO), Hospital Israelita Albert Einstein, Sao Paulo, SP, Brazil.
¹⁶ Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
¹⁷ Institute of Pathology, Aachen Medical University, RWTH Aachen, Aachen, Germany.
¹⁸ German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.
¹⁹ Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
²⁰ Department of Medicine, McMaster University, Firestone Institute for Respiratory Health, St Joseph's Healthcare, Hamilton, ON, Canada.
²¹ Infection Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, UK.
²² Viral Vector Laboratory, Cancer Institute of São Paulo, University of São Paulo, SP, Brazil.
²³ Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
²⁴ Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
²⁵ Department of Cellular and Developmental Biology, Northwestern University, Chicago, IL, USA.
²⁶ Laboratorio de Bioingeniería de Tejidos, Departamento de Estudios de Posgrado e Investigación, Universidad Nacional Autónoma de México, Mexico City, Mexico.
²⁷ Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
²⁸ Center for Advanced Tissue Imaging Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
²⁹ Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
³⁰ Florida Research and Innovation Center, Cleveland Clinic Lerner Research Institute, Port Saint Lucie, FL, USA.
³¹ Institute of Anatomy, University of Zurich, Zurich, Switzerland.
³² Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, UK.
³³ Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.

PMID: 39764400
PMCID: PMC11702815

The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods

Ziv Yaniv et al. ArXiv. 2024.

[Preprint]. 2024 Dec 17:arXiv:2412.12965v1.

Authors

Affiliations

¹ Bioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
² Critical Care Medicine and Pulmonary Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
³ Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
⁴ Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
⁵ UCL Institute of Ophthalmology and NIHR Moorfields Biomedical Research Centre, London, UK.
⁶ Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge Department of Medicine, Molecular Immunity Unit, Laboratory of Molecular Biology, Cambridge, UK.
⁷ McMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada.
⁸ Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany.
⁹ Department of Business Development, BioLegend Inc., San Diego, CA, USA.
¹⁰ Functional Immunogenomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
¹¹ Laboratory of Cell-Cell Interactions, Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
¹² Division of Rheumatology, Rush University Medical Center, Chicago, IL, USA.
¹³ Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA.
¹⁴ Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.
¹⁵ Center for Research in Immuno-oncology (CRIO), Hospital Israelita Albert Einstein, Sao Paulo, SP, Brazil.
¹⁶ Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
¹⁷ Institute of Pathology, Aachen Medical University, RWTH Aachen, Aachen, Germany.
¹⁸ German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.
¹⁹ Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
²⁰ Department of Medicine, McMaster University, Firestone Institute for Respiratory Health, St Joseph's Healthcare, Hamilton, ON, Canada.
²¹ Infection Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, UK.
²² Viral Vector Laboratory, Cancer Institute of São Paulo, University of São Paulo, SP, Brazil.
²³ Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
²⁴ Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
²⁵ Department of Cellular and Developmental Biology, Northwestern University, Chicago, IL, USA.
²⁶ Laboratorio de Bioingeniería de Tejidos, Departamento de Estudios de Posgrado e Investigación, Universidad Nacional Autónoma de México, Mexico City, Mexico.
²⁷ Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
²⁸ Center for Advanced Tissue Imaging Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
²⁹ Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
³⁰ Florida Research and Innovation Center, Cleveland Clinic Lerner Research Institute, Port Saint Lucie, FL, USA.
³¹ Institute of Anatomy, University of Zurich, Zurich, Switzerland.
³² Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, UK.
³³ Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.

PMID: 39764400
PMCID: PMC11702815

Abstract

The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the open-source software community and includes three facets: a development platform (GitHub), static website, and service for data archiving. The Knowledge-Base facilitates the practice of open science throughout the research life cycle by providing validation data for recommended and non-recommended reagents, e.g., primary and secondary antibodies. In addition to reporting negative data, the Knowledge-Base empowers method adoption and evolution by providing a venue for sharing protocols, videos, datasets, software, and publications. A dedicated discussion forum fosters a sense of community among researchers while addressing questions not covered in published manuscripts. Together, scientists from around the world are advancing scientific discovery at a faster pace, reducing wasted time and effort, and instilling greater confidence in the resulting data.

PubMed Disclaimer

Figures

**Figure 1.. 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.. 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. Website is automatically generated via Python scripts utilizing the GitHub continuous integration compute infrastructure and static website creation services (Jekyll).

**Figure 3.. 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.. 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.

See this image and copyright information in PMC

References

1. Agley J. Assessing changes in US public trust in science amid the COVID-19 pandemic. Public Health. 2020. Jun; 183:122–125. doi: 10.1016/j.puhe.2020.05.004. - DOI - PMC - PubMed
1. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O’Donovan C, Redaschi N, Yeh LSL. The Universal Protein Resource (UniProt). Nucleic Acids Res. 2005; 33:D154–D159. doi: 10.1093/nar/gki070. - DOI - PMC - PubMed
1. Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova-Seinstra E, Vasilevsky N. The Resource Identification Initiative: A cultural shift in publishing. Journal of Comparative Neurology. 2016; 524(1):8–22. doi: 10.1002/brb3.417. - DOI - PMC - PubMed
1. Bertram MG, Sundin J, Roche DG, Sánchez-Tójar A, Thoré ESJ, Brodin T. Open science. Curr Biol. 2023; 33(15):R792–R797. doi: 10.1016/j.cub.2023.05.036. - DOI - PubMed
1. Bespalov A, Steckler T, Skolnick P. Be positive about negatives-recommendations for the publication of negative (or null) results. European Neuropsychopharmacology. 2019; 29(12):1312–1320. doi: 10.1016/j.euroneuro.2019.10.007. - DOI - PubMed

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

This is a preprint.

The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods

Affiliations

The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods

Authors

Affiliations

Abstract

Figures

References

Publication types

Grants and funding

LinkOut - more resources

Full Text Sources