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

• DOI: 10.7554/elife.105737
• Publication Date: 2025-04-02T15:36:13Z
• Authors: Ziv Yaniv; Ifeanyichukwu U A...; Leanne Arakkal; Armando J Arroyo-...; Rebecca T Beuschel; Katy Börner; Colin J Chu; Beatrice Clark; Menna R Clatworthy; Jake Colautti; Fabian Coscia; Joshua Croteau; Saven Denha; Rose Dever; Walderez O Dutra; Sonja Fritzsche; Spencer Fullam; Michael Y Gerner; Anita Gola; Kenneth J Gollob; Jonathan M Hernandez; Jyh Liang Hor; Hiroshi Ichise; Zhixin Jing; Danny Jonigk; Evelyn Kandov; Wolfgang Kastenmü...; Joshua FE Koenig; Aanandita Kothurkar; Rosa K Kortekaas; Alexandra Y Kreins; Ian T Lamborn; Yuri Lin; Katia Luciano Per...; Aleksandra Lunich; Jean CS Luz; Ryan B MacDonald; Chen Makranz; Vivien I Maltez; John E McDonough; Ryan V Moriarty; Juan M Ocampo-God...; Vitoria M Olyntho; Annette Oxenius; Kartika Padhan; Kirsten Remmert; Nathan Richoz; Edward C Schrom; Wanjing Shang; Lihong Shi; Rochelle M Shih; Emily Speranza; Salome Stierli; Sarah A Teichmann; Tibor Z Veres; Megan Vierhout; Brianna T Wachter; Margaret Williams; Nathan Zangger; Ronald N Germain; Andrea J Radtke
• Keywords: FOS: Biological sciences; Image and Video Processing (eess.IV); FOS: Electrical engineering, electronic engineering, information engineering; Quantitative Biology - Tissues and Organs; Electrical Engineering and Systems Science - Image and Video Processing; Tissues and Organs (q-bio.TO)

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.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.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.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.