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arXiv · 2412.12965

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

Ziv Yaniv·Ifeanyichukwu U. Anidi·Leanne Arakkal·Armando J. Arroyo-Mejías·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 Kastenmüller·Joshua F. E. Koenig·Aanandita Kothurkar·Rosa K. Kortekaas·Alexandra Y. Kreins·Ian T. Lamborn·Yuri Lin·Katia Luciano Pereira Morais·Aleksandra Lunich·Jean C. S. Luz·Ryan B. MacDonald·Chen Makranz·Vivien I. Maltez·John E. McDonough·Ryan V. Moriarty·Juan M. Ocampo-Godinez·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·Adam K. Wade-Vallance·Margaret Williams·Nathan Zangger·Ronald N. Germain·Andrea J. Radtke
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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, such as 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.

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Ziv Yaniv, Ifeanyichukwu U. Anidi, Leanne Arakkal, Armando J. Arroyo-Mejías, 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 Kastenmüller, Joshua F. E. Koenig, Aanandita Kothurkar, Rosa K. Kortekaas, Alexandra Y. Kreins, Ian T. Lamborn, Yuri Lin, Katia Luciano Pereira Morais, Aleksandra Lunich, Jean C. S. Luz, Ryan B. MacDonald, Chen Makranz, Vivien I. Maltez, John E. McDonough, Ryan V. Moriarty, Juan M. Ocampo-Godinez, 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, Adam K. Wade-Vallance, Margaret Williams, Nathan Zangger, Ronald N. Germain, Andrea J. Radtke. 2025-10-12. The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods. https://arxiv.org/abs/2412.12965

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