Reviewer #2 (Public review): The IBEX Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluorescence Imaging Methods

Read full text
Authors: Ziv Rafael Yaniv, Ifeanyichukwu U. Anidi, Leanne Arakkal, Armando Arroyo-Mejías, Rebecca T. Beuschel, Katy Börner, Colin J. Chu, Beatrice Clark, Menna R Clatworthy, Jake Colautti, Fabian Coscia, Joshua Croteau
+50 more Saven Denha, Rose Dever, Walderez O Dutra, Sonja Fritzsche, Spencer Fullam, Michael Y Gerner, Anita Gola, Kenneth J Gollob, Jonathan Matthew Hernandez, Jyh Liang Hor, Hiroshi Ichise, Zhixin Jing, Danny David Jonigk, Evelyn Kandov, wolfgang kastenmüller, Joshua F. E. Koenig, Rosa K Kortekaas, Aanandita A. Kothurkar, Alexandra Y. Kreins, Ian T. Lamborn, Yuri Lin, Kátia L.P. Morais, Aleksandra Lunich, Jean CS 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 E. Speranza, Salome Stierli, Sarah A Teichmann, Tibor Z Veres, Megan Vierhout, Brianna T. Wachter, Adam K Wade-Vallance, Margaret Williams, Nathan Sébastien Zangger, Ronald N. Germain, Andrea J. Radtke
Cited by: 0

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.

Publication details

Publication date
5 January 2026