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

no code implementations • 17 Dec 2024 • 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, Margaret Williams, Nathan Zangger, Ronald N. Germain, Andrea J. Radtke

The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods.

scientific discovery

The IBEX Knowledge-Base: Achieving more together with open science

no code implementations • 26 Jul 2024 • Andrea J. Radtke, Ifeanyichukwu Anidi, Leanne Arakkal, Armando Arroyo-Mejias, Rebecca T. Beuschel, Katy Borner, Colin J. Chu, Beatrice Clark, Menna R. Clatworthy, Jake Colautti, 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 Kastenmueller, Joshua F. E. Koenig, Aanandita Kothurkar, Alexandra Y. Kreins, Ian Lamborn, Yuri Lin, Katia Luciano Pereira Morais, Aleksandra Lunich, Jean C. S. Luz, Ryan B. MacDonald, Chen Makranz, Vivien I. Maltez, Ryan V. Moriaty, Juan M. Ocampo-Godinez, Vitoria M. Olyntho, 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, Ziv Yaniv

Iterative Bleaching Extends multipleXity (IBEX) is a versatile method for highly multiplexed imaging of diverse tissues.

Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data

no code implementations • 23 Jan 2024 • Nikki Bialy, Frank Alber, Brenda Andrews, Michael Angelo, Brian Beliveau, Lacramioara Bintu, Alistair Boettiger, Ulrike Boehm, Claire M. Brown, Mahmoud Bukar Maina, James J. Chambers, Beth A. Cimini, Kevin Eliceiri, Rachel Errington, Orestis Faklaris, Nathalie Gaudreault, Ronald N. Germain, Wojtek Goscinski, David Grunwald, Michael Halter, Dorit Hanein, John W. Hickey, Judith Lacoste, Alex Laude, Emma Lundberg, Jian Ma, Leonel Malacrida, Josh Moore, Glyn Nelson, Elizabeth Kathleen Neumann, Roland Nitschke, Shuichi Onami, Jaime A. Pimentel, Anne L. Plant, Andrea J. Radtke, Bikash Sabata, Denis Schapiro, Johannes Schöneberg, Jeffrey M. Spraggins, Damir Sudar, Wouter-Michiel Adrien Maria Vierdag, Niels Volkmann, Carolina Wählby, Siyuan, Wang, Ziv Yaniv, Caterina Strambio-De-Castillia

Together with the molecular knowledge of genes and proteins, biological images promise to significantly enhance the scientific understanding of complex cellular systems and to advance predictive and personalized therapeutic products for human health.

IBEX: An open and extensible method for high content multiplex imaging of diverse tissues

no code implementations • 23 Jul 2021 • Andrea J. Radtke, Colin J. Chu, Ziv Yaniv, Li Yao, James Marr, Rebecca T. Beuschel, Hiroshi Ichise, Anita Gola, Juraj Kabat, Bradley Lowekamp, Emily Speranza, Joshua Croteau, Nishant Thakur, Danny Jonigk, Jeremy Davis, Jonathan M. Hernandez, Ronald N. Germain

We recently developed Iterative Bleaching Extends multi-pleXity (IBEX), an iterative immunolabeling and chemical bleaching method that enables multiplexed imaging (>65 parameters) in diverse tissues, including human organs relevant for international consortia efforts.

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging

no code implementations • 16 Jul 2021 • John W. Hickey, Elizabeth K. Neumann, Andrea J. Radtke, Jeannie M. Camarillo, Rebecca T. Beuschel, Alexandre Albanese, Elizabeth McDonough, Julia Hatler, Anne E. Wiblin, Jeremy Fisher, Josh Croteau, Eliza C. Small, Anup Sood, Richard M. Caprioli, R. Michael Angelo, Garry P. Nolan, Kwanghun Chung, Stephen M. Hewitt, Ronald N. Germain, Jeffrey M. Spraggins, Emma Lundberg, Michael P. Snyder, Neil L. Kelleher, Sinem K. Saka

Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions.