1. Imaging cellular activity across all organs reveals body-wide circuitsNature

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   Virginie M. S. Ruetten, Wei Zheng, Igor Siwanowicz, Brett D. Mensh, Mark Eddison, Amy Hu, Yunfeng Chi, Andrew L. Lemire, Caiying Guo, Mykola Kadobianskyi, Marc Renz, Sara Lelek-Greskovic, Yisheng He, Kari Close, Gudrun Ihrke, Aparna Dev, Alyson Petruncio, Yinan Wan, Rongwei Zhang, Mark C. Fishman, Florian Engert, Benjamin Judkewitz, Mikail Rubinov, Philipp J. Keller, Chie Satou, Guoqiang Yu, Paul W. Tillberg, Maneesh Sahani, Misha B. Ahrens

   Featured by EurekAlert, Brightsurf, ScienceAlert, CRBC News, The Times of India
2. Whole-brain, all-optical interrogation of neuronal dynamics underlying gut and vascular interoception in zebrafishNature Communications

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   Weiyu Chen*, Ben James*, Virginie M. S. Ruetten*, Sambashiva Banala, Ziqiang Wei, Xueying Yang, Greg Fleishman, Igor Siwanowicz, Mikail Rubinov, Jeremy Delahanty, Mark C. Fishman, Florian Engert, Maneesh Sahani, Luke D. Lavis, James E. Fitzgerald, Misha B. Ahrens

Preprints

1. A neuron-glia circuit anticipates hypoxia to regulate organismal oxygen usebioRxiv

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   Rongwei Zhang*, Ziqiang Wei*, Javier J. How, Michele Nardin, Sujatha Narayan, Amina Kinkhabwala, Weiyu Chen, Jing-Xuan Lim, Virginie M. S. Ruetten, Anuththara Rupashinge, Martin Haesemeyer, Brett D. Mensh, Mark C. Fishman, Florian Engert, Behtash Babadi, Jiulin Du, David A. Prober*, Misha B. Ahrens*

Protocols

1. WHOLISTIC ExM: Whole-Body Expansion Microscopy with Fluorescence Insitu Hybridization (WB-ExM FISH)protocols.io

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   Virginie Ruetten, Mark Eddision, Amy Hu, Misha B Ahrens, Paul Tillberg
2. WHOLISTIC ExM: Whole-Body Expansion Microscopy with Immunofluorescence and Histological Stainsprotocols.io

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   VMS. Ruetten, A Hu, M Eddison, K Close, Y He, MB Ahrens, P Tillberg

1. Fast, accurate, and versatile data analysis platform for the quantification of molecular spatiotemporal signalsCell

   Xuelong Mi*, Alex Bo-Yuan Chen*, Daniela Duarte, Erin Carey, Charlotte R. Taylor, Philipp N. Braaker, Mark Bright, Rafael G. Almeida, Jing-Xuan Lim, Virginie M. S. Ruetten, Yizhi Wang, Mengfan Wang, Weizhan Zhang, Wei Zheng, Michael E. Reitman, Yongkang Huang, Xiaoyu Wang, Lei Li, HanFei Deng, Song-Hai Shi, Kira E. Poskanzer, David A. Lyons, Axel Nimmerjahn, Misha B. Ahrens, Guoqiang Yu
2. Live imaging of the extracellular matrix with a glycan-binding fluorophoreNature Methods

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   Antonio Fiore, Guoqiang Yu, Jason J. Northey, Ronak Patel, Thomas A. Ravenscroft, Richard Ikegami, Wiert Kolkman, Pratik Kumar, Tanya L. Dilan, Virginie M. S. Ruetten, Misha B. Ahrens, Hari Shroff, Shaohe Wang, Valerie M. Weaver, Kayvon Pedram

Preprints

1. Emergence of functional heart-brain circuits in a vertebratebioRxiv

   Luis Hernandez-Nunez, Joana Avrami, Sky Shi, Areni Markarian, Areni Kim, Jonathan Boulanger-Weill, Virginie M. S. Ruetten, Arman Zarghani-Shiraz, Misha B. Ahrens, Florian Engert, Mark C. Fishman
2. Fishexplorer: A multimodal cellular atlas platform for neuronal circuit dissection in larval zebrafishbioRxiv

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   Sumit K. Vohra, Maren Eberle, Jonathan Boulanger-Weill, Mariela D. Petkova, Gregor F. P. Schuhknecht, Kristian J. Herrera, Florian Kämpf, Virginie M. S. Ruetten, Jeff W. Lichtman, Florian Engert, Owen Randlett, Armin Bahl, Yasuko Isoe, Hans-Christian Hege, Daniel Baum

Protocols

1. Labeling of Zebrafish Organs and Substructures in Light Data in Amira 3D Classic Segmentation Workroomprotocols.io

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   A Petruncio, A Dev, VMS. Ruetten, G Ihrke, A Weigel, CellMap Project Team
2. PhotoMap: unbiased mapping of Expansion Microscopy deformation fieldsprotocols.io

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   Virginie M. S. Ruetten, Amy Hu, Misha B Ahrens, Paul Tillberg

1. Whole body-brain functional imaging and interrogation platform: technology development, analysis methods and applicationsUCL (University College London)

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   VMS. Ruetten

1. Bright and High-Performance Genetically Encoded Ca2+ Indicator Based on mNeonGreen Fluorescent ProteinACS Sensors

   Landon Zarowny*, Abhi Aggarwal*, Virginie M. S. Ruetten, Ilya Kolb, The GENIE Project, Ronak Patel, Hsin-Yi Huang, Yu-Fen Chang, Tiffany Phan, Richard Kanyo, Misha B. Ahrens, W. Ted Allison, Kaspar Podgorski, Robert E. Campbell
2. Efficient communication over complex dynamical networks: The role of matrix non-normalityScience Advances

   G Baggio, VMS. Ruetten, G Hennequin, S Zampieri
3. Non-reversible Gaussian processes for identifying latent dynamical structure in neural dataAdvances in Neural Information Processing Systems

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   VMS. Ruetten, A Bernacchia, M Sahani, G Hennequin

1. Information transmission in dynamical networks: The normal network case2018 IEEE Conference on Decision and Control (CDC)

   G Baggio, VMS. Ruetten, G Hennequin, S Zampieri