Publications total: 35

Publications on the mesoSPIM initiative and instruments

Please cite these papers if you used a mesoSPIM microscope to acquire data for your project.

Nikita Vladimirov, Fabian Voigt, Thomas Naert, Gabriela R. Araujo, Ruiyao Cai, Anna Maria Reuss, Shan Zhao, Patricia Schmid, Sven Hildebrand, Martina Schaettin, Dominik Groos, José María Mateos, Philipp Bethge, Taiyo Yamamoto, Valentino Aerne, Alard Roebroeck, Ali Ertürk, Adriano Aguzzi, Urs Ziegler, Esther T Stoeckli, Laura Baudis, Soeren Sten Lienkamp, Fritjof Helmchen. The Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for large cleared samples, bioRxiv 2023.06.16.545256.
Fabian F. Voigt, Daniel Kirschenbaum, Evgenia Platonova, Stéphane Pagès, Robert A. A. Campbell, Rahel Kästli Martina Schaettin, Ladan Egolf, Alexander van der Bourg, Philipp Bethge, Karen Haenraets, Noémie Frézel, Thomas Topilko, Paola Perin, Daniel Hillier, Sven Hildebrand, Anna Schueth, Alard Roebroeck, Botond Roska, Esther Stoeckli, Roberto Pizzala, Nicolas Renier, Hanns Ulrich Zeilhofer, Theofanis Karayannis, Urs Ziegler, Laura Batti, Anthony Holtmaat, Christian Lüscher, Adriano Aguzzi, and Fritjof Helmchen:
The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue; Nature Methods, 2019 (Preprint)

mesoSPIM covers

Reviews, tutorials, and protocols

Ruiyao Cai, Zeynep Ilgin Kolabas, Chenchen Pan, Hongcheng Mai, Shan Zhao, Doris Kaltenecker, Fabian F. Voigt, Muge Molbay, Tzu-lun Ohn, Cécile Vincke, Mihail I. Todorov, Fritjof Helmchen, Jo A. Van Ginderachter and Ali Ertürk: Whole-mouse clearing and imaging at the cellular level with vDISCO, Nature Protocols, January 25th, 2023
Kevin M. Dean, Tonmoy Chakraborty, Stephan Daetwyler, Jinlong Lin, Gerard Garrelts, Ons M’Saad, Hannahmariam T. Mekbib,Fabian F. Voigt, Martina Schaettin, Esther T. Stoeckli, Fritjof Helmchen, Joerg Bewersdorf and Reto Fiolka: Isotropic imaging across spatial scales with axially swept light-sheet microscopy, Nature Protocols, July 13th, 2022
Kurt R. Weiss, Fabian F. Voigt, Douglas P. Shepherd & Jan Huisken: Tutorial: practical considerations for tissue clearing and imaging, Nature Protocols, May 21st, 2021

Application publications

Preprints and manuscripts

Dominik Groos, Anna Maria Reuss, Peter Rupprecht, Tevye Stachniak, Shuting Han, Christopher Lewis, Yaroslav Sych, Martin Wieckhorst, Theofanis Karayannis, Adriano Aguzzi, Fritjof Helmchen. Distinct hypothalamus-habenula circuits govern risk preference. bioRxiv 2023.01.04.522571.
Gwendolin Schoenfeld, Sepp Kollmorgen, Christopher M Lewis, Philipp Bethge, Anna Maria Reuss, Adriano Aguzzi, Valerio Mante, and Fritjof Helmchen: Dendritic integration of sensory and reward information facilitates learning, bioRxiv Preprint, December 30th, 2021
Romain Guiet, Oliver Burri, Nicolas Chiaruttini, Oliver Hagens, Arne Seitz: DEVILS: a tool for the visualization of large datasets with a high dynamic range, F1000 Research Manuscript, November 27th, 2020

2023

Darche M, Borella Y, Verschueren A, Gantar I, Pagès S, Batti L, Paques M. Light sheet fluorescence microscopy of cleared human eyes. Nature Communications Biology 2023.
Squair JW, Milano M, de Coucy A, Gautier M, Skinnider MA, James ND, Cho N, Lasne A, Kathe C, Hutson TH, Ceto S, Baud L, Galan K, Aureli V, Laskaratos A, Barraud Q, Deming TJ, Kohman RE, Schneider BL, He Z, Bloch J, Sofroniew MV, Courtine G, Anderson MA. Recovery of walking after paralysis by regenerating characterized neurons to their natural target region. Science, 2023.
Elijah D. Lowenstein, Pierre-Louis Ruffault, Aristotelis Misios, Kate L. Osman, Huimin Li, Rachel S. Greenberg, Rebecca Thompson, Kun Song, Stephan Dietrich, Xun Li, Nikita Vladimirov, Andrew Woehler, Jean-François Brunet, Niccolò Zampieri, Ralf Kühn, Stephen D. Liberles, Shiqi Jia, Gary R. Lewin, Nikolaus Rajewsky, Teresa E. Lever, Carmen Birchmeier. Prox2 and Runx3 vagal sensory neurons regulate esophageal motility. Neuron, 2023.

2022

Grand K, Stoltz M, Rizzo L, Röck R, Kaminski M, Salinas G, Getwan M, Naert T, Pichler R, Lienkamp S. HNF1B Alters an Evolutionarily Conserved Nephrogenic Program of Target Genes. J Am Soc Nephrol., 2022 Dec 15:ASN.2022010076. doi: 10.1681/ASN.2022010076. PMID: 36522156.
Daniel Kirschenbaum, Ehsan Dadgar-Kiani, Francesca Catto, Fabian F. Voigt, Chiara Trevisan, Oliver Bichsel, Hamid Shirani, K. Peter R. Nilsson, Karl J. Frontzek, Paolo Paganetti, Fritjof Helmchen, Jin Hyung Lee, Adriano Aguzzi: Whole-brain microscopy reveals distinct temporal and spatial efficacy of anti-Aβ therapies, EMBO Molecular Medicine, Nov 16th, 2022, e16789
Claudia Kathe, Michael A. Skinnider, Thomas H. Hutson, Nicola Regazzi, Matthieu Gautier, Robin Demesmaeker, Salif Komi, Steven Ceto, Nicholas D. James, Newton Cho, Laetitia Baud, Katia Galan, Kaya J. E. Matson, Andreas Rowald, Kyungjin Kim, Ruijia Wang, Karen Minassian, John O. Prior, Leonie Asboth, Quentin Barraud, Stéphanie P. Lacour, Ariel J. Levine, Fabien Wagner, Jocelyne Bloch, Jordan W. Squair & Grégoire Courtine The neurons that restore walking after paralysis. Nature, 2022 Nov 9. doi: 10.1038/s41586-022-05385-7. PMID: 36352232.
Steven Schepanski, Mattia Chini, Veronika Sternemann, Christopher Urbschat, Kristin Thiele, Ting Sun, Yu Zhao, Mareike Poburski, Anna Woestemeier, Marie-Theres Thieme, Dimitra E. Zazara, Malik Alawi, Nicole Fischer, Joerg Heeren, Nikita Vladimirov, Andrew Woehler, Victor G. Puelles, Stefan Bonn, Nicola Gagliani, Ileana L. Hanganu-Opatz & Petra C. Arck: Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice, Nature Communications, August 5, 2022.
Hei Ming Lai, Yumi Tang, Zachary Y. H. Lau, Robert A. A. Campbell, Juno C. N. Yau, Caleb C. Y. Chan, Danny C. W. Chan, Tin Yan Wong, Harriet K. T. Wong, Leo Y. C. Yan, William K. K. Wu, Sunny H. Wong, Ka-Wai Kwok, Yun-Kwok Wing, Henry H. N. Lam, Ho-Keung Ng, Thomas D. Mrsic-Flogel, Vincent C. T. Mok, Jason Y. K. Chan & Ho Ko: Antibody stabilization for thermally accellerated deep immunostaining, Nature Methods, September 1st, 2022
Ruiqing Ni, Zhenyue Chen, Xosé Luís Deán-Ben, Fabian F. Voigt, Daniel Kirschenbaum, Gloria Shi, Alessia Villois, Quanyu Zhou, Alessandro Crimi, Paolo Arosio, Roger M. Nitsch, K. Peter R. Nilsson, Adriano Aguzzi, Fritjof Helmchen, Jan Klohs, and Daniel Razansky: Multiscale optical and optoacoustic imaging of amyloid-β deposits in mice, Nature Biomedical Engineering, July 14th, 2022 (bioRxiv Preprint)
Krystal Alfonso, Gabriela R. Araujo, Laura Baudis, Nathaniel Bowden, Bernadette K. Cogswell, Anna Erickson, Michelle Galloway, Adam A. Hecht, Rathsara R. H. Herath Mudiyanselage, Patrick Huber, Igor Jovanovic, Giti A. Khodaparast, Brenden A. Magill, Thomas O’Donnell, Nicholas W. G. Smith, and Xianyi Zhang: Passive low energy nuclear recoil detection with color centers – PALEOCCENE, Snowmass White Paper, March 10th, 2022.

2021

Thomas Naert, Özgün Çiçek, Paulina Ogar, Max Bürgi, Michael M. Kaminski, Yuxiao Xu, Kelli Grand, Marko Vujanovic, Daniel Prata, Friedhelm Hildebrandt, Thomas Brox, Olaf Ronneberger, Fabian F. Voigt, Fritjof Helmchen, Johannes Loffing, Marko Horb, Helen Rankin Willsey, Soeren S. Lienkamp: Deep learning is widely applicable to phenotyping embryonic development and disease; Development, 148, 21, November 5th, 2021
Claudia Kathe, Frédéric Michoud, Philipp Schönle, Andreas Rowald, Noé Brun, Jimmy Ravier, Ivan Furfaro, Valentina Paggi, Kyungjin Kim, Sadaf Soloukey, Leonie Asboth, Thomas H. Hutson, Ileana Jelescu, Antoine Philippides, Noaf Alwahab, Jérôme Gandar, Daniel Huber, Chris I. De Zeeuw, Quentin Barraud, Qiuting Huang, Stéphanie P. Lacour, and Grégoire Courtine: Wireless closed-loop optogenetics across the entire dorsoventral spinal cord in mice, Nature Biotechnology, September 27th, 2021
Camilla Olianti, Francesco Giardini, Erica Lazzeri, Irene Costantini, Ludovico Silvestri, Raffaele Coppini, Elisabetta Cerbai, Francesco S.Pavone, Leonardo Sacconi: Optical clearing in cardiac imaging: A comparative study, Progress in Biophysics and Molecular Biology, August 4th, 2021
Paola Perin, Riccardo Rossetti, Carolina Ricci, Daniele Cossellu, Simone Lazzarini, Philipp Bethge, Fabian F. Voigt, Fritjof Helmchen, Laura Batti, Ivana Gantar, and Roberto Pizzala: 3D reconstruction of the clarified rat hindbrain choroid plexus, Frontiers in Cell and Developmental Biology, July 29th, 2021
Laura Ferlauto, Paola Vagni, Adele Fanelli, Elodie Geneviève Zollinger, Katia Monsorno, Rosa Chiara Paolicelli, and Diego Ghezzi: All-polymeric transient neural probe for prolonged in-vivo electrophysiological recordings, Biomaterials, July 1st, 2021 (bioRxiv Preprint)
Joseph Clerke, Patricia Preston-Ferrer, Audrey Tissot, Laura Batti, Fabian F. Voigt, Stephane Pagès, Andrea Burgalossi, and Manuel Mameli: Output-specific reorganization of excitatory transmission at habenula-midbrain synapses during cocaine withdrawal; Frontiers in Synaptic Neuroscience, March 31st, 2021
Yasir Gallero-Salas, Shuting Han, Yaroslav Sych, Fabian F. Voigt, Balazs Laurenczy, Ariel Gilad, and Fritjof Helmchen: Sensory and Behavioral Components of Neocortical Signal Flow in Discrimination Tasks with Short-Term Memory, Neuron, 109:1-14, 2021, online: November 6th, 2020 (bioRxiv preprint)

2020

Rahel Kastli, Rasmus Vighagen, Alexander van der Bourg, Ali Ozgur Argunsah, Asim Iqbal, Fabian F. Voigt, Daniel Kirschenbaum, Adriano Aguzzi, Fritjof Helmchen, and Theofanis Karayannis: Developmental Divergence of Sensory Stimulus Representation in Cortical Interneurons, Nature Communications, November 12th, 2020 (bioRxiv preprint)
Abhishek Banerjee, Giuseppe Parente, Jasper Anton Teutsch, Christopher Lewis, Fabian F. Voigt, and Fritjof Helmchen: Value-guided remapping of sensory circuits by lateral orbitofrontal cortex in reversal learning, Nature, September 10th, 2020 (bioRxiv preprint)
Noémie Frézel, Jose Maria Mateos, Evgenia Platonova, Urs Ziegler, Hendrik Wildner, and Hanns Ulrich Zeilhofer: In-depth characterization of layer 5 output neurons of the primary somatosensory cortex innervating the mouse dorsalspinal cord, Cerebral Cortex Communications, August 20th, 2020 (bioRxiv preprint)
Morgane Humbel, Mergim Ramosaj, Virginie Zimmer, Sara Regio, Ludiwine Aeby, Sylvain Moser, Alexia Boizot, Mélanie Sipion, Maria Rey, and Nicole Déglon: Maximizing lentiviral vector gene transfer in the CNS; Gene Therapy, July 6th, 2020
Jennifer Romanos, Dietmar Benke, Daniela Pietrobon, Hanns Ulrich Zeilhofer, Mirko Santello: Astrocyte dysfunction increases cortical dendritic excitability and promotes cranial pain infamilial migraine; Science Advances, June 5th, 2020
Madlaina Boillat, Pierre-Mehdi Hammoudi, Sunil Kumar Dogga, Stéphane Pagès, Maged Goubran, Ivan Rodriguez, and Dominique Soldati-Favre: Neuroinflammation-Associated Aspecific Manipulation of Mouse Predator Fear by Toxoplasma gondii; Cell Reports, January 14th, 2020

2019

Yvette Zarb, Ulrike Weber-Stadlbauer, Daniel Kirschenbaum, Diana Rita Kindler, Juliet Richetto, Daniel Keller, Rosa Rademakers, Dennis W. Dickson, Andreas Pasch, Tatiana Byzova, Khayrun Nahar, Fabian F. Voigt, Fritjof Helmchen, Andreas Boss, Adriano Aguzzi, Jan Klohs, and Annika Keller: Ossified blood vessels in primary familial brain calcification elicit a neurotoxic astrocyte response; Brain, awz032, February 25th, 2019
Paola Perin, Fabian F. Voigt, Philipp Bethge, Fritjof Helmchen, and Roberto Pizzala: iDISCO+ for the Study of Neuroimmune Architecture of the Rat Auditory Brainstem; Frontiers in Neuroanatomy, 13, 15, February 13th, 2019
Mariana Diales Rocha, Daniel Normen Düring, Philipp Bethge, Fabian F. Voigt, Staffan Hildebrand, Fritjof Helmchen, Alexander Pfeifer, Richard Hans Robert Hahnloser, and Manfred Gahr: Tissue Clearing and Light Sheet Microscopy: Imaging the Unsectioned Adult Zebra Finch Brain at Cellular Resolution; Frontiers in Neuroanatomy, 13, 13, February 14th, 2019

2018

Annika Keller, Mario Nuvolone, Irina Abakumova, Andra Chincisan, Regina Reimann, Merve Avar, Daniel Heinzer, Simone Hornemann, Josephin Wagner, Daniel Kirschenbaum, Fabian F. Voigt, Caihong Zhu, Luca Regli, Fritjof Helmchen, and Adriano Aguzzi: Prion pathogenesis is unaltered in a mouse strain with a permeable blood-brain barrier; PLOS Pathogens, 14, 11, November 29th, 2018