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Mitani TT, Susaki EA, Matsumoto K, Ueda HR. Realization of cellomics to dive into the whole-body or whole-organ cell cloud. Nat Methods 2024:10.1038/s41592-024-02307-5. [PMID: 38871985 DOI: 10.1038/s41592-024-02307-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Affiliation(s)
- Tomoki T Mitani
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
- Department of Systems Biology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Etsuo A Susaki
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Katsuhiko Matsumoto
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Hiroki R Ueda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan.
- Department of Systems Pharmacology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan.
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2
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Vladimirov N, Voigt FF, Naert T, Araujo GR, Cai R, Reuss AM, Zhao S, Schmid P, Hildebrand S, Schaettin M, Groos D, Mateos JM, Bethge P, Yamamoto T, Aerne V, Roebroeck A, Ertürk A, Aguzzi A, Ziegler U, Stoeckli E, Baudis L, Lienkamp SS, Helmchen F. The Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for large cleared samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545256. [PMID: 38168219 PMCID: PMC10760166 DOI: 10.1101/2023.06.16.545256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In 2015, we launched the mesoSPIM initiative (www.mesospim.org), an open-source project for making light-sheet microscopy of large cleared tissues more accessible. Meanwhile, the demand for imaging larger samples at higher speed and resolution has increased, requiring major improvements in the capabilities of light-sheet microscopy. Here, we introduce the next-generation mesoSPIM ("Benchtop") with significantly increased field of view, improved resolution, higher throughput, more affordable cost and simpler assembly compared to the original version. We developed a new method for testing objectives, enabling us to select detection objectives optimal for light-sheet imaging with large-sensor sCMOS cameras. The new mesoSPIM achieves high spatial resolution (1.5 μm laterally, 3.3 μm axially) across the entire field of view, a magnification up to 20x, and supports sample sizes ranging from sub-mm up to several centimetres, while being compatible with multiple clearing techniques. The new microscope serves a broad range of applications in neuroscience, developmental biology, and even physics.
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Affiliation(s)
- Nikita Vladimirov
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- University Research Priority Program (URPP) Adaptive Brain Circuits in Development and Learning (AdaBD), University of Zurich, Zurich, Switzerland
- Center for Microscopy and Image Analysis (ZMB), University of Zurich, Zurich, Switzerland
| | - Fabian F. Voigt
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
- Present address: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Thomas Naert
- Institute of Anatomy and Zurich Kidney Center (ZKC), University of Zurich, Zurich, Switzerland
| | | | - Ruiyao Cai
- Present address: Department of Biology, Stanford University, Stanford, CA, USA
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, Munich, German
| | - Anna Maria Reuss
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
- Institute of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - Shan Zhao
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Patricia Schmid
- Institute of Anatomy and Zurich Kidney Center (ZKC), University of Zurich, Zurich, Switzerland
| | - Sven Hildebrand
- Department of Cognitive Neuroscience, Faculty of Psychology & Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Martina Schaettin
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Dominik Groos
- Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - José María Mateos
- Center for Microscopy and Image Analysis (ZMB), University of Zurich, Zurich, Switzerland
| | - Philipp Bethge
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
| | - Taiyo Yamamoto
- Institute of Anatomy and Zurich Kidney Center (ZKC), University of Zurich, Zurich, Switzerland
| | - Valentino Aerne
- Department of Physics, University of Zurich, Zurich, Switzerland
| | - Alard Roebroeck
- Department of Cognitive Neuroscience, Faculty of Psychology & Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Ali Ertürk
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, Munich, German
| | - Adriano Aguzzi
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
- Institute of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - Urs Ziegler
- Center for Microscopy and Image Analysis (ZMB), University of Zurich, Zurich, Switzerland
| | - Esther Stoeckli
- University Research Priority Program (URPP) Adaptive Brain Circuits in Development and Learning (AdaBD), University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Laura Baudis
- Department of Physics, University of Zurich, Zurich, Switzerland
| | - Soeren S. Lienkamp
- Institute of Anatomy and Zurich Kidney Center (ZKC), University of Zurich, Zurich, Switzerland
| | - Fritjof Helmchen
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- University Research Priority Program (URPP) Adaptive Brain Circuits in Development and Learning (AdaBD), University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
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Timonidis N, Bakker R, Rubio-Teves M, Alonso-Martínez C, Garcia-Amado M, Clascá F, Tiesinga PHE. Translating single-neuron axonal reconstructions into meso-scale connectivity statistics in the mouse somatosensory thalamus. Front Neuroinform 2023; 17:1272243. [PMID: 38107469 PMCID: PMC10722239 DOI: 10.3389/fninf.2023.1272243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
Characterizing the connectomic and morphological diversity of thalamic neurons is key for better understanding how the thalamus relays sensory inputs to the cortex. The recent public release of complete single-neuron morphological reconstructions enables the analysis of previously inaccessible connectivity patterns from individual neurons. Here we focus on the Ventral Posteromedial (VPM) nucleus and characterize the full diversity of 257 VPM neurons, obtained by combining data from the MouseLight and Braintell projects. Neurons were clustered according to their most dominantly targeted cortical area and further subdivided by their jointly targeted areas. We obtained a 2D embedding of morphological diversity using the dissimilarity between all pairs of axonal trees. The curved shape of the embedding allowed us to characterize neurons by a 1-dimensional coordinate. The coordinate values were aligned both with the progression of soma position along the dorsal-ventral and lateral-medial axes and with that of axonal terminals along the posterior-anterior and medial-lateral axes, as well as with an increase in the number of branching points, distance from soma and branching width. Taken together, we have developed a novel workflow for linking three challenging aspects of connectomics, namely the topography, higher order connectivity patterns and morphological diversity, with VPM as a test-case. The workflow is linked to a unified access portal that contains the morphologies and integrated with 2D cortical flatmap and subcortical visualization tools. The workflow and resulting processed data have been made available in Python, and can thus be used for modeling and experimentally validating new hypotheses on thalamocortical connectivity.
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Affiliation(s)
- Nestor Timonidis
- Neuroinformatics Department, Donders Centre for Neuroscience, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Rembrandt Bakker
- Neuroinformatics Department, Donders Centre for Neuroscience, Radboud University Nijmegen, Nijmegen, Netherlands
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA BRAIN Institute I, Jülich Research Centre, Jülich, Germany
| | - Mario Rubio-Teves
- Department of Anatomy and Neuroscience, School of Medicine, Autónoma de Madrid University, Madrid, Spain
| | - Carmen Alonso-Martínez
- Department of Anatomy and Neuroscience, School of Medicine, Autónoma de Madrid University, Madrid, Spain
| | - Maria Garcia-Amado
- Department of Anatomy and Neuroscience, School of Medicine, Autónoma de Madrid University, Madrid, Spain
| | - Francisco Clascá
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA BRAIN Institute I, Jülich Research Centre, Jülich, Germany
| | - Paul H. E. Tiesinga
- Neuroinformatics Department, Donders Centre for Neuroscience, Radboud University Nijmegen, Nijmegen, Netherlands
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Balaram P, Takasaki K, Hellevik A, Tandukar J, Turschak E, MacLennan B, Ouellette N, Torres R, Laughland C, Gliko O, Seshamani S, Perlman E, Taormina M, Peterson E, Juneau Z, Potekhina L, Glaser A, Chandrashekar J, Logsdon M, Cao K, Dylla C, Hatanaka G, Chatterjee S, Ting J, Vumbaco D, Waters J, Bair W, Tsao D, Gao R, Reid C. Microscale visualization of cellular features in adult macaque visual cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.02.565381. [PMID: 37961179 PMCID: PMC10635096 DOI: 10.1101/2023.11.02.565381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Expansion microscopy and light sheet imaging enable fine-scale resolution of intracellular features that comprise neural circuits. Most current techniques visualize sparsely distributed features across whole brains or densely distributed features within individual brain regions. Here, we visualize dense distributions of immunolabeled proteins across early visual cortical areas in adult macaque monkeys. This process may be combined with multiphoton or magnetic resonance imaging to produce multimodal atlases in large, gyrencephalic brains.
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