1
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Costantini I, Morgan L, Yang J, Balbastre Y, Varadarajan D, Pesce L, Scardigli M, Mazzamuto G, Gavryusev V, Castelli FM, Roffilli M, Silvestri L, Laffey J, Raia S, Varghese M, Wicinski B, Chang S, Chen IA, Wang H, Cordero D, Vera M, Nolan J, Nestor K, Mora J, Iglesias JE, Garcia Pallares E, Evancic K, Augustinack JC, Fogarty M, Dalca AV, Frosch MP, Magnain C, Frost R, van der Kouwe A, Chen SC, Boas DA, Pavone FS, Fischl B, Hof PR. A cellular resolution atlas of Broca's area. SCIENCE ADVANCES 2023; 9:eadg3844. [PMID: 37824623 PMCID: PMC10569704 DOI: 10.1126/sciadv.adg3844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/03/2023] [Indexed: 10/14/2023]
Abstract
Brain cells are arranged in laminar, nuclear, or columnar structures, spanning a range of scales. Here, we construct a reliable cell census in the frontal lobe of human cerebral cortex at micrometer resolution in a magnetic resonance imaging (MRI)-referenced system using innovative imaging and analysis methodologies. MRI establishes a macroscopic reference coordinate system of laminar and cytoarchitectural boundaries. Cell counting is obtained with a digital stereological approach on the 3D reconstruction at cellular resolution from a custom-made inverted confocal light-sheet fluorescence microscope (LSFM). Mesoscale optical coherence tomography enables the registration of the distorted histological cell typing obtained with LSFM to the MRI-based atlas coordinate system. The outcome is an integrated high-resolution cellular census of Broca's area in a human postmortem specimen, within a whole-brain reference space atlas.
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Affiliation(s)
- Irene Costantini
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino (FI), Italy
- Department of Biology, University of Florence, Florence, Italy
- National Institute of Optics (INO), National Research Council (CNR), Sesto Fiorentino, Italy
| | - Leah Morgan
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | - Jiarui Yang
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Yael Balbastre
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Divya Varadarajan
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Luca Pesce
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino (FI), Italy
| | - Marina Scardigli
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino (FI), Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino (FI), Italy
- Division of Physiology, Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Giacomo Mazzamuto
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino (FI), Italy
- National Institute of Optics (INO), National Research Council (CNR), Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino (FI), Italy
| | - Vladislav Gavryusev
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino (FI), Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino (FI), Italy
| | - Filippo Maria Castelli
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino (FI), Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino (FI), Italy
- Bioretics srl, Cesena, Italy
| | | | - Ludovico Silvestri
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino (FI), Italy
- National Institute of Optics (INO), National Research Council (CNR), Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino (FI), Italy
| | - Jessie Laffey
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sophia Raia
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Merina Varghese
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bridget Wicinski
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shuaibin Chang
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | | | - Hui Wang
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Devani Cordero
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | - Matthew Vera
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | - Jackson Nolan
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | - Kimberly Nestor
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Jocelyn Mora
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Juan Eugenio Iglesias
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Erendira Garcia Pallares
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | - Kathryn Evancic
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Jean C. Augustinack
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Morgan Fogarty
- Imaging Science Program, Washington University McKelvey School of Engineering, St. Louis, MO, USA
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Adrian V. Dalca
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew P. Frosch
- C.S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Caroline Magnain
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Robert Frost
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Andre van der Kouwe
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Department of Human Biology, University of Cape Town, Cape Town, South Africa
| | - Shih-Chi Chen
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - David A. Boas
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Francesco Saverio Pavone
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino (FI), Italy
- National Institute of Optics (INO), National Research Council (CNR), Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino (FI), Italy
| | - Bruce Fischl
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- HST, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Patrick R. Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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2
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Franceschini A, Mazzamuto G, Checcucci C, Chicchi L, Fanelli D, Costantini I, Passani MB, Silva BA, Pavone FS, Silvestri L. Brain-wide neuron quantification toolkit reveals strong sexual dimorphism in the evolution of fear memory. Cell Rep 2023; 42:112908. [PMID: 37516963 DOI: 10.1016/j.celrep.2023.112908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/07/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023] Open
Abstract
Fear responses are functionally adaptive behaviors that are strengthened as memories. Indeed, detailed knowledge of the neural circuitry modulating fear memory could be the turning point for the comprehension of this emotion and its pathological states. A comprehensive understanding of the circuits mediating memory encoding, consolidation, and retrieval presents the fundamental technological challenge of analyzing activity in the entire brain with single-neuron resolution. In this context, we develop the brain-wide neuron quantification toolkit (BRANT) for mapping whole-brain neuronal activation at micron-scale resolution, combining tissue clearing, high-resolution light-sheet microscopy, and automated image analysis. The robustness and scalability of this method allow us to quantify the evolution of activity patterns across multiple phases of memory in mice. This approach highlights a strong sexual dimorphism in recruited circuits, which has no counterpart in the behavior. The methodology presented here paves the way for a comprehensive characterization of the evolution of fear memory.
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Affiliation(s)
- Alessandra Franceschini
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy; Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy.
| | - Giacomo Mazzamuto
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy; Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy; National Institute of Optics - National Research Council (CNR-INO), Sesto Fiorentino, Italy
| | - Curzio Checcucci
- Department of Information Engineering (DINFO), University of Florence, Florence, Italy
| | - Lorenzo Chicchi
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
| | - Duccio Fanelli
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
| | - Irene Costantini
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy; Department of Biology, University of Florence, Florence, Italy
| | | | - Bianca Ambrogina Silva
- National Research Council of Italy, Institute of Neuroscience, Milan, Italy; IRCCS Humanitas Research Hospital, Lab of Circuits Neuroscience, Rozzano, Milan, Italy
| | - Francesco Saverio Pavone
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy; Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy; National Institute of Optics - National Research Council (CNR-INO), Sesto Fiorentino, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy; Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy; National Institute of Optics - National Research Council (CNR-INO), Sesto Fiorentino, Italy.
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3
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Pernet V, Joly S, Spiegel S, Meli I, Idriss S, Maigler F, Mdzomba JB, Roenneke AK, Franceschini A, Silvestri L, Pavone FS, Calamai M, Schindowski K, Chan A. Nogo-A antibody delivery through the olfactory mucosa mitigates experimental autoimmune encephalomyelitis in the mouse CNS. Cell Death Discov 2023; 9:290. [PMID: 37558696 PMCID: PMC10412545 DOI: 10.1038/s41420-023-01588-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/18/2023] [Accepted: 07/28/2023] [Indexed: 08/11/2023] Open
Abstract
Systemic administration of Nogo-A-neutralizing antibody ameliorates experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis. However, the blood-brain barrier (BBB) is a major obstacle limiting the passage of systemically applied antibody to the CNS. To bypass the BBB, in the present study we tested the intranasal route of administration by targeting the olfactory mucosa with the Nogo-A-blocking antibody 11C7 mAb in myelin oligodendrocyte glycoprotein-induced EAE. Antibodies were specifically administered onto the olfactory mucosa using a microcatheter. Antibody distribution was examined in the CNS by ELISA and light-sheet microscopy. The effects of 11C7 mAb on Nogo-A signaling were assessed by Western blotting. EAE-induced deficits were monitored daily. Demyelination was observed on spinal cord histological sections. Gene expression changes were followed by trancriptomic analyses. A sensitive capture ELISA revealed a rapid and widespread distribution of 11C7 mAb in the CNS, including the olfactory bulb, the cerebellum and the lumbar spinal cord, but not in the CSF. Light-sheet microscopy allowed to observe antibody accumulation in the parenchyma, thus demonstrating nose-to-brain transfer of IgG. At the functional level, the widespread penetration of 11C7 mAb in the CNS, including the thoracolumbar spinal cord, resulted in the improvement of motor symptoms and in the preservation of myelin in the spinal cord of EAE mice. This was accompanied by Nogo-A signaling downregulation, as reflected by the decreased level of phosphorylated cofilin observed by Western blotting in the cerebellum. In the brain of EAE score-matched animals, 11C7 modified the expression of genes that can influence neurotransmission and cognitive functions, independently of the demyelination phenotype in the spinal cord. In conclusion, our data show the feasibility of olfactory mucosa-directed administration for the delivery of therapeutic antibodies targeting CNS antigens in EAE mice.
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Affiliation(s)
- Vincent Pernet
- Department of Neurology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Center for experimental neurology (ZEN), Bern University Hospital, University of Bern, Bern, Switzerland.
- Centre de recherche du CHU de Québec-Université Laval and Department of Molecular Medicine, Faculté de médecine, Université Laval, Québec, Québec, Canada.
| | - Sandrine Joly
- Department of Neurology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Center for experimental neurology (ZEN), Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Sebastian Spiegel
- Department of Neurology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Center for experimental neurology (ZEN), Bern University Hospital, University of Bern, Bern, Switzerland
- Institute of Applied Biotechnology, Biberach University of Applied Science, Hubertus-Liebrecht-Strasse 35, Biberach, Germany
- Department of Biomedical Research, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Ivo Meli
- Department of Neurology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Center for experimental neurology (ZEN), Bern University Hospital, University of Bern, Bern, Switzerland
| | - Sherif Idriss
- Department of Neurology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Center for experimental neurology (ZEN), Bern University Hospital, University of Bern, Bern, Switzerland
| | - Frank Maigler
- Institute of Applied Biotechnology, Biberach University of Applied Science, Hubertus-Liebrecht-Strasse 35, Biberach, Germany
| | - Julius Baya Mdzomba
- Department of Neurology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Center for experimental neurology (ZEN), Bern University Hospital, University of Bern, Bern, Switzerland
| | - Anna K Roenneke
- Department of Neurology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Center for experimental neurology (ZEN), Bern University Hospital, University of Bern, Bern, Switzerland
| | - Alessandra Franceschini
- LENS- European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto-Fiorentino (Firenze), Italy
| | - Ludovico Silvestri
- LENS- European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto-Fiorentino (Firenze), Italy
| | - Francesco S Pavone
- LENS- European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto-Fiorentino (Firenze), Italy
| | - Martino Calamai
- LENS- European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto-Fiorentino (Firenze), Italy
- National Institute of Optics - National Research Council (CNR-INO), Sesto Fiorentino, Italy
| | - Katharina Schindowski
- Institute of Applied Biotechnology, Biberach University of Applied Science, Hubertus-Liebrecht-Strasse 35, Biberach, Germany
| | - Andrew Chan
- Department of Neurology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Center for experimental neurology (ZEN), Bern University Hospital, University of Bern, Bern, Switzerland.
- Department of Biomedical Research, University of Bern, Bern, Switzerland.
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4
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Cell3: a new vision for study of the endomembrane system in mammalian cells. Biosci Rep 2021; 41:230388. [PMID: 34874399 PMCID: PMC8655501 DOI: 10.1042/bsr20210850c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 11/17/2022] Open
Abstract
The endomembrane system of mammalian cells provides massive capacity for the segregation of biochemical reactions into discrete locations. The individual organelles of the endomembrane system also require the ability to precisely transport material between these compartments in order to maintain cell homeostasis; this process is termed membrane traffic. For several decades, researchers have been systematically identifying and dissecting the molecular machinery that governs membrane trafficking pathways, with the overwhelming majority of these studies being carried out in cultured cells growing as monolayers. In recent years, a number of methodological innovations have provided the opportunity for cultured cells to be grown as 3-dimensional (3D) assemblies, for example as spheroids and organoids. These structures have the potential to better replicate the cellular environment found in tissues and present an exciting new opportunity for the study of cell function. In this mini-review, we summarize the main methods used to generate 3D cell models and highlight emerging studies that have started to use these models to study basic cellular processes. We also describe a number of pieces of work that potentially provide the basis for adaptation for deeper study of how membrane traffic is coordinated in multicellular assemblies. Finally, we comment on some of the technological challenges that still need to be overcome if 3D cell biology is to become a mainstream tool toward deepening our understanding of the endomembrane system in mammalian cells.
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5
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Universal autofocus for quantitative volumetric microscopy of whole mouse brains. Nat Methods 2021; 18:953-958. [PMID: 34312564 DOI: 10.1038/s41592-021-01208-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 06/14/2021] [Indexed: 11/08/2022]
Abstract
Unbiased quantitative analysis of macroscopic biological samples demands fast imaging systems capable of maintaining high resolution across large volumes. Here we introduce RAPID (rapid autofocusing via pupil-split image phase detection), a real-time autofocus method applicable in every widefield-based microscope. RAPID-enabled light-sheet microscopy reliably reconstructs intact, cleared mouse brains with subcellular resolution, and allowed us to characterize the three-dimensional (3D) spatial clustering of somatostatin-positive neurons in the whole encephalon, including densely labeled areas. Furthermore, it enabled 3D morphological analysis of microglia across the entire brain. Beyond light-sheet microscopy, we demonstrate that RAPID maintains high image quality in various settings, from in vivo fluorescence imaging to 3D tracking of fast-moving organisms. RAPID thus provides a flexible autofocus solution that is suitable for traditional automated microscopy tasks as well as for quantitative analysis of large biological specimens.
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6
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Ricci P, Gavryusev V, Müllenbroich C, Turrini L, de Vito G, Silvestri L, Sancataldo G, Pavone FS. Removing striping artifacts in light-sheet fluorescence microscopy: a review. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 168:52-65. [PMID: 34274370 DOI: 10.1016/j.pbiomolbio.2021.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/21/2021] [Accepted: 07/12/2021] [Indexed: 11/24/2022]
Abstract
In recent years, light-sheet fluorescence microscopy (LSFM) has found a broad application for imaging of diverse biological samples, ranging from sub-cellular structures to whole animals, both in-vivo and ex-vivo, owing to its many advantages relative to point-scanning methods. By providing the selective illumination of sample single planes, LSFM achieves an intrinsic optical sectioning and direct 2D image acquisition, with low out-of-focus fluorescence background, sample photo-damage and photo-bleaching. On the other hand, such an illumination scheme is prone to light absorption or scattering effects, which lead to uneven illumination and striping artifacts in the images, oriented along the light sheet propagation direction. Several methods have been developed to address this issue, ranging from fully optical solutions to entirely digital post-processing approaches. In this work, we present them, outlining their advantages, performance and limitations.
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Affiliation(s)
- Pietro Ricci
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy
| | - Vladislav Gavryusev
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy
| | | | - Lapo Turrini
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy
| | - Giuseppe de Vito
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; University of Florence, Department of Neuroscience, Psychology, Drug Research and Child Health, Florence, 50139, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy; National Institute of Optics, National Research Council, Sesto Fiorentino, 50019, Italy
| | - Giuseppe Sancataldo
- University of Palermo, Department of Physics and Chemistry, Palermo, 90128, Italy.
| | - Francesco Saverio Pavone
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy; National Institute of Optics, National Research Council, Sesto Fiorentino, 50019, Italy.
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7
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Ricci P, Sancataldo G, Gavryusev V, Franceschini A, Müllenbroich MC, Silvestri L, Pavone FS. Fast multi-directional DSLM for confocal detection without striping artifacts. BIOMEDICAL OPTICS EXPRESS 2020; 11:3111-3124. [PMID: 32637245 PMCID: PMC7316030 DOI: 10.1364/boe.390916] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/19/2020] [Accepted: 04/28/2020] [Indexed: 05/02/2023]
Abstract
In recent years light-sheet fluorescence microscopy (LSFM) has become a cornerstone technology for neuroscience, improving the quality and capabilities of 3D imaging. By selectively illuminating a single plane, it provides intrinsic optical sectioning and fast image recording, while minimizing out of focus fluorescence background, sample photo-damage and photo-bleaching. However, images acquired with LSFM are often affected by light absorption or scattering effects, leading to un-even illumination and striping artifacts. In this work we present an optical solution to this problem, via fast multi-directional illumination of the sample, based on an acousto-optical deflector (AOD). We demonstrate that this pivoting system is compatible with confocal detection in digital scanned laser light-sheet fluorescence microscopy (DSLM) by using a pivoted elliptical-Gaussian beam. We tested its performance by acquiring signals emitted by specific fluorophores in several mouse brain areas, comparing the pivoting beam illumination and a traditional static one, measuring the point spread function response and quantifying the striping reduction. We observed real-time shadow suppression, while preserving the advantages of confocal detection for image contrast.
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Affiliation(s)
- Pietro Ricci
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy
- University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy
| | - Giuseppe Sancataldo
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy
- University of Palermo, Department of Physics and Chemistry, Palermo, 90128, Italy
| | - Vladislav Gavryusev
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy
- University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy
| | - Alessandra Franceschini
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy
- National Institute of Optics, Sesto Fiorentino, 50019, Italy
| | | | - Ludovico Silvestri
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy
- University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy
- National Institute of Optics, Sesto Fiorentino, 50019, Italy
| | - Francesco Saverio Pavone
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy
- University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy
- National Institute of Optics, Sesto Fiorentino, 50019, Italy
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8
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Li R, Liu A, Wu T, Xiao W, Tang LI, Chen L. Digital scanned laser light-sheet fluorescence lifetime microscopy with wide-field time-gated imaging. J Microsc 2020; 279:69-76. [PMID: 32307699 DOI: 10.1111/jmi.12898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/21/2020] [Accepted: 04/14/2020] [Indexed: 01/01/2023]
Abstract
We develop a multidimensional fluorescence imaging technique by implementing a wide-field time-gated fluorescence lifetime imaging into digital scanned laser light-sheet microscopy (FLIM-DSLM) to measure 3D fluorescence lifetime distribution in mesoscopic specimens with high resolution. This is achieved by acquiring a series of time-gated images at different relative time delays with respect of excitation pulses at different depths. The lifetime is determined for each voxel by iteratively fitting to single exponential decay. The performance of the developed system is evaluated with the measurements of a lifetime reference Rhodamine 6G solution and a subresolution fluorescent bead phantom. We also demonstrate the application performances of this system to ex vivo and in vivo imaging of Tg(kdrl:EGFP) transgenic zebrafish embryos, illustrating the lifetime differences between the GFP signal and the autofluorescence signal. The results show that FLIM-DSLM can be used for sample size up to a few millimetres and can be utilised as a powerful and robust method for biomedical research, for example as a readout of protein-protein interactions via Förster resonance energy transfer.
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Affiliation(s)
- R Li
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China.,College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
| | - A Liu
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China.,College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
| | - T Wu
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China.,College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
| | - W Xiao
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China.,College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
| | - L I Tang
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China.,College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
| | - Lingling Chen
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China.,College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
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9
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Costantini I, Cicchi R, Silvestri L, Vanzi F, Pavone FS. In-vivo and ex-vivo optical clearing methods for biological tissues: review. BIOMEDICAL OPTICS EXPRESS 2019; 10:5251-5267. [PMID: 31646045 PMCID: PMC6788593 DOI: 10.1364/boe.10.005251] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 05/05/2023]
Abstract
Every optical imaging technique is limited in its penetration depth by scattering occurring in biological tissues. Possible solutions to overcome this problem consist of limiting the detrimental effects of scattering by reducing optical inhomogeneities within the sample. This can be achieved either by using physical methods (such as refractive index matching solutions) or by chemical methods (such as the removal of scatterers), based on tissue transformation protocols. This review provides an overview of the current state-of-the-art methods used for both ex-vivo and in-vivo optical clearing of biological tissues. We start with a brief history of the development of the most widespread clearing methods across the new millennium, then we describe the working principles of both physical and chemical methods. Clearing methods are then reviewed, pointing the attention of the reader on both physical and chemical methods, classified based on the tissue size and type for each specific application. A small section is reserved for methods that have already found in-vivo applications at the research level. Finally, a detailed discussion highlighting both the most relevant results achieved and the new ongoing developments in this field is reported in the last part, together with future perspectives for the clearing methodology.
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Affiliation(s)
- Irene Costantini
- National Institute of Optics, National Research Council, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
- European Laboratory for Non-linear Spectroscopy, University of Florence, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Riccardo Cicchi
- National Institute of Optics, National Research Council, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
- European Laboratory for Non-linear Spectroscopy, University of Florence, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Ludovico Silvestri
- National Institute of Optics, National Research Council, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
- European Laboratory for Non-linear Spectroscopy, University of Florence, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via Sansone 1, Sesto Fiorentino, 50019, Italy
| | - Francesco Vanzi
- European Laboratory for Non-linear Spectroscopy, University of Florence, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019, Italy
| | - Francesco Saverio Pavone
- National Institute of Optics, National Research Council, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
- European Laboratory for Non-linear Spectroscopy, University of Florence, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via Sansone 1, Sesto Fiorentino, 50019, Italy
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10
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LIU A, XIAO W, LI R, LIU L, CHEN L. Comparison of optical projection tomography and light‐sheet fluorescence microscopy. J Microsc 2019; 275:3-10. [DOI: 10.1111/jmi.12796] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/18/2019] [Accepted: 04/18/2019] [Indexed: 01/21/2023]
Affiliation(s)
- A. LIU
- College of Health Science and Environmental EngineeringShenzhen Technology University Shenzhen China
- College of Optoelectronics EngineeringShenzhen University Shenzhen China
| | - W. XIAO
- College of Health Science and Environmental EngineeringShenzhen Technology University Shenzhen China
- College of Optoelectronics EngineeringShenzhen University Shenzhen China
| | - R. LI
- College of Health Science and Environmental EngineeringShenzhen Technology University Shenzhen China
- College of Optoelectronics EngineeringShenzhen University Shenzhen China
| | - L. LIU
- College of Health Science and Environmental EngineeringShenzhen Technology University Shenzhen China
- College of Optoelectronics EngineeringShenzhen University Shenzhen China
| | - L. CHEN
- College of Health Science and Environmental EngineeringShenzhen Technology University Shenzhen China
- College of Optoelectronics EngineeringShenzhen University Shenzhen China
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11
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Di Giovanna AP, Credi C, Franceschini A, Müllenbroich MC, Silvestri L, Pavone FS. Tailored Sample Mounting for Light-Sheet Fluorescence Microscopy of Clarified Specimens by Polydimethylsiloxane Casting. Front Neuroanat 2019; 13:35. [PMID: 30971902 PMCID: PMC6445857 DOI: 10.3389/fnana.2019.00035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/08/2019] [Indexed: 12/22/2022] Open
Abstract
The combination of biological tissue clearing methods with light-sheet fluorescence microscopy (LSFM) allows acquiring images of specific biological structures of interest at whole organ scale and microscopic resolution. Differently to classical epifluorescence techniques, where the sample is cut into slices, LSFM preserves the whole organ architecture, which is of particular relevance for investigations of long-range neuronal circuits. This imaging modality comes with the need of new protocols for sample mounting. Gel matrix, hooks, tips, glues, and quartz cuvettes have been used to keep whole rodent organs in place during image acquisitions. The last one has the advantage of avoiding sample damage and optical aberrations when using a quartz refractive index (RI) matching solution. However, commercially available quartz cuvettes for such large samples are expensive. We propose the use of polydimethylsiloxane (PDMS) for creating tailor-made cuvettes for sample holding. For validation, we compared PDMS and quartz cuvettes by measuring light transmittance and performing whole mouse-brain imaging with LSFM. Moreover, imaging can be performed using an inexpensive RI matching solution, which further reduces the cost of the imaging process. Worth of note, the RI matching solution used in combination with PDMS leads to a moderate expansion of the sample with respect to its original size, which may represent an advantage when investigating small components, such as neuronal processes. Overall, we found the use of custom-made PDMS cuvettes advantageous in term of cost, image quality, or preservation of sample integrity with respect to other whole-mouse brain mounting strategies adopted for LSFM.
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Affiliation(s)
| | - Caterina Credi
- European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto Fiorentino, Italy.,Department of Information Engineering (DINFO), University of Florence, Florence, Italy
| | - Alessandra Franceschini
- European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto Fiorentino, Italy
| | | | - Ludovico Silvestri
- European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto Fiorentino, Italy.,National Institute of Optics, National Research Council, Florence, Italy
| | - Francesco Saverio Pavone
- European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto Fiorentino, Italy.,National Institute of Optics, National Research Council, Florence, Italy.,Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
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12
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High-Fidelity Imaging in Brain-Wide Structural Studies Using Light-Sheet Microscopy. eNeuro 2018; 5:eN-TMNT-0124-18. [PMID: 30627630 PMCID: PMC6325532 DOI: 10.1523/eneuro.0124-18.2018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/26/2018] [Accepted: 08/22/2018] [Indexed: 11/21/2022] Open
Abstract
Light-sheet microscopy (LSM) has proven a useful tool in neuroscience to image whole brains with high frame rates at cellular resolution and, in combination with tissue clearing methods, is often employed to reconstruct the cyto-architecture over the intact mouse brain. Inherently to LSM, however, residual opaque objects, always present to some extent even in extremely well optically cleared samples, cause stripe artifacts, which, in the best case, severely affect image homogeneity and, in the worst case, completely obscure features of interest. Here, demonstrating two example applications in intact optically cleared mouse brains, we report how Bessel beams reduce streaking artifacts and produce high-fidelity structural data for the brain-wide morphology of neuronal and vascular networks. We found that a third of the imaged volume of the brain was affected by strong striated image intensity inhomogeneity and, furthermore, a significant amount of information content lost with Gaussian illumination was accessible when interrogated with Bessel beams. In conclusion, Bessel beams produce high-fidelity structural data of improved image homogeneity and might significantly relax demands placed on the automated tools to count, trace, or segment fluorescent features of interest.
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13
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Ovečka M, von Wangenheim D, Tomančák P, Šamajová O, Komis G, Šamaj J. Multiscale imaging of plant development by light-sheet fluorescence microscopy. NATURE PLANTS 2018; 4:639-650. [PMID: 30185982 DOI: 10.1038/s41477-018-0238-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/31/2018] [Indexed: 05/21/2023]
Abstract
Light-sheet fluorescence microscopy (LSFM) methods collectively represent the major breakthrough in developmental bio-imaging of living multicellular organisms. They are becoming a mainstream approach through the development of both commercial and custom-made LSFM platforms that are adjusted to diverse biological applications. Based on high-speed acquisition rates under conditions of low light exposure and minimal photo-damage of the biological sample, these methods provide ideal means for long-term and in-depth data acquisition during organ imaging at single-cell resolution. The introduction of LSFM methods into biology extended our understanding of pattern formation and developmental progress of multicellular organisms from embryogenesis to adult body. Moreover, LSFM imaging allowed the dynamic visualization of biological processes under almost natural conditions. Here, we review the most important, recent biological applications of LSFM methods in developmental studies of established and emerging plant model species, together with up-to-date methods of data editing and evaluation for modelling of complex biological processes. Recent applications in animal models push LSFM into the forefront of current bio-imaging approaches. Since LSFM is now the single most effective method for fast imaging of multicellular organisms, allowing quantitative analyses of their long-term development, its broader use in plant developmental biology will likely bring new insights.
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Affiliation(s)
- Miroslav Ovečka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - Daniel von Wangenheim
- Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Pavel Tomančák
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Olga Šamajová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - George Komis
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic.
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14
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Di Giovanna AP, Tibo A, Silvestri L, Müllenbroich MC, Costantini I, Allegra Mascaro AL, Sacconi L, Frasconi P, Pavone FS. Whole-Brain Vasculature Reconstruction at the Single Capillary Level. Sci Rep 2018; 8:12573. [PMID: 30135559 PMCID: PMC6105658 DOI: 10.1038/s41598-018-30533-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 07/27/2018] [Indexed: 02/03/2023] Open
Abstract
The distinct organization of the brain’s vascular network ensures that it is adequately supplied with oxygen and nutrients. However, despite this fundamental role, a detailed reconstruction of the brain-wide vasculature at the capillary level remains elusive, due to insufficient image quality using the best available techniques. Here, we demonstrate a novel approach that improves vascular demarcation by combining CLARITY with a vascular staining approach that can fill the entire blood vessel lumen and imaging with light-sheet fluorescence microscopy. This method significantly improves image contrast, particularly in depth, thereby allowing reliable application of automatic segmentation algorithms, which play an increasingly important role in high-throughput imaging of the terabyte-sized datasets now routinely produced. Furthermore, our novel method is compatible with endogenous fluorescence, thus allowing simultaneous investigations of vasculature and genetically targeted neurons. We believe our new method will be valuable for future brain-wide investigations of the capillary network.
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Affiliation(s)
- Antonino Paolo Di Giovanna
- European Laboratory for Non-Linear Spectroscopy, University of Florence, Via Nello Carrara 1, Sesto Fiorentino, 50019, Italy
| | - Alessandro Tibo
- Department of Information Engineering (DINFO), University of Florence, Via di S. Marta 3, Florence, 50139, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-Linear Spectroscopy, University of Florence, Via Nello Carrara 1, Sesto Fiorentino, 50019, Italy.,National Institute of Optics, National Research Council, Largo Fermi 6, Florence, 50125, Italy
| | - Marie Caroline Müllenbroich
- European Laboratory for Non-Linear Spectroscopy, University of Florence, Via Nello Carrara 1, Sesto Fiorentino, 50019, Italy.,National Institute of Optics, National Research Council, Largo Fermi 6, Florence, 50125, Italy
| | - Irene Costantini
- European Laboratory for Non-Linear Spectroscopy, University of Florence, Via Nello Carrara 1, Sesto Fiorentino, 50019, Italy
| | - Anna Letizia Allegra Mascaro
- European Laboratory for Non-Linear Spectroscopy, University of Florence, Via Nello Carrara 1, Sesto Fiorentino, 50019, Italy.,Neuroscience Institute, National Research Council, Via Giuseppe Moruzzi 1, Pisa, 56125, Italy
| | - Leonardo Sacconi
- European Laboratory for Non-Linear Spectroscopy, University of Florence, Via Nello Carrara 1, Sesto Fiorentino, 50019, Italy.,National Institute of Optics, National Research Council, Largo Fermi 6, Florence, 50125, Italy
| | - Paolo Frasconi
- Department of Information Engineering (DINFO), University of Florence, Via di S. Marta 3, Florence, 50139, Italy
| | - Francesco Saverio Pavone
- European Laboratory for Non-Linear Spectroscopy, University of Florence, Via Nello Carrara 1, Sesto Fiorentino, 50019, Italy. .,National Institute of Optics, National Research Council, Largo Fermi 6, Florence, 50125, Italy. .,Department of Physics and Astronomy, University of Florence, Via Sansone 1, Sesto Fiorentino, 50019, Italy.
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15
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Ando K, Laborde Q, Brion JP, Duyckaerts C. 3D imaging in the postmortem human brain with CLARITY and CUBIC. HANDBOOK OF CLINICAL NEUROLOGY 2018; 150:303-317. [PMID: 29496149 DOI: 10.1016/b978-0-444-63639-3.00021-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Recent innovations in tissue clearing and imaging technologies have enabled us to analyse biological systems directly in three-dimensions using thick samples. In this review, we discuss two of these recently reported tissue-clearing technologies (CLARITY and CUBIC) that are compatible with archival formalin-fixed human brain materials that have been fixed in formalin for a long period of time. We will discuss the pros and cons of these two technologies, examples of visualisation of Alzheimer neuropathological hallmarks and the exact protocols that we regularly use in the laboratory.
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Affiliation(s)
- Kunie Ando
- Laboratory of Histology, Neuroanatomy and Neuropathology, ULB Neuroscience Institute, Université Libre de Bruxelles, Brussels, Belgium; Laboratoire de Neuropathologie Escourolle, Hôpital de la Pitié-Salpêtrière, Paris, France.
| | - Quentin Laborde
- Laboratoire de Neuropathologie Escourolle, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Jean-Pierre Brion
- Laboratory of Histology, Neuroanatomy and Neuropathology, ULB Neuroscience Institute, Université Libre de Bruxelles, Brussels, Belgium
| | - Charles Duyckaerts
- Laboratoire de Neuropathologie Escourolle, Hôpital de la Pitié-Salpêtrière, Paris, France
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