1
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Damstra HGJ, Mohar B, Eddison M, Akhmanova A, Kapitein LC, Tillberg PW. Ten-fold Robust Expansion Microscopy. Bio Protoc 2023; 13:e4698. [PMID: 37397797 PMCID: PMC10308184 DOI: 10.21769/bioprotoc.4698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/03/2023] [Accepted: 04/09/2023] [Indexed: 07/04/2023] Open
Abstract
Expansion microscopy (ExM) is a powerful technique to overcome the diffraction limit of light microscopy that can be applied in both tissues and cells. In ExM, samples are embedded in a swellable polymer gel to physically expand the sample and isotropically increase resolution in x, y, and z. By systematic exploration of the ExM recipe space, we developed a novel ExM method termed Ten-fold Robust Expansion Microscopy (TREx) that, as the original ExM method, requires no specialized equipment or procedures. TREx enables ten-fold expansion of both thick mouse brain tissue sections and cultured human cells, can be handled easily, and enables high-resolution subcellular imaging with a single expansion step. Furthermore, TREx can provide ultrastructural context to subcellular protein localization by combining antibody-stained samples with off-the-shelf small molecule stains for both total protein and membranes.
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Affiliation(s)
- Hugo G. J. Damstra
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Boaz Mohar
- Janelia Research Campus, HHMI, Ashburn, Virginia 20147, USA
| | - Mark Eddison
- Janelia Research Campus, HHMI, Ashburn, Virginia 20147, USA
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Lukas C. Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
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2
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Aggarwal A, Liu R, Chen Y, Ralowicz AJ, Bergerson SJ, Tomaska F, Mohar B, Hanson TL, Hasseman JP, Reep D, Tsegaye G, Yao P, Ji X, Kloos M, Walpita D, Patel R, Mohr MA, Tillberg PW, Looger LL, Marvin JS, Hoppa MB, Konnerth A, Kleinfeld D, Schreiter ER, Podgorski K. Glutamate indicators with improved activation kinetics and localization for imaging synaptic transmission. Nat Methods 2023; 20:925-934. [PMID: 37142767 PMCID: PMC10250197 DOI: 10.1038/s41592-023-01863-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 03/21/2023] [Indexed: 05/06/2023]
Abstract
The fluorescent glutamate indicator iGluSnFR enables imaging of neurotransmission with genetic and molecular specificity. However, existing iGluSnFR variants exhibit low in vivo signal-to-noise ratios, saturating activation kinetics and exclusion from postsynaptic densities. Using a multiassay screen in bacteria, soluble protein and cultured neurons, we generated variants with improved signal-to-noise ratios and kinetics. We developed surface display constructs that improve iGluSnFR's nanoscopic localization to postsynapses. The resulting indicator iGluSnFR3 exhibits rapid nonsaturating activation kinetics and reports synaptic glutamate release with decreased saturation and increased specificity versus extrasynaptic signals in cultured neurons. Simultaneous imaging and electrophysiology at individual boutons in mouse visual cortex showed that iGluSnFR3 transients report single action potentials with high specificity. In vibrissal sensory cortex layer 4, we used iGluSnFR3 to characterize distinct patterns of touch-evoked feedforward input from thalamocortical boutons and both feedforward and recurrent input onto L4 cortical neuron dendritic spines.
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Affiliation(s)
- Abhi Aggarwal
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Rui Liu
- Department of Physics, University of California, San Diego, La Jolla, CA, USA
| | - Yang Chen
- Institute of Neuroscience and Cluster for Systems Neurology (SyNergy), Technical University of Munich (TUM), Munich, Germany
| | - Amelia J Ralowicz
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | | | - Filip Tomaska
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Physiology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Boaz Mohar
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Timothy L Hanson
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jeremy P Hasseman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Daniel Reep
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Getahun Tsegaye
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Pantong Yao
- Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Xiang Ji
- Department of Physics, University of California, San Diego, La Jolla, CA, USA
| | - Marinus Kloos
- Institute of Neuroscience and Cluster for Systems Neurology (SyNergy), Technical University of Munich (TUM), Munich, Germany
| | - Deepika Walpita
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Ronak Patel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Manuel A Mohr
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH) Zurich, Basel, Switzerland
| | - Paul W Tillberg
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Howard Hughes Medical Institute, Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Jonathan S Marvin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Michael B Hoppa
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Arthur Konnerth
- Institute of Neuroscience and Cluster for Systems Neurology (SyNergy), Technical University of Munich (TUM), Munich, Germany
| | - David Kleinfeld
- Department of Physics, University of California, San Diego, La Jolla, CA, USA
- Section of Neurobiology, University of California, San Diego, La Jolla, CA, USA
| | - Eric R Schreiter
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Kaspar Podgorski
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
- Allen Institute for Neural Dynamics, Seattle, WA, USA.
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3
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Wang Y, Krabbe S, Eddison M, Henry FE, Fleishman G, Lemire AL, Wang L, Korff W, Tillberg PW, Lüthi A, Sternson SM. Multimodal mapping of cell types and projections in the central nucleus of the amygdala. eLife 2023; 12:84262. [PMID: 36661218 PMCID: PMC9977318 DOI: 10.7554/elife.84262] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
The central nucleus of the amygdala (CEA) is a brain region that integrates external and internal sensory information and executes innate and adaptive behaviors through distinct output pathways. Despite its complex functions, the diversity of molecularly defined neuronal types in the CEA and their contributions to major axonal projection targets have not been examined systematically. Here, we performed single-cell RNA-sequencing (scRNA-seq) to classify molecularly defined cell types in the CEA and identified marker genes to map the location of these neuronal types using expansion-assisted iterative fluorescence in situ hybridization (EASI-FISH). We developed new methods to integrate EASI-FISH with 5-plex retrograde axonal labeling to determine the spatial, morphological, and connectivity properties of ~30,000 molecularly defined CEA neurons. Our study revealed spatiomolecular organization of the CEA, with medial and lateral CEA associated with distinct molecularly defined cell families. We also found a long-range axon projection network from the CEA, where target regions receive inputs from multiple molecularly defined cell types. Axon collateralization was found primarily among projections to hindbrain targets, which are distinct from forebrain projections. This resource reports marker gene combinations for molecularly defined cell types and axon-projection types, which will be useful for selective interrogation of these neuronal populations to study their contributions to the diverse functions of the CEA.
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Affiliation(s)
- Yuhan Wang
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Sabine Krabbe
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Mark Eddison
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Fredrick E Henry
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Greg Fleishman
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Andrew L Lemire
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Lihua Wang
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Wyatt Korff
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Paul W Tillberg
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Andreas Lüthi
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Scott M Sternson
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- Howard Hughes Medical Institute & Department of Neurosciences, University of California, San DiegoSan DiegoUnited States
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4
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Lillvis JL, Otsuna H, Ding X, Pisarev I, Kawase T, Colonell J, Rokicki K, Goina C, Gao R, Hu A, Wang K, Bogovic J, Milkie DE, Meienberg L, Mensh BD, Boyden ES, Saalfeld S, Tillberg PW, Dickson BJ. Rapid reconstruction of neural circuits using tissue expansion and light sheet microscopy. eLife 2022; 11:81248. [DOI: 10.7554/elife.81248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022] Open
Abstract
Brain function is mediated by the physiological coordination of a vast, intricately connected network of molecular and cellular components. The physiological properties of neural network components can be quantified with high throughput. The ability to assess many animals per study has been critical in relating physiological properties to behavior. By contrast, the synaptic structure of neural circuits is presently quantifiable only with low throughput. This low throughput hampers efforts to understand how variations in network structure relate to variations in behavior. For neuroanatomical reconstruction there is a methodological gulf between electron-microscopic (EM) methods, which yield dense connectomes at considerable expense and low throughput, and light-microscopic (LM) methods, which provide molecular and cell-type specificity at high throughput but without synaptic resolution. To bridge this gulf, we developed a high-throughput analysis pipeline and imaging protocol using tissue expansion and light sheet microscopy (ExLLSM) to rapidly reconstruct selected circuits across many animals with single-synapse resolution and molecular contrast. Using Drosophila to validate this approach, we demonstrate that it yields synaptic counts similar to those obtained by EM, enables synaptic connectivity to be compared across sex and experience, and can be used to correlate structural connectivity, functional connectivity, and behavior. This approach fills a critical methodological gap in studying variability in the structure and function of neural circuits across individuals within and between species.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Edward S Boyden
- MIT McGovern Institute for Brain Research, Massachusetts Institute of Technology
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5
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Damstra HGJ, Mohar B, Eddison M, Akhmanova A, Kapitein LC, Tillberg PW. Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx). eLife 2022; 11:73775. [PMID: 35179128 PMCID: PMC8887890 DOI: 10.7554/elife.73775] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/30/2022] [Indexed: 12/18/2022] Open
Abstract
Expansion microscopy (ExM) is a powerful technique to overcome the diffraction limit of light microscopy that can be applied in both tissues and cells. In ExM, samples are embedded in a swellable polymer gel to physically expand the sample and isotropically increase resolution in x, y, and z. The maximum resolution increase is limited by the expansion factor of the gel, which is four-fold for the original ExM protocol. Variations on the original ExM method have been reported that allow for greater expansion factors but at the cost of ease of adoption or versatility. Here, we systematically explore the ExM recipe space and present a novel method termed Ten-fold Robust Expansion Microscopy (TREx) that, like the original ExM method, requires no specialized equipment or procedures. We demonstrate that TREx gels expand 10-fold, can be handled easily, and can be applied to both thick mouse brain tissue sections and cultured human cells enabling high-resolution subcellular imaging with a single expansion step. Furthermore, we show that TREx can provide ultrastructural context to subcellular protein localization by combining antibody-stained samples with off-the-shelf small-molecule stains for both total protein and membranes.
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Affiliation(s)
- Hugo G J Damstra
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Boaz Mohar
- Janelia Research Campus, HHMI, Ashburn, United States
| | - Mark Eddison
- Janelia Research Campus, HHMI, Ashburn, United States
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Lukas C Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
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6
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Damstra HGJ, Mohar B, Eddison M, Akhmanova A, Kapitein LC, Tillberg PW. Correction: Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx). eLife 2022; 11:85169. [PMID: 36444779 PMCID: PMC9708063 DOI: 10.7554/elife.85169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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7
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Wang Y, Eddison M, Fleishman G, Weigert M, Xu S, Wang T, Rokicki K, Goina C, Henry FE, Lemire AL, Schmidt U, Yang H, Svoboda K, Myers EW, Saalfeld S, Korff W, Sternson SM, Tillberg PW. EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization. Cell 2021; 184:6361-6377.e24. [PMID: 34875226 DOI: 10.1016/j.cell.2021.11.024] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 08/22/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022]
Abstract
Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 μm) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine spatially and molecularly defined subregions. EASI-FISH also facilitates iterative reanalysis of scRNA-seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.
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Affiliation(s)
- Yuhan Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Mark Eddison
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Greg Fleishman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Martin Weigert
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Institute of Bioengineering, School of Life Sciences, EPFL, 1015 Lausanne, Switzerland
| | - Shengjin Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Tim Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Konrad Rokicki
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Cristian Goina
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Fredrick E Henry
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Andrew L Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Uwe Schmidt
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Hui Yang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Karel Svoboda
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Stephan Saalfeld
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Wyatt Korff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Scott M Sternson
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Paul W Tillberg
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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8
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Abstract
Expansion microscopy (ExM) is a physical form of magnification that increases the effective resolving power of any microscope. Here, we describe the fundamental principles of ExM, as well as how recently developed ExM variants build upon and apply those principles. We examine applications of ExM in cell and developmental biology for the study of nanoscale structures as well as ExM's potential for scalable mapping of nanoscale structures across large sample volumes. Finally, we explore how the unique anchoring and hydrogel embedding properties enable postexpansion molecular interrogation in a purified chemical environment. ExM promises to play an important role complementary to emerging live-cell imaging techniques, because of its relative ease of adoption and modification and its compatibility with tissue specimens up to at least 200 μm thick.
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Affiliation(s)
| | - Fei Chen
- Broad Institute of Harvard and MIT, Boston, Massachusetts 02142, USA
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9
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Oran D, Rodriques SG, Gao R, Asano S, Skylar-Scott MA, Chen F, Tillberg PW, Marblestone AH, Boyden ES. 3D nanofabrication by volumetric deposition and controlled shrinkage of patterned scaffolds. Science 2019; 362:1281-1285. [PMID: 30545883 DOI: 10.1126/science.aau5119] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/02/2018] [Indexed: 12/26/2022]
Abstract
Lithographic nanofabrication is often limited to successive fabrication of two-dimensional (2D) layers. We present a strategy for the direct assembly of 3D nanomaterials consisting of metals, semiconductors, and biomolecules arranged in virtually any 3D geometry. We used hydrogels as scaffolds for volumetric deposition of materials at defined points in space. We then optically patterned these scaffolds in three dimensions, attached one or more functional materials, and then shrank and dehydrated them in a controlled way to achieve nanoscale feature sizes in a solid substrate. We demonstrate that our process, Implosion Fabrication (ImpFab), can directly write highly conductive, 3D silver nanostructures within an acrylic scaffold via volumetric silver deposition. Using ImpFab, we achieve resolutions in the tens of nanometers and complex, non-self-supporting 3D geometries of interest for optical metamaterials.
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Affiliation(s)
- Daniel Oran
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Samuel G Rodriques
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ruixuan Gao
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shoh Asano
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Pfizer Internal Medicine Research Unit, Cambridge, MA 02139, USA
| | - Mark A Skylar-Scott
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.,Wyss Institute for Biologically Inspired Engineering, Cambridge, MA 02138, USA
| | - Fei Chen
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Paul W Tillberg
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Adam H Marblestone
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edward S Boyden
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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10
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Asano SM, Gao R, Wassie AT, Tillberg PW, Chen F, Boyden ES. Expansion Microscopy: Protocols for Imaging Proteins and RNA in Cells and Tissues. ACTA ACUST UNITED AC 2018; 80:e56. [PMID: 30070431 DOI: 10.1002/cpcb.56] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Expansion microscopy (ExM) is a recently developed technique that enables nanoscale-resolution imaging of preserved cells and tissues on conventional diffraction-limited microscopes via isotropic physical expansion of the specimens before imaging. In ExM, biomolecules and/or fluorescent labels in the specimen are linked to a dense, expandable polymer matrix synthesized evenly throughout the specimen, which undergoes 3-dimensional expansion by ∼4.5 fold linearly when immersed in water. Since our first report, versions of ExM optimized for visualization of proteins, RNA, and other biomolecules have emerged. Here we describe best-practice, step-by-step ExM protocols for performing analysis of proteins (protein retention ExM, or proExM) as well as RNAs (expansion fluorescence in situ hybridization, or ExFISH), using chemicals and hardware found in a typical biology lab. Furthermore, a detailed protocol for handling and mounting expanded samples and for imaging them with confocal and light-sheet microscopes is provided. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Shoh M Asano
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts.,Internal Medicine Research Unit, Pfizer Inc., Cambridge, Massachusetts
| | - Ruixuan Gao
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts
| | - Asmamaw T Wassie
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts.,Department of Biological Engineering, MIT, Cambridge, Massachusetts
| | | | - Fei Chen
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Edward S Boyden
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts.,Department of Biological Engineering, MIT, Cambridge, Massachusetts.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts.,Koch Institute, MIT, Cambridge, Massachusetts
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11
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Wang Y, Woehrstein JB, Donoghue N, Dai M, Avendaño MS, Schackmann RC, Zoeller JJ, Wang SSH, Tillberg PW, Park D, Lapan SW, Boyden ES, Brugge JS, Kaeser PS, Church GM, Agasti SS, Jungmann R, Yin P. Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues. Nano Lett 2017; 17:6131-6139. [PMID: 28933153 PMCID: PMC5658129 DOI: 10.1021/acs.nanolett.7b02716] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
To decipher the molecular mechanisms of biological function, it is critical to map the molecular composition of individual cells or even more importantly tissue samples in the context of their biological environment in situ. Immunofluorescence (IF) provides specific labeling for molecular profiling. However, conventional IF methods have finite multiplexing capabilities due to spectral overlap of the fluorophores. Various sequential imaging methods have been developed to circumvent this spectral limit but are not widely adopted due to the common limitation of requiring multirounds of slow (typically over 2 h at room temperature to overnight at 4 °C in practice) immunostaining. We present here a practical and robust method, which we call DNA Exchange Imaging (DEI), for rapid in situ spectrally unlimited multiplexing. This technique overcomes speed restrictions by allowing for single-round immunostaining with DNA-barcoded antibodies, followed by rapid (less than 10 min) buffer exchange of fluorophore-bearing DNA imager strands. The programmability of DEI allows us to apply it to diverse microscopy platforms (with Exchange Confocal, Exchange-SIM, Exchange-STED, and Exchange-PAINT demonstrated here) at multiple desired resolution scales (from ∼300 nm down to sub-20 nm). We optimized and validated the use of DEI in complex biological samples, including primary neuron cultures and tissue sections. These results collectively suggest DNA exchange as a versatile, practical platform for rapid, highly multiplexed in situ imaging, potentially enabling new applications ranging from basic science, to drug discovery, and to clinical pathology.
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Affiliation(s)
- Yu Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Johannes B. Woehrstein
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Noah Donoghue
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Warren Alpert Medical School, Brown University, Providence, Rhode Island, 02903, USA
| | - Mingjie Dai
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Program in Biophysics, Harvard University, Boston, Massachusetts, 02138, USA
| | - Maier S. Avendaño
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Ron C.J. Schackmann
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Jason J. Zoeller
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Shan Shan H. Wang
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Program in Neuroscience, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Paul W. Tillberg
- Media Lab, MIT, Cambridge, Massachusetts, 02139, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, Massachusetts 02139, USA
| | - Demian Park
- Media Lab, MIT, Cambridge, Massachusetts, 02139, USA
| | - Sylvain W. Lapan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Edward S. Boyden
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, 02139, USA
- Media Lab, MIT, Cambridge, Massachusetts, 02139, USA
| | - Joan S. Brugge
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Pascal S. Kaeser
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - George M. Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Sarit S. Agasti
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
- P.Y. (; 617-432-7731), R.J. (), and S.S.A. ()
| | - Ralf Jungmann
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
- P.Y. (; 617-432-7731), R.J. (), and S.S.A. ()
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
- P.Y. (; 617-432-7731), R.J. (), and S.S.A. ()
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12
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Tillberg PW, Chen F, Piatkevich KD, Zhao Y, Yu CCJ, English BP, Gao L, Martorell A, Suk HJ, Yoshida F, DeGennaro EM, Roossien DH, Gong G, Seneviratne U, Tannenbaum SR, Desimone R, Cai D, Boyden ES. Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies. Nat Biotechnol 2016; 34:987-92. [PMID: 27376584 PMCID: PMC5068827 DOI: 10.1038/nbt.3625] [Citation(s) in RCA: 358] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 05/30/2016] [Indexed: 01/22/2023]
Abstract
Expansion microscopy (ExM) enables imaging of preserved specimens with nanoscale precision on diffraction-limited instead of specialized super-resolution microscopes. ExM works by physically separating fluorescent probes after anchoring them to a swellable gel. The first ExM method did not result in the retention of native proteins in the gel and relied on custom-made reagents that are not widely available. Here we describe protein retention ExM (proExM), a variant of ExM in which proteins are anchored to the swellable gel, allowing the use of conventional fluorescently labeled antibodies and streptavidin, and fluorescent proteins. We validated and demonstrated the utility of proExM for multicolor super-resolution (∼70 nm) imaging of cells and mammalian tissues on conventional microscopes.
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Affiliation(s)
- Paul W Tillberg
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Massachusetts Institute of Technology Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Fei Chen
- Massachusetts Institute of Technology Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kiryl D Piatkevich
- Massachusetts Institute of Technology Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Yongxin Zhao
- Massachusetts Institute of Technology Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Chih-Chieh Jay Yu
- Massachusetts Institute of Technology Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Brian P English
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Linyi Gao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Anthony Martorell
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ho-Jun Suk
- Massachusetts Institute of Technology Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Fumiaki Yoshida
- Osaka University Medical School, Suita, Osaka, Japan.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ellen M DeGennaro
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Guanyu Gong
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Uthpala Seneviratne
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Steven R Tannenbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Robert Desimone
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Dawen Cai
- University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Edward S Boyden
- Massachusetts Institute of Technology Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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13
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Zhang YS, Chang JB, Alvarez MM, Trujillo-de Santiago G, Aleman J, Batzaya B, Krishnadoss V, Ramanujam AA, Kazemzadeh-Narbat M, Chen F, Tillberg PW, Dokmeci MR, Boyden ES, Khademhosseini A. Hybrid Microscopy: Enabling Inexpensive High-Performance Imaging through Combined Physical and Optical Magnifications. Sci Rep 2016; 6:22691. [PMID: 26975883 PMCID: PMC4792139 DOI: 10.1038/srep22691] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/18/2016] [Indexed: 11/08/2022] Open
Abstract
To date, much effort has been expended on making high-performance microscopes through better instrumentation. Recently, it was discovered that physical magnification of specimens was possible, through a technique called expansion microscopy (ExM), raising the question of whether physical magnification, coupled to inexpensive optics, could together match the performance of high-end optical equipment, at a tiny fraction of the price. Here we show that such "hybrid microscopy" methods--combining physical and optical magnifications--can indeed achieve high performance at low cost. By physically magnifying objects, then imaging them on cheap miniature fluorescence microscopes ("mini-microscopes"), it is possible to image at a resolution comparable to that previously attainable only with benchtop microscopes that present costs orders of magnitude higher. We believe that this unprecedented hybrid technology that combines expansion microscopy, based on physical magnification, and mini-microscopy, relying on conventional optics--a process we refer to as Expansion Mini-Microscopy (ExMM)--is a highly promising alternative method for performing cost-effective, high-resolution imaging of biological samples. With further advancement of the technology, we believe that ExMM will find widespread applications for high-resolution imaging particularly in research and healthcare scenarios in undeveloped countries or remote places.
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Affiliation(s)
- Yu Shrike Zhang
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02139, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge 02139, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston 02115, MA, USA
| | | | - Mario Moisés Alvarez
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02139, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge 02139, MA, USA
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, CP 64849, Monterrey, Nuevo León, México
- Microsystems Technologies Laboratories, MIT, Cambridge, 02139, MA, USA
| | - Grissel Trujillo-de Santiago
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02139, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge 02139, MA, USA
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, CP 64849, Monterrey, Nuevo León, México
- Microsystems Technologies Laboratories, MIT, Cambridge, 02139, MA, USA
| | - Julio Aleman
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02139, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge 02139, MA, USA
| | - Byambaa Batzaya
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02139, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge 02139, MA, USA
| | - Vaishali Krishnadoss
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02139, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge 02139, MA, USA
- School of Chemical & Biotechnology, SASTRA University, Tamil Nadu 613401, India
| | - Aishwarya Aravamudhan Ramanujam
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02139, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge 02139, MA, USA
- School of Chemical & Biotechnology, SASTRA University, Tamil Nadu 613401, India
| | - Mehdi Kazemzadeh-Narbat
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02139, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge 02139, MA, USA
| | - Fei Chen
- Department of Biological Engineering, MIT, Cambridge 02139, MA, USA
| | - Paul W. Tillberg
- Department of Electrical Engineering and Computer Science, MIT, Cambridge 02139, MA, USA
| | - Mehmet Remzi Dokmeci
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02139, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge 02139, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston 02115, MA, USA
| | - Edward S. Boyden
- Media Lab, MIT, Cambridge 02139, MA, USA
- Department of Biological Engineering, MIT, Cambridge 02139, MA, USA
- McGovern Institute, MIT, Cambridge 02139, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge 02139, MA, USA
- Center for Neurobiological Engineering, MIT, Cambridge 02139, MA, USA
| | - Ali Khademhosseini
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02139, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge 02139, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston 02115, MA, USA
- Department of Bioindustrial Technologies, College of Animal Bioscience and Technology, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
- Department of Physics, King Abdulaziz University, Jeddah 21569, Saudi Arabia
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14
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Abstract
In optical microscopy, fine structural details are resolved by using refraction to magnify images of a specimen. We discovered that by synthesizing a swellable polymer network within a specimen, it can be physically expanded, resulting in physical magnification. By covalently anchoring specific labels located within the specimen directly to the polymer network, labels spaced closer than the optical diffraction limit can be isotropically separated and optically resolved, a process we call expansion microscopy (ExM). Thus, this process can be used to perform scalable superresolution microscopy with diffraction-limited microscopes. We demonstrate ExM with apparent ~70-nanometer lateral resolution in both cultured cells and brain tissue, performing three-color superresolution imaging of ~10(7) cubic micrometers of the mouse hippocampus with a conventional confocal microscope.
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Affiliation(s)
- Fei Chen
- Department of Biological Engineering, Massachussetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Paul W Tillberg
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - Edward S Boyden
- Department of Biological Engineering, Massachussetts Institute of Technology (MIT), Cambridge, MA, USA. Media Lab, MIT, Cambridge, MA, USA. McGovern Institute, MIT, Cambridge, MA, USA. Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA. Center for Neurobiological Engineering, MIT, Cambridge, MA, USA.
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