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Chandler T, Guo M, Su Y, Chen J, Wu Y, Liu J, Agashe A, Fischer RS, Mehta SB, Kumar A, Baskin TI, Jamouillé V, Liu H, Swaminathan V, Nain A, Oldenbourg R, Riviére PL, Shroff H. Three-dimensional spatio-angular fluorescence microscopy with a polarized dual-view inverted selective-plane illumination microscope (pol-diSPIM). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.09.584243. [PMID: 38712306 PMCID: PMC11071302 DOI: 10.1101/2024.03.09.584243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Polarized fluorescence microscopy is a valuable tool for measuring molecular orientations, but techniques for recovering three-dimensional orientations and positions of fluorescent ensembles are limited. We report a polarized dual-view light-sheet system for determining the three-dimensional orientations and diffraction-limited positions of ensembles of fluorescent dipoles that label biological structures, and we share a set of visualization, histogram, and profiling tools for interpreting these positions and orientations. We model our samples, their excitation, and their detection using coarse-grained representations we call orientation distribution functions (ODFs). We apply ODFs to create physics-informed models of image formation with spatio-angular point-spread and transfer functions. We use theory and experiment to conclude that light-sheet tilting is a necessary part of our design for recovering all three-dimensional orientations. We use our system to extend known two-dimensional results to three dimensions in FM1-43-labelled giant unilamellar vesicles, fast-scarlet-labelled cellulose in xylem cells, and phalloidin-labelled actin in U2OS cells. Additionally, we observe phalloidin-labelled actin in mouse fibroblasts grown on grids of labelled nanowires and identify correlations between local actin alignment and global cell-scale orientation, indicating cellular coordination across length scales.
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Affiliation(s)
- Talon Chandler
- CZ Biohub SF, San Francisco, 94158, California, USA
- Department of Radiology, University of Chicago, Chicago, 60637, Illinois, USA
| | - Min Guo
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, 20892, Maryland, USA
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, 20892, Maryland, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, 20892, Maryland, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, 20147, Virginia, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, 20892, Maryland, USA
| | - Yicong Wu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, 20892, Maryland, USA
| | - Junyu Liu
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Atharva Agashe
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, 24061, Virginia, USA
| | - Robert S. Fischer
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, Maryland, USA
| | - Shalin B. Mehta
- CZ Biohub SF, San Francisco, 94158, California, USA
- Department of Radiology, University of Chicago, Chicago, 60637, Illinois, USA
- Bell Center, Marine Biological Laboratory, Woods Hole, 02543, Massachusetts, USA
| | - Abhishek Kumar
- Bell Center, Marine Biological Laboratory, Woods Hole, 02543, Massachusetts, USA
| | - Tobias I. Baskin
- Biology Department, University of Massachusetts, Amherst, 01003, Maryland, USA
- Whitman Center, Marine Biological Laboratory, Woods Hole, 02543, Massachusetts, USA
| | - Valentin Jamouillé
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, Maryland, USA
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, V5A 1S6, British Columbia, Canada
| | - Huafeng Liu
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Vinay Swaminathan
- Department of Clinical Sciences, Lund University, Lund, SE-221 00, Scania, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, SE-221 00, Scania, Sweden
| | - Amrinder Nain
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, 24061, Virginia, USA
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, 24061, Virginia, USA
| | - Rudolf Oldenbourg
- Bell Center, Marine Biological Laboratory, Woods Hole, 02543, Massachusetts, USA
| | - Patrick La Riviére
- Department of Radiology, University of Chicago, Chicago, 60637, Illinois, USA
- Whitman Center, Marine Biological Laboratory, Woods Hole, 02543, Massachusetts, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, 20892, Maryland, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, 20892, Maryland, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, 20147, Virginia, USA
- Whitman Center, Marine Biological Laboratory, Woods Hole, 02543, Massachusetts, USA
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Schnupfhagn C, Schumacher T, Markus P, Papastavrou G, Aftenieva O, König TAF, Dudko V, Matejdes M, Breu J, Lippitz M. Disentangling the Orientations of Spectrally Overlapping Transition Dipoles in Dense Dye Layers. NANO LETTERS 2022; 22:7499-7505. [PMID: 36094390 DOI: 10.1021/acs.nanolett.2c02438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The transition dipole orientations of dye assemblies in heterostructures have a crucial impact on the efficiency of novel optoelectronic devices such as organic thin-film transistors and light-emitting diodes. These devices are frequently based on heterojunctions and tandem structures featuring multiple optical transitions. Precise knowledge of preferred orientations, spatial order, and spatial variations is highly relevant. We present a fast and universal large-area screening method to determine the transition dipole orientations in dye assemblies with diffraction-limited spatial resolution. Moreover, our hyperspectral imaging approach disentangles the orientations of different chromophores. As a demonstration, we apply our technique to dye monolayers with two optical transitions sandwiched between two ultrathin silicate nanosheets. A comprehensive model for dipole orientation distributions in monolayers reveals a long-range orientational order and a strong correlation between the two transitions.
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Affiliation(s)
| | | | - Paul Markus
- Physical Chemistry II, University of Bayreuth, Bayreuth 95447, Germany
| | - Georg Papastavrou
- Physical Chemistry II, University of Bayreuth, Bayreuth 95447, Germany
| | - Olha Aftenieva
- Institute of Physical Chemistry and Polymer Physics, Leibniz-Institut für Polymerforschung Dresden e.V., Dresden 01069, Germany
- Center for Advancing Electronics Dresden (CFAED), Technische Universität Dresden, Helmholtzstraße 18, Dresden 01069, Germany
| | - Tobias A F König
- Institute of Physical Chemistry and Polymer Physics, Leibniz-Institut für Polymerforschung Dresden e.V., Dresden 01069, Germany
- Center for Advancing Electronics Dresden (CFAED), Technische Universität Dresden, Helmholtzstraße 18, Dresden 01069, Germany
| | - Volodymyr Dudko
- Inorganic Chemistry I, University of Bayreuth, Bayreuth 95447, Germany
| | - Marian Matejdes
- Inorganic Chemistry I, University of Bayreuth, Bayreuth 95447, Germany
| | - Josef Breu
- Inorganic Chemistry I, University of Bayreuth, Bayreuth 95447, Germany
| | - Markus Lippitz
- Experimental Physics III, University of Bayreuth, Bayreuth 95447, Germany
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Wu T, Lu J, Lew MD. Dipole-spread-function engineering for simultaneously measuring the 3D orientations and 3D positions of fluorescent molecules. OPTICA 2022; 9:505-511. [PMID: 35601691 PMCID: PMC9122034 DOI: 10.1364/optica.451899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/03/2022] [Indexed: 06/01/2023]
Abstract
Interactions between biomolecules are characterized by both where they occur and how they are organized, e.g., the alignment of lipid molecules to form a membrane. However, spatial and angular information are mixed within the image of a fluorescent molecule-the microscope's dipole-spread function (DSF). We demonstrate the pixOL algorithm for simultaneously optimizing all pixels within a phase mask to produce an engineered Green's tensor-the dipole extension of point-spread function engineering. The pixOL DSF achieves optimal precision for measuring simultaneously the 3D orientation and 3D location of a single molecule, i.e., 4.1° orientation, 0.44 sr wobble angle, 23.2 nm lateral localization, and 19.5 nm axial localization precisions in simulations over a 700-nm depth range using 2500 detected photons. The pixOL microscope accurately and precisely resolves the 3D positions and 3D orientations of Nile red within a spherical supported lipid bilayer, resolving both membrane defects and differences in cholesterol concentration in 6 dimensions.
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Affiliation(s)
- Tingting Wu
- Department of Electrical and Systems Engineering, Washington University in St. Louis, Missouri 63130, USA
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, Missouri 63130, USA
| | - Jin Lu
- Department of Electrical and Systems Engineering, Washington University in St. Louis, Missouri 63130, USA
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, Missouri 63130, USA
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering, Washington University in St. Louis, Missouri 63130, USA
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, Missouri 63130, USA
- Institute of Materials Science and Engineering, Washington University in St. Louis, Missouri 63130, USA
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Thorsen RØ, Hulleman CN, Rieger B, Stallinga S. Photon efficient orientation estimation using polarization modulation in single-molecule localization microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:2835-2858. [PMID: 35774337 PMCID: PMC9203119 DOI: 10.1364/boe.452159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 06/01/2023]
Abstract
Combining orientation estimation with localization microscopy opens up the possibility to analyze the underlying orientation of biomolecules on the nanometer scale. Inspired by the recent improvement of the localization precision by shifting excitation patterns (MINFLUX, SIMFLUX), we have adapted the idea towards the modulation of excitation polarization to enhance the orientation precision. For this modality two modes are analyzed: i) normally incident excitation with three polarization steps to retrieve the in-plane angle of emitters and ii) obliquely incident excitation with p-polarization with five different azimuthal angles of incidence to retrieve the full orientation. Firstly, we present a theoretical study of the lower precision limit with a Cramér-Rao bound for these modes. For the oblique incidence mode we find a favorable isotropic orientation precision for all molecular orientations if the polar angle of incidence is equal to arccos 2 / 3 ≈ 35 degrees. Secondly, a simulation study is performed to assess the performance for low signal-to-background ratios and how inaccurate illumination polarization angles affect the outcome. We show that a precision, at the Cramér-Rao bound (CRB) limit, of just 2.4 and 1.6 degrees in the azimuthal and polar angles can be achieved with only 1000 detected signal photons and 10 background photons per pixel (about twice better than reported earlier). Lastly, the alignment and calibration of an optical microscope with polarization control is described in detail. With this microscope a proof-of-principle experiment is carried out, demonstrating an experimental in-plane precision close to the CRB limit for signal photon counts ranging from 400 to 10,000.
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Affiliation(s)
- Rasmus Ø Thorsen
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
- These authors contributed equally
| | - Christiaan N Hulleman
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
- These authors contributed equally
| | - Bernd Rieger
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
- These authors contributed equally
| | - Sjoerd Stallinga
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
- These authors contributed equally
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Blanchard AT, Brockman JM, Salaita K, Mattheyses AL. Variable incidence angle linear dichroism (VALiD): a technique for unique 3D orientation measurement of fluorescent ensembles. OPTICS EXPRESS 2020; 28:10039-10061. [PMID: 32225599 PMCID: PMC7340377 DOI: 10.1364/oe.381676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 06/02/2023]
Abstract
A fundamental challenge with fluorophore orientation measurement is degeneracy, which is the inability to distinguish between multiple unique fluorophore orientations. Techniques exist for the non-degenerate measurement of the orientations of single, static fluorophores. However, such techniques are unsuitable for densely labeled and/or dynamic samples common to biological research. Accordingly, a rapid, widefield microscopy technique that can measure orientation parameters for ensembles of fluorophores in a non-degenerate manner is desirable. We propose that exciting samples with polarized light and multiple incidence angles could enable such a technique. We use Monte Carlo simulations to validate this approach for specific axially symmetric ensembles of fluorophores and obtain optimal experimental parameters for its future implementation.
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Affiliation(s)
- Aaron T. Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
| | - Joshua M. Brockman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
| | - Khalid Salaita
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Alexa L. Mattheyses
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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