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Song S, Kim J, Moon T, Seong B, Kim W, Yoo CH, Choi JK, Joo C. Polarization-sensitive intensity diffraction tomography. LIGHT, SCIENCE & APPLICATIONS 2023; 12:124. [PMID: 37202421 DOI: 10.1038/s41377-023-01151-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 04/07/2023] [Accepted: 04/10/2023] [Indexed: 05/20/2023]
Abstract
Optical anisotropy, which is an intrinsic property of many materials, originates from the structural arrangement of molecular structures, and to date, various polarization-sensitive imaging (PSI) methods have been developed to investigate the nature of anisotropic materials. In particular, the recently developed tomographic PSI technologies enable the investigation of anisotropic materials through volumetric mappings of the anisotropy distribution of these materials. However, these reported methods mostly operate on a single scattering model, and are thus not suitable for three-dimensional (3D) PSI imaging of multiple scattering samples. Here, we present a novel reference-free 3D polarization-sensitive computational imaging technique-polarization-sensitive intensity diffraction tomography (PS-IDT)-that enables the reconstruction of 3D anisotropy distribution of both weakly and multiple scattering specimens from multiple intensity-only measurements. A 3D anisotropic object is illuminated by circularly polarized plane waves at various illumination angles to encode the isotropic and anisotropic structural information into 2D intensity information. These information are then recorded separately through two orthogonal analyzer states, and a 3D Jones matrix is iteratively reconstructed based on the vectorial multi-slice beam propagation model and gradient descent method. We demonstrate the 3D anisotropy imaging capabilities of PS-IDT by presenting 3D anisotropy maps of various samples, including potato starch granules and tardigrade.
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Affiliation(s)
- Seungri Song
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jeongsoo Kim
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Taegyun Moon
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Baekcheon Seong
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Woovin Kim
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Chang-Hyuk Yoo
- Small Machines Company, Ltd., Seoul, 04808, Republic of Korea
| | - Jun-Kyu Choi
- Small Machines Company, Ltd., Seoul, 04808, Republic of Korea
| | - Chulmin Joo
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
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2
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Zhan Z, Li C, Liu X, Sun X, He C, Kuang C, Liu X. Simultaneous super-resolution estimation of single-molecule position and orientation with minimal photon fluxes. OPTICS EXPRESS 2022; 30:22051-22065. [PMID: 36224912 DOI: 10.1364/oe.456557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/24/2022] [Indexed: 06/16/2023]
Abstract
The orientation of a single molecule provides valuable information on fundamental biological processes. We report a technique for the simultaneous estimation of single-molecule 2D position and 2D orientation with ultra-high localization precision (∼2-nm precision with ∼500 photons under a typical 100-nm diameter of excitation beam pattern), which is also compatible with tracking in living cells. In the proposed method, the theoretical precision limits are calculated, and the localization and orientation performance along with potential applications are explored using numerical simulations. Compared to other camera-based orientation measurement methods, it is confirmed that the proposed method can obtain reasonable estimates even under very weak signals (∼15 photons). Moreover, the maximum likelihood estimator (MLE) is found to converge to the theoretical limit when the total number of photons is less than 100.
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Li Y, Shi W, Liu S, Cavka I, Wu YL, Matti U, Wu D, Koehler S, Ries J. Global fitting for high-accuracy multi-channel single-molecule localization. Nat Commun 2022; 13:3133. [PMID: 35668089 PMCID: PMC9170706 DOI: 10.1038/s41467-022-30719-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/16/2022] [Indexed: 11/09/2022] Open
Abstract
Multi-channel detection in single-molecule localization microscopy greatly increases information content for various biological applications. Here, we present globLoc, a graphics processing unit based global fitting algorithm with flexible PSF modeling and parameter sharing, to extract maximum information from multi-channel single molecule data. As signals in multi-channel data are highly correlated, globLoc links parameters such as 3D coordinates or photon counts across channels, improving localization precision and robustness. We show, both in simulations and experiments, that global fitting can substantially improve the 3D localization precision for biplane and 4Pi single-molecule localization microscopy and color assignment for ratiometric multicolor imaging.
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Affiliation(s)
- Yiming Li
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China. .,European Molecular Biology Laboratory, Cell Biology and Biophysics, 69117, Heidelberg, Germany.
| | - Wei Shi
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Sheng Liu
- European Molecular Biology Laboratory, Cell Biology and Biophysics, 69117, Heidelberg, Germany
| | - Ivana Cavka
- European Molecular Biology Laboratory, Cell Biology and Biophysics, 69117, Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Yu-Le Wu
- European Molecular Biology Laboratory, Cell Biology and Biophysics, 69117, Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Ulf Matti
- European Molecular Biology Laboratory, Cell Biology and Biophysics, 69117, Heidelberg, Germany
| | - Decheng Wu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Simone Koehler
- European Molecular Biology Laboratory, Cell Biology and Biophysics, 69117, Heidelberg, Germany
| | - Jonas Ries
- European Molecular Biology Laboratory, Cell Biology and Biophysics, 69117, Heidelberg, Germany.
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Optical Polarization-Based Measurement Methods for Characterization of Self-Assembled Peptides' and Amino Acids' Micro- and Nanostructures. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27061802. [PMID: 35335166 PMCID: PMC8953639 DOI: 10.3390/molecules27061802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 11/30/2022]
Abstract
In recent years, self-assembled peptides’ and amino acids’ (SAPA) micro- and nanostructures have gained much research interest. Here, description of how SAPA architectures can be characterized using polarization-based optical measurement methods is provided. The measurement methods discussed include: polarized Raman spectroscopy, polarized imaging microscopy, birefringence imaging, and fluorescence polarization. An example of linear polarized waveguiding in an amino acid Histidine microstructure is discussed. The implementation of a polarization-based measurement method for monitoring peptide self-assembly processes and for deriving molecular orientation of peptides is also described.
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Mukherjee S, Thomas C, Wilson R, Simmerman E, Hung ST, Jimenez R. Characterizing Dark State Kinetics and Single Molecule Fluorescence of FusionRed and FusionRed-MQ at Low Irradiances. Phys Chem Chem Phys 2022; 24:14310-14323. [DOI: 10.1039/d2cp00889k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The presence of dark states causes fluorescence intermittency of single molecules due to transitions between “on” and “off” states. Genetically encodable markers such as fluorescent proteins (FPs) exhibit dark states...
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He C, He H, Chang J, Chen B, Ma H, Booth MJ. Polarisation optics for biomedical and clinical applications: a review. LIGHT, SCIENCE & APPLICATIONS 2021; 10:194. [PMID: 34552045 PMCID: PMC8458371 DOI: 10.1038/s41377-021-00639-x] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 05/13/2023]
Abstract
Many polarisation techniques have been harnessed for decades in biological and clinical research, each based upon measurement of the vectorial properties of light or the vectorial transformations imposed on light by objects. Various advanced vector measurement/sensing techniques, physical interpretation methods, and approaches to analyse biomedically relevant information have been developed and harnessed. In this review, we focus mainly on summarising methodologies and applications related to tissue polarimetry, with an emphasis on the adoption of the Stokes-Mueller formalism. Several recent breakthroughs, development trends, and potential multimodal uses in conjunction with other techniques are also presented. The primary goal of the review is to give the reader a general overview in the use of vectorial information that can be obtained by polarisation optics for applications in biomedical and clinical research.
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Affiliation(s)
- Chao He
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
| | - Honghui He
- Guangdong Engineering Center of Polarisation Imaging and Sensing Technology, Tsinghua Shenzhen International Graduate School, Tsinghua University, 518055, Shenzhen, China.
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, 518055, Shenzhen, China.
| | - Jintao Chang
- Guangdong Engineering Center of Polarisation Imaging and Sensing Technology, Tsinghua Shenzhen International Graduate School, Tsinghua University, 518055, Shenzhen, China
- Department of Physics, Tsinghua University, 100084, Beijing, China
| | - Binguo Chen
- Guangdong Engineering Center of Polarisation Imaging and Sensing Technology, Tsinghua Shenzhen International Graduate School, Tsinghua University, 518055, Shenzhen, China
- Department of Biomedical Engineering, Tsinghua University, 100084, Beijing, China
| | - Hui Ma
- Guangdong Engineering Center of Polarisation Imaging and Sensing Technology, Tsinghua Shenzhen International Graduate School, Tsinghua University, 518055, Shenzhen, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, 518055, Shenzhen, China
- Department of Physics, Tsinghua University, 100084, Beijing, China
| | - Martin J Booth
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
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Shepherd JW, Payne-Dwyer AL, Lee JE, Syeda A, Leake MC. Combining single-molecule super-resolved localization microscopy with fluorescence polarization imaging to study cellular processes. JPHYS PHOTONICS 2021. [DOI: 10.1088/2515-7647/ac015d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Super-resolution microscopy has catalyzed valuable insights into the sub-cellular, mechanistic details of many different biological processes across a wide range of cell types. Fluorescence polarization spectroscopy tools have also enabled important insights into cellular processes through identifying orientational changes of biological molecules typically at an ensemble level. Here, we combine these two biophysical methodologies in a single home-made instrument to enable the simultaneous detection of orthogonal fluorescence polarization signals from single fluorescent protein molecules used as common reporters on the localization of proteins in cellular processes. These enable measurement of spatial location to a super-resolved precision better than the diffraction-limited optical resolution, as well as estimation of molecular stoichiometry based on the brightness of individual fluorophores. In this innovation we have adapted a millisecond timescale microscope used for single-molecule detection to enable splitting of fluorescence polarization emissions into two separate imaging channels for s- and p-polarization signals, which are imaged onto separate halves of the same high sensitivity back-illuminated CMOS camera detector. We applied this fluorescence polarization super-resolved imaging modality to a range of test fluorescent samples relevant to the study of biological processes, including purified monomeric green fluorescent protein, single combed DNA molecules, and protein assemblies and complexes from live Escherichia coli and Saccharomyces cerevisiae cells. Our findings are qualitative but demonstrate promise in showing how fluorescence polarization and super-resolved localization microscopy can be combined on the same sample to enable simultaneous measurements of polarization and stoichiometry of tracked molecular complexes, as well as the translational diffusion coefficient.
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