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Grassi E, Laptenok SP, Genchi L, Serdaroglu A, Liberale C. Frequency-modulation stimulated Raman scattering microscopy with an acousto-optic tunable filter. OPTICS EXPRESS 2023; 31:18290-18299. [PMID: 37381542 DOI: 10.1364/oe.486337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/05/2023] [Indexed: 06/30/2023]
Abstract
Stimulated Raman scattering (SRS) microscopy is increasingly employed for highly specific, label-free, and high-speed bioimaging. Despite its benefits, SRS is susceptible to spurious background signals caused by competing effects, which lower the possible imaging contrast and sensitivity. An efficient approach to suppress these undesired background signals is frequency-modulation (FM) SRS, which exploits the competing effects' weak spectral dependence compared to the SRS signal's high spectral specificity. We propose an FM-SRS scheme realized with an acousto-optic tunable filter, which presents a few advantages compared to other solutions presented in the literature. In particular, it can perform automated measurements from the fingerprint to the CH-stretching region of the vibrational spectrum without any manual adjustment of the optical setup. Moreover, it allows simple all-electronic control of the spectral separation and relative intensities of the pair of probed wavenumbers.
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Wallmeier K, Würthwein T, Lemberger N, Brinkmann M, Hellwig T, Fallnich C. Frequency modulation stimulated Raman scattering scheme for real-time background correction with a single light source. BIOMEDICAL OPTICS EXPRESS 2023; 14:315-325. [PMID: 36698676 PMCID: PMC9841997 DOI: 10.1364/boe.476513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
A frequency modulation (FM) scheme for stimulated Raman scattering (SRS) is presented with a single fiber-based light source. Pulse-to-pulse wavelength-switching allows real-time subtraction of parasitic signals leaving only the resonant SRS signal with a noise reduction of up to 30 % compared to digital subtraction schemes, leading effectively to a contrast improvement by a factor of up to 8.3. The wide tuning range of the light source from 1500 cm-1 to 3000 cm-1 and the possibility to separately adjust the resonant and the nonresonant wavenumber for every specimen allow to investigate a variety of samples with high contrast and high signal-to-noise ratio, e. g., for medical diagnostics.
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Affiliation(s)
- Kristin Wallmeier
- University of Münster
, Institute of Applied Physics, Corrensstraße 2, 48149 Münster, Germany
| | - Thomas Würthwein
- University of Münster
, Institute of Applied Physics, Corrensstraße 2, 48149 Münster, Germany
| | - Nick Lemberger
- University of Münster
, Institute of Applied Physics, Corrensstraße 2, 48149 Münster, Germany
| | | | - Tim Hellwig
- Refined Laser Systems GmbH, Mendelstraße 11, 48149 Münster, Germany
| | - Carsten Fallnich
- University of Münster
, Institute of Applied Physics, Corrensstraße 2, 48149 Münster, Germany
- University of Münster, Cells in Motion Interfaculty Centre, Münster, Germany
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Zahn J, Germond A, Lundgren AY, Cicerone MT. Discriminating cell line specific features of antibiotic-resistant strains of Escherichia coli from Raman spectra via machine learning analysis. JOURNAL OF BIOPHOTONICS 2022; 15:e202100274. [PMID: 35238159 PMCID: PMC9262779 DOI: 10.1002/jbio.202100274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/02/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
While Raman spectroscopy can provide label-free discrimination between highly similar biological species, the discrimination is often marginal, and optimal use of spectral information is imperative. Here, we compare two machine learning models, an artificial neural network and a support vector machine, for discriminating between Raman spectra of 11 bacterial mutants of Escherichia coli MDS42. While we find that both models discriminate the 11 bacterial strains with similarly high accuracy, sensitivity and specificity, it is clear that the models form different class boundaries. By extracting strain-specific (and function-specific) spectral features utilized by the models, we find that both models utilize a small subset of high intensity peaks while separate subsets of lower intensity peaks are utilized by only one method or the other. This analysis highlights the need for methods to use the complete spectral information more effectively, beginning with a better understanding of the distinct information gained from each model.
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Affiliation(s)
- Jessica Zahn
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA 30332, USA
| | - Arno Germond
- INRAE, UR 370 Qualité des Produits Animaux (QuaPA) Équipe Imagerie & Transferts (IT), 63122 Saint-Gènes-Champanelle, France
| | - Alice Y Lundgren
- Department of Mathematics, Brigham Young University, 275 TMCB, Provo, UT 84602, USA
| | - Marcus T Cicerone
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA 30332, USA
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Ge X, Pereira FC, Mitteregger M, Berry D, Zhang M, Hausmann B, Zhang J, Schintlmeister A, Wagner M, Cheng JX. SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level. Proc Natl Acad Sci U S A 2022; 119:e2203519119. [PMID: 35727976 PMCID: PMC9245642 DOI: 10.1073/pnas.2203519119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/08/2022] [Indexed: 12/26/2022] Open
Abstract
One of the biggest challenges in microbiome research in environmental and medical samples is to better understand functional properties of microbial community members at a single-cell level. Single-cell isotope probing has become a key tool for this purpose, but the current detection methods for determination of isotope incorporation into single cells do not allow high-throughput analyses. Here, we report on the development of an imaging-based approach termed stimulated Raman scattering-two-photon fluorescence in situ hybridization (SRS-FISH) for high-throughput metabolism and identity analyses of microbial communities with single-cell resolution. SRS-FISH offers an imaging speed of 10 to 100 ms per cell, which is two to three orders of magnitude faster than achievable by state-of-the-art methods. Using this technique, we delineated metabolic responses of 30,000 individual cells to various mucosal sugars in the human gut microbiome via incorporation of deuterium from heavy water as an activity marker. Application of SRS-FISH to investigate the utilization of host-derived nutrients by two major human gut microbiome taxa revealed that response to mucosal sugars tends to be dominated by Bacteroidales, with an unexpected finding that Clostridia can outperform Bacteroidales at foraging fucose. With high sensitivity and speed, SRS-FISH will enable researchers to probe the fine-scale temporal, spatial, and individual activity patterns of microbial cells in complex communities with unprecedented detail.
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Affiliation(s)
- Xiaowei Ge
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
| | - Fátima C. Pereira
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Matthias Mitteregger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Meng Zhang
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Jing Zhang
- Department of Biomedical Engineering, Photonics Center, Boston University, Boston, MA 02215
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
- Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Ji-Xin Cheng
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
- Department of Biomedical Engineering, Photonics Center, Boston University, Boston, MA 02215
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Koike K, Smith NI, Fujita K. Spectral focusing in picosecond pulsed stimulated Raman scattering microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:995-1004. [PMID: 35284158 PMCID: PMC8884224 DOI: 10.1364/boe.445640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
We introduce spectral focusing of picosecond laser pulses in stimulated Raman scattering (SRS) microscopy to improve spectral resolution, reduce nonlinear background signals, and decrease nonlinear photodamage. We produce a pair of 14 ps pump and Stokes laser pulses by spectral focusing of a 2 ps laser and achieve a spectral resolution of 2 cm-1. Due to instantaneous narrow-band excitation, we find that the chirped 14 ps laser pulses can be used to improve the signal-to-background ratio in SRS microscopy of various samples such as polymer particles and small molecules in HeLa cells. The lower peak powers produced by chirped picosecond laser pulses also reduce nonlinear photodamage, allowing long-term SRS imaging of living cells with higher SNR.
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Affiliation(s)
- Kota Koike
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- AIST-Osaka University Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Nicholas I. Smith
- Immunology Frontier Research Center, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Katsumasa Fujita
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- AIST-Osaka University Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Transdimensional Life Imaging Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Tsikritsis D, Legge EJ, Belsey NA. Practical considerations for quantitative and reproducible measurements with stimulated Raman scattering microscopy. Analyst 2022; 147:4642-4656. [DOI: 10.1039/d2an00817c] [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
This tutorial review presents the most important practical considerations for sample preparation, instrument set-up, image acquisition and data analysis to obtain reproducible SRS measurements.
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Affiliation(s)
- Dimitrios Tsikritsis
- Chemical and Biological Sciences Department, National Physical Laboratory, Hampton Road, Teddington, Middlesex, TW11 0LW, UK
| | - Elizabeth J. Legge
- Chemical and Biological Sciences Department, National Physical Laboratory, Hampton Road, Teddington, Middlesex, TW11 0LW, UK
| | - Natalie A. Belsey
- Chemical and Biological Sciences Department, National Physical Laboratory, Hampton Road, Teddington, Middlesex, TW11 0LW, UK
- Department of Chemical & Process Engineering, University of Surrey, Guildford, GU2 7XH, UK
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Heuke S, Rimke I, Sarri B, Gasecka P, Appay R, Legoff L, Volz P, Büttner E, Rigneault H. Shot-noise limited tunable dual-vibrational frequency stimulated Raman scattering microscopy. BIOMEDICAL OPTICS EXPRESS 2021; 12:7780-7789. [PMID: 35003866 PMCID: PMC8713670 DOI: 10.1364/boe.446348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/14/2021] [Indexed: 06/14/2023]
Abstract
We present a shot-noise limited SRS implementation providing a >200 mW per excitation wavelength that is optimized for addressing two molecular vibrations simultaneously. As the key to producing a 3 ps laser of different colors out of a single fs-laser (15 nm FWHM), we use ultra-steep angle-tunable optical filters to extract 2 narrow-band Stokes laser beams (1-2 nm & 1-2 ps), which are separated by 100 cm-1. The center part of the fs-laser is frequency doubled to pump an optical parametric oscillator (OPO). The temporal width of the OPO's output (1 ps) is matched to the Stokes beams and can be tuned from 650-980 nm to address simultaneously two Raman shifts separated by 100 cm-1 that are located between 500 cm-1 and 5000 cm-1. We demonstrate background-free SRS imaging of C-D labeled biological samples (bacteria and Drosophila). Furthermore, high quality virtual stimulated Raman histology imaging of a brain adenocarcinoma is shown for pixel dwell times of 16 µs.
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Affiliation(s)
- Sandro Heuke
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
- contributed equally to this work
| | - Ingo Rimke
- APE Angewandte Physik & Elektronik GmbH, Berlin, Germany
- contributed equally to this work
| | - Barbara Sarri
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
- Lightcore Technologies, Cannes, France
| | - Paulina Gasecka
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
| | - Romain Appay
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
- APHM, CHU Timone, Service d’Anatomie Pathologique et de Neuropathologie, Marseille, France
| | - Loic Legoff
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
| | - Peter Volz
- APE Angewandte Physik & Elektronik GmbH, Berlin, Germany
| | - Edlef Büttner
- APE Angewandte Physik & Elektronik GmbH, Berlin, Germany
| | - Hervé Rigneault
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
- Lightcore Technologies, Cannes, France
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Heuke S, Lombardini A, Büttner E, Rigneault H. Simultaneous stimulated Raman gain and loss detection (SRGAL). OPTICS EXPRESS 2020; 28:29619-29630. [PMID: 33114857 PMCID: PMC7679185 DOI: 10.1364/oe.400298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The fidelity of stimulated Raman scattering (SRS) microscopy images is impaired by artifacts such as thermal lensing, cross-phase modulation and multi-photon absorption. These artifacts affect differently the stimulated Raman loss (SRL) and stimulated Raman gain (SRG) channels making SRL and SRG image comparisons attractive to identify and correct SRS image artifacts. To provide answer to the question: "Can I trust my SRS images?", we designed a novel, but straightforward SRS scheme that enables the dectection of the stimulated Raman gain and loss (SRGAL) simultaneously at the same pixel level. As an advantage over the conventional SRS imaging scheme, SRGAL doubles the SRS signal by acquiring both SRL as well as SRG and allows for the identification of SRS artifacts and their reduction via a balanced summation of the SRL and SRG images.
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Affiliation(s)
- Sandro Heuke
- Aix Marseille Univ, CNRS, Centrale Marseille, Turing Center for Living Systems, Institut Fresnel, Marseille, France
| | - Alberto Lombardini
- Aix Marseille Univ, CNRS, Centrale Marseille, Turing Center for Living Systems, Institut Fresnel, Marseille, France
- Current address: Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - Edlef Büttner
- APE Angewandte Physik & Elektronik GmbH, Berlin, Germany
| | - Hervé Rigneault
- Aix Marseille Univ, CNRS, Centrale Marseille, Turing Center for Living Systems, Institut Fresnel, Marseille, France
- Lightcore Technologies, Marseille, France
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