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Kong B, Blümel R, Ylä-Oijala P, Wallén H, Sihvola A, Kohler A. Signatures of top versus bottom illuminations and their predicted implications for infrared transmission microspectroscopy. JOURNAL OF BIOPHOTONICS 2024:e202400079. [PMID: 39128483 DOI: 10.1002/jbio.202400079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/13/2024] [Accepted: 06/10/2024] [Indexed: 08/13/2024]
Abstract
Since both top and bottom illuminations are widely used in infrared transmission measurements, in this paper, we study the effects of different illuminations on the signatures in infrared microspectroscopy. By simulating a series of dielectric samples, we show that their extinction efficiency,Q ext $$ {Q}_{\mathrm{ext}} $$ , remains unchanged when the direction of the incident plane wave is reversed, even though the field distributions both inside and outside of the sample may be dramatically different. We find features inQ ext $$ {Q}_{\mathrm{ext}} $$ that are correlated with whispering gallery modes for one beam direction and correspond to completely different field distributions for the opposite beam direction. In addition, by linking the optical theorem and the reciprocity relation of far-field scattered field, we rigorously prove the invariance ofQ ext $$ {Q}_{\mathrm{ext}} $$ for arbitrary dielectric targets under opposite plane-wave illuminations. Furthermore, we show the difference in the apparent absorbance spectrum for opposite beam directions when considering numerical apertures.
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Affiliation(s)
- Beibei Kong
- Faculty of Science and Technology, Norwegian University of Life Sciences, Aas, Norway
| | - Reinhold Blümel
- Department of Physics, Wesleyan University, Middletown, Connecticut, USA
| | - Pasi Ylä-Oijala
- Department of Electronics and Nanoengineering, Aalto University, Espoo, Finland
| | - Henrik Wallén
- Department of Electronics and Nanoengineering, Aalto University, Espoo, Finland
| | - Ari Sihvola
- Department of Electronics and Nanoengineering, Aalto University, Espoo, Finland
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Aas, Norway
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2
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Iyer RR, Applegate CC, Arogundade OH, Bangru S, Berg IC, Emon B, Porras-Gomez M, Hsieh PH, Jeong Y, Kim Y, Knox HJ, Moghaddam AO, Renteria CA, Richard C, Santaliz-Casiano A, Sengupta S, Wang J, Zambuto SG, Zeballos MA, Pool M, Bhargava R, Gaskins HR. Inspiring a convergent engineering approach to measure and model the tissue microenvironment. Heliyon 2024; 10:e32546. [PMID: 38975228 PMCID: PMC11226808 DOI: 10.1016/j.heliyon.2024.e32546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/22/2024] [Accepted: 06/05/2024] [Indexed: 07/09/2024] Open
Abstract
Understanding the molecular and physical complexity of the tissue microenvironment (TiME) in the context of its spatiotemporal organization has remained an enduring challenge. Recent advances in engineering and data science are now promising the ability to study the structure, functions, and dynamics of the TiME in unprecedented detail; however, many advances still occur in silos that rarely integrate information to study the TiME in its full detail. This review provides an integrative overview of the engineering principles underlying chemical, optical, electrical, mechanical, and computational science to probe, sense, model, and fabricate the TiME. In individual sections, we first summarize the underlying principles, capabilities, and scope of emerging technologies, the breakthrough discoveries enabled by each technology and recent, promising innovations. We provide perspectives on the potential of these advances in answering critical questions about the TiME and its role in various disease and developmental processes. Finally, we present an integrative view that appreciates the major scientific and educational aspects in the study of the TiME.
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Affiliation(s)
- Rishyashring R. Iyer
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Catherine C. Applegate
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Opeyemi H. Arogundade
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sushant Bangru
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ian C. Berg
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Bashar Emon
- Department of Mechanical Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Marilyn Porras-Gomez
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Pei-Hsuan Hsieh
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yoon Jeong
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yongdeok Kim
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hailey J. Knox
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Amir Ostadi Moghaddam
- Department of Mechanical Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Carlos A. Renteria
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Craig Richard
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ashlie Santaliz-Casiano
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sourya Sengupta
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jason Wang
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Samantha G. Zambuto
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Maria A. Zeballos
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Marcia Pool
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Rohit Bhargava
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Mechanical Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemical and Biochemical Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- NIH/NIBIB P41 Center for Label-free Imaging and Multiscale Biophotonics (CLIMB), University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - H. Rex Gaskins
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Biomedical and Translational Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Pathobiology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
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3
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Hanninen A. Vibrational imaging of metabolites for improved microbial cell strains. JOURNAL OF BIOMEDICAL OPTICS 2024; 29:S22711. [PMID: 38952688 PMCID: PMC11216725 DOI: 10.1117/1.jbo.29.s2.s22711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 07/03/2024]
Abstract
Significance Biomanufacturing utilizes modified microbial systems to sustainably produce commercially important biomolecules for use in agricultural, energy, food, material, and pharmaceutical industries. However, technological challenges related to non-destructive and high-throughput metabolite screening need to be addressed to fully unlock the potential of synthetic biology and sustainable biomanufacturing. Aim This perspective outlines current analytical screening tools used in industrial cell strain development programs and introduces label-free vibrational spectro-microscopy as an alternative contrast mechanism. Approach We provide an overview of the analytical instrumentation currently used in the "test" portion of the design, build, test, and learn cycle of synthetic biology. We then highlight recent progress in Raman scattering and infrared absorption imaging techniques, which have enabled improved molecular specificity and sensitivity. Results Recent developments in high-resolution chemical imaging methods allow for greater throughput without compromising the image contrast. We provide a roadmap of future work needed to support integration with microfluidics for rapid screening at the single-cell level. Conclusions Quantifying the net expression of metabolites allows for the identification of cells with metabolic pathways that result in increased biomolecule production, which is essential for improving the yield and reducing the cost of industrial biomanufacturing. Technological advancements in vibrational microscopy instrumentation will greatly benefit biofoundries as a complementary approach for non-destructive cell screening.
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Baghel D, de Oliveira AP, Satyarthy S, Chase WE, Banerjee S, Ghosh A. Structural characterization of amyloid aggregates with spatially resolved infrared spectroscopy. Methods Enzymol 2024; 697:113-150. [PMID: 38816120 PMCID: PMC11147165 DOI: 10.1016/bs.mie.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
The self-assembly of proteins and peptides into ordered structures called amyloid fibrils is a hallmark of numerous diseases, impacting the brain, heart, and other organs. The structure of amyloid aggregates is central to their function and thus has been extensively studied. However, the structural heterogeneities between aggregates as they evolve throughout the aggregation pathway are still not well understood. Conventional biophysical spectroscopic methods are bulk techniques and only report on the average structural parameters. Understanding the structure of individual aggregate species in a heterogeneous ensemble necessitates spatial resolution on the length scale of the aggregates. Recent technological advances have led to augmentation of infrared (IR) spectroscopy with imaging modalities, wherein the photothermal response of the sample upon vibrational excitation is leveraged to provide spatial resolution beyond the diffraction limit. These combined approaches are ideally suited to map out the structural heterogeneity of amyloid ensembles. AFM-IR, which integrates IR spectroscopy with atomic force microscopy enables identification of the structural facets the oligomers and fibrils at individual aggregate level with nanoscale resolution. These capabilities can be extended to chemical mapping in diseased tissue specimens with submicron resolution using optical photothermal microscopy, which combines IR spectroscopy with optical imaging. This book chapter provides the basic premise of these novel techniques and provides the typical methodology for using these approaches for amyloid structure determination. Detailed procedures pertaining to sample preparation and data acquisition and analysis are discussed and the aggregation of the amyloid β peptide is provided as a case study to provide the reader the experimental parameters necessary to use these techniques to complement their research efforts.
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Affiliation(s)
- Divya Baghel
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States
| | - Ana Pacheco de Oliveira
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States
| | - Saumya Satyarthy
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States
| | - William E Chase
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States
| | - Siddhartha Banerjee
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States
| | - Ayanjeet Ghosh
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States.
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Nazeer SS, Venkataraman RK, Jayasree RS, Bayry J. Infrared Spectroscopy for Rapid Triage of Cancer Using Blood Derivatives: A Reality Check. Anal Chem 2024; 96:957-965. [PMID: 38164878 DOI: 10.1021/acs.analchem.3c02590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Infrared (IR) spectroscopy of serum/plasma represents an alluring molecular diagnostic tool, especially for cancer, as it can provide a molecular fingerprint of clinical samples based on vibrational modes of chemical bonds. However, despite the superior performance, the routine adoption of this technique for clinical settings has remained elusive. This is due to the potential confounding factors that are often overlooked and pose a significant barrier to clinical translation. In this Perspective, we summarize the concerns associated with various confounding factors, such as fluid sampling, optical effects, hemolysis, abnormal cardiovascular and/or hepatic functions, infections, alcoholism, diet style, age, and gender of a patient or normal control cohort, and improper selection of numerical methods that ultimately would lead to improper spectral diagnosis. We also propose some precautionary measures to overcome the challenges associated with these confounding factors.
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Affiliation(s)
- Shaiju S Nazeer
- Department of Chemistry, Indian Institute of Space Sciences and Technology, Thiruvananthapuram, Kerala 695547, India
| | - Ravi Kumar Venkataraman
- Ultrafast Laser Spectroscopy Lab, Center for Integrative Petroleum Research, King Fahd University of Petroleum and Minerals, Dhahran 31261, Kingdom of Saudi Arabia
| | - Ramapurath S Jayasree
- Division of Biophotonics and Imaging, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695012, India
| | - Jagadeesh Bayry
- Department of Biological Sciences and Engineering, Indian Institute of Technology Palakkad, Palakkad 678623, India
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6
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Kassem A, Abbas L, Coutinho O, Opara S, Najaf H, Kasperek D, Pokhrel K, Li X, Tiquia-Arashiro S. Applications of Fourier Transform-Infrared spectroscopy in microbial cell biology and environmental microbiology: advances, challenges, and future perspectives. Front Microbiol 2023; 14:1304081. [PMID: 38075889 PMCID: PMC10703385 DOI: 10.3389/fmicb.2023.1304081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/03/2023] [Indexed: 01/02/2024] Open
Abstract
Microorganisms play pivotal roles in shaping ecosystems and biogeochemical cycles. Their intricate interactions involve complex biochemical processes. Fourier Transform-Infrared (FT-IR) spectroscopy is a powerful tool for monitoring these interactions, revealing microorganism composition and responses to the environment. This review explores the diversity of applications of FT-IR spectroscopy within the field of microbiology, highlighting its specific utility in microbial cell biology and environmental microbiology. It emphasizes key applications such as microbial identification, process monitoring, cell wall analysis, biofilm examination, stress response assessment, and environmental interaction investigation, showcasing the crucial role of FT-IR in advancing our understanding of microbial systems. Furthermore, we address challenges including sample complexity, data interpretation nuances, and the need for integration with complementary techniques. Future prospects for FT-IR in environmental microbiology include a wide range of transformative applications and advancements. These include the development of comprehensive and standardized FT-IR libraries for precise microbial identification, the integration of advanced analytical techniques, the adoption of high-throughput and single-cell analysis, real-time environmental monitoring using portable FT-IR systems and the incorporation of FT-IR data into ecological modeling for predictive insights into microbial responses to environmental changes. These innovative avenues promise to significantly advance our understanding of microorganisms and their complex interactions within various ecosystems.
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Affiliation(s)
- Amin Kassem
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Lana Abbas
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Oliver Coutinho
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Somie Opara
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Hawraa Najaf
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Diana Kasperek
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Keshav Pokhrel
- Department of Mathematics and Statistics, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Xiaohua Li
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Sonia Tiquia-Arashiro
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
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7
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Martin FL. Translating Biospectroscopy Techniques to Clinical Settings: A New Paradigm in Point-of-Care Screening and/or Diagnostics. J Pers Med 2023; 13:1511. [PMID: 37888122 PMCID: PMC10608143 DOI: 10.3390/jpm13101511] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023] Open
Abstract
As healthcare tools increasingly move towards a more digital and computational format, there is an increasing need for sensor-based technologies that allow for rapid screening and/or diagnostics [...].
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Affiliation(s)
- Francis L Martin
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK
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8
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Wang H, Lee D, Cao Y, Bi X, Du J, Miao K, Wei L. Bond-selective fluorescence imaging with single-molecule sensitivity. NATURE PHOTONICS 2023; 17:846-855. [PMID: 38162388 PMCID: PMC10756635 DOI: 10.1038/s41566-023-01243-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/25/2023] [Indexed: 01/03/2024]
Abstract
Bioimaging harnessing optical contrasts and chemical specificity is of vital importance in probing complex biology. Vibrational spectroscopy based on mid-infrared (mid-IR) excitation can reveal rich chemical information about molecular distributions. However, its full potential for bioimaging is hindered by the achievable sensitivity. Here, we report bond selective fluorescence-detected infrared-excited (BonFIRE) spectral microscopy. BonFIRE employs two-photon excitation in the mid-IR and near-IR to upconvert vibrational excitations to electronic states for fluorescence detection, thus encoding vibrational information into fluorescence. The system utilizes tuneable narrowband picosecond pulses to ensure high sensitivity, biocompatibility, and robustness for bond-selective biological interrogations over a wide spectrum of reporter molecules. We demonstrate BonFIRE spectral imaging in both fingerprint and cell-silent spectroscopic windows with single-molecule sensitivity for common fluorescent dyes. We then demonstrate BonFIRE imaging on various intracellular targets in fixed and live cells, neurons, and tissues, with promises for further vibrational multiplexing. For dynamic bioanalysis in living systems, we implement a high-frequency modulation scheme and demonstrate time-lapse BonFIRE microscopy of live HeLa cells. We expect BonFIRE to expand the bioimaging toolbox by providing a new level of bond-specific vibrational information and facilitate functional imaging and sensing for biological investigations.
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Affiliation(s)
- Haomin Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Dongkwan Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Yulu Cao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Xiaotian Bi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Jiajun Du
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Kun Miao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Lu Wei
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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9
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Yeh K, Sharma I, Falahkheirkhah K, Confer MP, Orr AC, Liu YT, Phal Y, Ho RJ, Mehta M, Bhargava A, Mei W, Cheng G, Cheville JC, Bhargava R. Infrared spectroscopic laser scanning confocal microscopy for whole-slide chemical imaging. Nat Commun 2023; 14:5215. [PMID: 37626026 PMCID: PMC10457288 DOI: 10.1038/s41467-023-40740-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Chemical imaging, especially mid-infrared spectroscopic microscopy, enables label-free biomedical analyses while achieving expansive molecular sensitivity. However, its slow speed and poor image quality impede widespread adoption. We present a microscope that provides high-throughput recording, low noise, and high spatial resolution where the bottom-up design of its optical train facilitates dual-axis galvo laser scanning of a diffraction-limited focal point over large areas using custom, compound, infinity-corrected refractive objectives. We demonstrate whole-slide, speckle-free imaging in ~3 min per discrete wavelength at 10× magnification (2 μm/pixel) and high-resolution capability with its 20× counterpart (1 μm/pixel), both offering spatial quality at theoretical limits while maintaining high signal-to-noise ratios (>100:1). The data quality enables applications of modern machine learning and capabilities not previously feasible - 3D reconstructions using serial sections, comprehensive assessments of whole model organisms, and histological assessments of disease in time comparable to clinical workflows. Distinct from conventional approaches that focus on morphological investigations or immunostaining techniques, this development makes label-free imaging of minimally processed tissue practical.
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Affiliation(s)
- Kevin Yeh
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ishaan Sharma
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Kianoush Falahkheirkhah
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Matthew P Confer
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Andres C Orr
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yen-Ting Liu
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yamuna Phal
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ruo-Jing Ho
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Manu Mehta
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ankita Bhargava
- University of Illinois Laboratory High School, Urbana, IL, 61801, USA
| | - Wenyan Mei
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Georgina Cheng
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carle Health, Urbana, IL, 61801, USA
| | - John C Cheville
- Department of Laboratory Medicine and Pathology, College of Medicine and Science, Mayo Clinic, Rochester, MN, 55905, USA
| | - Rohit Bhargava
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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10
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Al Jedani S, Smith CI, Ingham J, Whitley CA, Ellis BG, Triantafyllou A, Gunning PJ, Gardner P, Risk JM, Shaw RJ, Weightman P, Barrett SD. Tissue discrimination in head and neck cancer using image fusion of IR and optical microscopy. Analyst 2023; 148:4189-4194. [PMID: 37529901 PMCID: PMC10440831 DOI: 10.1039/d3an00692a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/27/2023] [Indexed: 08/03/2023]
Abstract
A regression-based fusion algorithm has been used to merge hyperspectral Fourier transform infrared (FTIR) data with an H&E image of oral squamous cell carcinoma metastases in cervical lymphoid nodal tissue. This provides insight into the success of the ratio of FTIR absorbances at 1252 cm-1 and 1285 cm-1 in discriminating between these tissue types. The success is due to absorbances at these two wavenumbers being dominated by contributions from DNA and collagen, respectively. A pixel-by-pixel fit of the fused spectra to the FTIR spectra of collagen, DNA and cytokeratin reveals the contributions of these molecules to the tissue at high spatial resolution.
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Affiliation(s)
- Safaa Al Jedani
- Department of Physics, University of Liverpool, L69 7ZE, UK.
- Department of Physics, University of Jeddah, Saudi Arabia
| | | | - James Ingham
- Department of Physics, University of Liverpool, L69 7ZE, UK.
| | - Conor A Whitley
- Department of Physics, University of Liverpool, L69 7ZE, UK.
| | - Barnaby G Ellis
- Department of Physics, University of Liverpool, L69 7ZE, UK.
| | - Asterios Triantafyllou
- Department of Cellular Pathology, Liverpool Clinical Laboratories, University of Liverpool, Liverpool, L7 8YE, UK
| | - Philip J Gunning
- Liverpool Head and Neck Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, L7 8TX, UK
| | - Peter Gardner
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Janet M Risk
- Liverpool Head and Neck Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, L7 8TX, UK
| | - Richard J Shaw
- Liverpool Head and Neck Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, L7 8TX, UK
- Head and Neck Surgery, Liverpool University Foundation NHS Trust, Aintree Hospital, Liverpool, L9 7AL, UK
| | - Peter Weightman
- Department of Physics, University of Liverpool, L69 7ZE, UK.
| | - Steve D Barrett
- Department of Physics, University of Liverpool, L69 7ZE, UK.
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11
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Bhargava R, Yeh K, Kenkel S. High-Fidelity Micro- and Nano-Scale Infrared Spectroscopic Imaging. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:562. [PMID: 37613310 PMCID: PMC11057005 DOI: 10.1093/micmic/ozad067.268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Rohit Bhargava
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Departments of Bioengineering, Chemical and Biomolecular Engineering, Electrical and Computer Engineering, Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Cancer Center at Illinois, University of Illinois at Urbana- Champaign, Urbana, IL, United States
| | - Kevin Yeh
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Seth Kenkel
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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12
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Bhargava R. Digital Histopathology by Infrared Spectroscopic Imaging. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:205-230. [PMID: 37068745 PMCID: PMC10408309 DOI: 10.1146/annurev-anchem-101422-090956] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Infrared (IR) spectroscopic imaging records spatially resolved molecular vibrational spectra, enabling a comprehensive measurement of the chemical makeup and heterogeneity of biological tissues. Combining this novel contrast mechanism in microscopy with the use of artificial intelligence can transform the practice of histopathology, which currently relies largely on human examination of morphologic patterns within stained tissue. First, this review summarizes IR imaging instrumentation especially suited to histopathology, analyses of its performance, and major trends. Second, an overview of data processing methods and application of machine learning is given, with an emphasis on the emerging use of deep learning. Third, a discussion on workflows in pathology is provided, with four categories proposed based on the complexity of methods and the analytical performance needed. Last, a set of guidelines, termed experimental and analytical specifications for spectroscopic imaging in histopathology, are proposed to help standardize the diversity of approaches in this emerging area.
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Affiliation(s)
- Rohit Bhargava
- Department of Bioengineering; Department of Electrical and Computer Engineering; Department of Mechanical Science and Engineering; Department of Chemical and Biomolecular Engineering; Department of Chemistry; Cancer Center at Illinois; and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA;
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13
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Alkhuder K. Raman Scattering-Based Optical Sensing Of Chronic Liver Diseases. Photodiagnosis Photodyn Ther 2023; 42:103505. [PMID: 36965755 DOI: 10.1016/j.pdpdt.2023.103505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/26/2023] [Accepted: 03/07/2023] [Indexed: 03/27/2023]
Abstract
Chronic liver diseases (CLDs) are a major public health problem. Despite the progress achieved in fighting against viral hepatitis, the emergence of non-alcoholic fatty liver disease might pose a serious challenge to the public's health in the coming decades. Medical management of CLDs represents a substantial burden on the public health infrastructures. The health care cost of these diseases is an additional burden that weighs heavily on the economies of developing countries. Effective management of CLDs requires the adoption of reliable and cost-effective screening and diagnosing methods to ensure early detection and accurate clinical assessment of these diseases. Vibrational spectroscopies have emerged as universal analytical methods with promising applications in various industrial and biomedical fields. These revolutionary analytical techniques rely on analyzing the interaction between a light beam and the test sample to generate a spectral fingerprint. This latter is defined by the analyte's chemical structure and the molecular vibrations of its functional groups. Raman spectroscopy and surface-enhanced Raman spectroscopy have been used in combination with various chemometric tests to diagnose a wide range of malignant, metabolic and infectious diseases. The aim of the current review is to cast light on the use of these optical sensing methods in the diagnosis of CLDs. The vast majority of research works that investigated the potential application of these spectroscopic techniques in screening and detecting CLDs were discussed here. The advantages and limitations of these modern analytical methods, as compared with the routine and gold standard diagnostic approaches, were also reviewed in details.
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14
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Hsieh PH, Phal Y, Prasanth KV, Bhargava R. Cell Phase Identification in a Three-Dimensional Engineered Tumor Model by Infrared Spectroscopic Imaging. Anal Chem 2023; 95:3349-3357. [PMID: 36574385 PMCID: PMC10214899 DOI: 10.1021/acs.analchem.2c04554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cell cycle progression plays a vital role in regulating proliferation, metabolism, and apoptosis. Three-dimensional (3D) cell cultures have emerged as an important class of in vitro disease models, and incorporating the variation occurring from cell cycle progression in these systems is critical. Here, we report the use of Fourier transform infrared (FT-IR) spectroscopic imaging to identify subtle biochemical changes within cells, indicative of the G1/S and G2/M phases of the cell cycle. Following previous studies, we first synchronized samples from two-dimensional (2D) cell cultures, confirmed their states by flow cytometry and DNA quantification, and recorded spectra. We determined two critical wavenumbers (1059 and 1219 cm-1) as spectral indicators of the cell cycle for a set of isogenic breast cancer cell lines (MCF10AT series). These two simple spectral markers were then applied to distinguish cell cycle stages in a 3D cell culture model using four cell lines that represent the main stages of cancer progression from normal cells to metastatic disease. Temporal dependence of spectral biomarkers during acini maturation validated the hypothesis that the cells are more proliferative in the early stages of acini development; later stages of the culture showed stability in the overall composition but unique spatial differences in cells in the two phases. Altogether, this study presents a computational and quantitative approach for cell phase analysis in tissue-like 3D structures without any biomarker staining and provides a means to characterize the impact of the cell cycle on 3D biological systems and disease diagnostic studies using IR imaging.
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Affiliation(s)
- Pei-Hsuan Hsieh
- Department of Bioengineering and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yamuna Phal
- Department of Electrical and Computer Engineering and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Rohit Bhargava
- Departments of Bioengineering, Electrical and Computer Engineering, Mechanical Science and Engineering, Chemical and Biomolecular Engineering, and Chemistry, Beckman Institute for Advanced Science and Technology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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15
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Thuiya Hennadige YIKDS, Akbar PN, Blümel R. Space-resolved chemical information from infrared extinction spectra. Sci Rep 2023; 13:557. [PMID: 36631640 PMCID: PMC9834313 DOI: 10.1038/s41598-023-27619-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023] Open
Abstract
A new method is presented for the extraction of the complex index of refraction from the extinction efficiency, [Formula: see text], of homogeneous and layered dielectric spheres that simultaneously removes scattering effects and corrects measured extinction spectra for systematic experimental errors such as baseline shifts, tilts, curvature, and scaling. No reference spectrum is required and fit functions may be used that automatically satisfy the Kramers-Kronig relations. Thus, the method yields the complex refractive index of a sample for unambiguous interpretation of the chemical information of the sample. In the case of homogeneous spheres, the method also determines the radius of the sphere. In the case of layered spheres, the method determines the substances within each layer. Only a single-element detector is required. Using numerically computed [Formula: see text] data of polymethyl-methacrylate and polystyrene homogeneous and layered spheres, we show that the new reconstruction algorithm is accurate and reliable. Reconstructing the complex refractive index from a published, experimentally measured raw absorbance spectrum shows that the new method simultaneously corrects spectra for scattering effects and, given shape information, corrects raw spectra for systematic errors that result in spectral distortions such as baseline shifts, tilts, curvature, and scaling.
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Affiliation(s)
| | - Proity Nayeeb Akbar
- grid.268117.b0000 0001 2293 7601Present Address: Department of Physics, Wesleyan University, 265 Church Street, Middletown, CT 06459-0155 USA
| | - Reinhold Blümel
- grid.268117.b0000 0001 2293 7601Present Address: Department of Physics, Wesleyan University, 265 Church Street, Middletown, CT 06459-0155 USA
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16
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Knez D, Toulson BW, Chen A, Ettenberg MH, Nguyen H, Potma EO, Fishman DA. Spectral imaging at high definition and high speed in the mid-infrared. SCIENCE ADVANCES 2022; 8:eade4247. [PMID: 36383646 PMCID: PMC9668290 DOI: 10.1126/sciadv.ade4247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Spectral imaging in the mid-infrared (MIR) range provides simultaneous morphological and chemical information of a wide variety of samples. However, current MIR technologies struggle to produce high-definition images over a broad spectral range at acquisition rates that are compatible with real-time processes. We present a novel spectral imaging technique based on nondegenerate two-photon absorption of temporally chirped optical MIR pulses. This approach avoids complex image processing or reconstruction and enables high-speed acquisition of spectral data cubes (xyω) at high-pixel density in under a second.
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Affiliation(s)
- David Knez
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Benjamin W. Toulson
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Anabel Chen
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Martin H. Ettenberg
- Princeton Infrared Technologies Inc., 7 Deerpark Dr. Suite E, Monmouth Junction, NJ 08852, USA
| | - Hai Nguyen
- Princeton Infrared Technologies Inc., 7 Deerpark Dr. Suite E, Monmouth Junction, NJ 08852, USA
| | - Eric O. Potma
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Dmitry A. Fishman
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
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17
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Siriwong S, Tanthanuch W, Srisamut D, Chantarakhon C, Kamkajon K, Thumanu K. Performance Evaluation of Focal Plane Array (FPA)-FTIR and Synchrotron Radiation (SR)-FTIR Microspectroscopy to Classify Rice Components. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-10. [PMID: 36062386 DOI: 10.1017/s1431927622012454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The development of biochemical analysis techniques to study heterogeneous biological samples is increasing. These techniques include synchrotron radiation Fourier transform infrared (SR-FTIR) microspectroscopy. This method has been applied to analyze biological tissue with multivariate statistical analysis to classify the components revealed by the spectral data. This study aims to compare the efficiencies of SR-FTIR microspectroscopy and focal plane array (FPA)-FTIR microspectroscopy when classifying rice tissue components. Spectral data were acquired for mapping the same sample areas from both techniques. Principal component analysis and cluster imaging were used to investigate the biochemical variations of the tissue types. The classification was based on the functional groups of pectin, protein, and polysaccharide. Four layers from SR-FTIR microspectroscopy including pericarp, aleurone layer, sub-aleurone layer, and endosperm were classified using cluster imaging, while FPA-FTIR microspectroscopy could classify only three layers of pericarp, aleurone layer, and endosperm. Moreover, SR-FTIR microspectroscopy increased the image contrast of the biochemical distribution in rice tissue more efficiently than FPA-FTIR microspectroscopy. We have demonstrated the capability of the high-resolution synchrotron technique and its ability to clarify small structures in rice tissue. The use of this technique might increase in future studies of tissue characterization.
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Affiliation(s)
- Supatcharee Siriwong
- Research Facility Department, Synchrotron Light Research Institute (Public Organization), Mueang District, Nakhon Ratchasima, 30000, Thailand
| | - Waraporn Tanthanuch
- Research Facility Department, Synchrotron Light Research Institute (Public Organization), Mueang District, Nakhon Ratchasima, 30000, Thailand
| | - Duangjai Srisamut
- Research Facility Department, Synchrotron Light Research Institute (Public Organization), Mueang District, Nakhon Ratchasima, 30000, Thailand
| | - Chulalak Chantarakhon
- Research Facility Department, Synchrotron Light Research Institute (Public Organization), Mueang District, Nakhon Ratchasima, 30000, Thailand
| | - Kanokwan Kamkajon
- Center of Calcium and Bone Research (COCAB), Department of Physiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Kanjana Thumanu
- Research Facility Department, Synchrotron Light Research Institute (Public Organization), Mueang District, Nakhon Ratchasima, 30000, Thailand
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18
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Effects of the coupling of dielectric spherical particles on signatures in infrared microspectroscopy. Sci Rep 2022; 12:13327. [PMID: 35922455 PMCID: PMC9349280 DOI: 10.1038/s41598-022-16857-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/18/2022] [Indexed: 11/08/2022] Open
Abstract
Infrared microspectroscopy is a powerful tool in the analysis of biological samples. However, strong electromagnetic scattering may occur since the wavelength of the incident radiation and the samples may be of comparable size. Based on the Mie theory of single spheres, correction algorithms have been developed to retrieve pure absorbance spectra. Studies of the scattering characteristics of samples of different types, obtained by microspectroscopy, have been performed. However, the detailed, microscopic effects of the coupling of the samples on signatures in spectra, obtained by infrared microspectroscopy, are still not clear. The aim of this paper is to investigate how the coupling of spherical samples influences the spectra. Applying the surface integral equation (SIE) method, we simulate small dielectric spheres, arranged as double-spheres or small arrays of spheres. We find that the coupling of the spheres hardly influences the broad oscillations observed in infrared spectra (the Mie wiggles) unless the radii of the spheres are different or the angle between the direction of the incident radiation and the normal of the plane where the spheres are located is large. Sharp resonance features in the spectra (the Mie ripples) are affected by the coupling of the spheres and this effect depends on the polarization of the incident wave. Experiments are performed to verify our conclusions.
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19
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Zhou J, Cai H, Ren Y, Li S, Jiang C, Lv Z, Qu G, Tan Y, Shi J, Wang T, Liu Q. Research on NCFCP compact broadband NIR detector imaging and energy transfer function. OPTICS EXPRESS 2022; 30:23716-23724. [PMID: 36225046 DOI: 10.1364/oe.460761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/06/2022] [Indexed: 06/16/2023]
Abstract
Nonlinear crystal frequency conversion imaging with direct detection by silicon-based detectors is an effective way to break through the limitations for existing near-infrared (NIR) detectors with expensive cost and high noise. In this paper, a broadband NIR detector imaging scheme based on the principle of nonlinear crystal frequency conversion (NCFCP) was proposed. A thin film of nonlinear crystal frequency conversion material (NCFCM) combined with a silicon-based detector was used to form a broadband NIR detector. The theoretically investigated energy transfer function was used as a guidance for experiment. Meanwhile, the relationship between the imaging effect and the energy transfer of the NCFCP-based compact broadband NIR detector in the NIR band was measured experimentally. The accuracy of the theoretical study had been verified by the measured transfer results.
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20
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Phal Y, Pfister L, Carney PS, Bhargava R. Resolution Limit in Infrared Chemical Imaging. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2022; 126:9777-9783. [PMID: 38476191 PMCID: PMC10928383 DOI: 10.1021/acs.jpcc.2c00740] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Chemical imaging combines the spatial specificity of optical microscopy with the spectral selectivity of vibrational spectroscopy. Mid-infrared (IR) absorption imaging instruments are now able to capture high-quality spectra with microscopic spatial detail, but the limits of their ability to resolve spatial and spectral objects remain less understood. In particular, the sensitivity of measurements to chemical and spatial changes and rules for optical design have been presented, but the influence of spectral information on spatial sensitivity is as yet relatively unexplored. We report an information theory-based approach to quantify the spatial localization capability of spectral data in chemical imaging. We explicitly consider the joint effects of the signal-to-noise ratio and spectral separation that have significance in experimental settings to derive resolution limits in IR spectroscopic imaging.
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Affiliation(s)
- Yamuna Phal
- Department of Electrical and Computer Engineering, University of Illinois at Urbana - Champaign, Urbana, Illinois 61801, United States; Beckman Institute for Advanced Science and Technology, Urbana, Illinois 61801, United States
| | - Luke Pfister
- Dynamic Imaging & Radiography Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - P Scott Carney
- Institute of Optics, University of Rochester, Rochester, New York 14627, United States
| | - Rohit Bhargava
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Beckman Institute for Advanced Science and Technology, Urbana, Illinois 61801, United States; Departments of Bioengineering, Chemical and Biomolecular Engineering, Mechanical Science and Engineering, and Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Cancer Center at Illinois, Beckman Institute for Advanced Science and Technology, Urbana, Illinois 61801, United States
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21
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Azizian Kalkhoran M, Douglas Winter A, Cinque G. Beamshaping for infrared hyperspectral imaging: a sequential optimization for infrared source coupling. OPTICS LETTERS 2022; 47:2959-2962. [PMID: 35709025 DOI: 10.1364/ol.456049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Focal plane array (FPA) detectors have escalated Fourier transform infrared (FTIR) microspectroscopy to a potent hyperspectral imaging method. Yet, despite the instrumental multiplex/multichannel advantages, the fidelity of the hyperspectral images relies on the throughput as the total flux of the source is divided among each FPA pixel. Additionally, maintaining the spectral resolution requires a certain level of collimation of the beam which adversely affect the flux of high étendue source. To this end, we propose an implementation of two deformable mirror (DM) sensorless adaptive optics system for infrared (IR) source coupling. The deflection shape of each DM membrane is optimized individually to deal with the beam intensity and the rays' direction in a separate manner, while preserving the spectral quality across the entire mid-IR range. This paper contemplates the choice of metrics in sequential optimization in conjunction with two variations of stochastic parallel gradient descent optimization algorithm. We discuss this approach with respect to a state-of-the-art FTIR microscope.
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22
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Russell BJ, Cadusch JJ, Meng J, Wen D, Crozier KB. Mid-infrared spectral reconstruction with dielectric metasurfaces and dictionary learning. OPTICS LETTERS 2022; 47:2490-2493. [PMID: 35561383 DOI: 10.1364/ol.448858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Mid-infrared (MIR) spectroscopy has numerous industrial applications and is usually performed with Fourier-transform infrared (FTIR) spectrometers. While these work well for many purposes, there is currently much interest in alternative approaches that are smaller and lighter, i.e., MIR microspectrometers. Here we investigate all-dielectric metasurfaces as spectral filters for MIR microspectrometers. Two metasurface types are studied. For the first, we design, fabricate, and test a metasurface with a narrow and angularly tunable transmission stop band. We use it to reconstruct the transmission spectra of various materials. The second metasurface, investigated theoretically, possesses narrow passband features via symmetry-protected bound states in the continuum.
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23
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Nakagawa K, Shimura Y, Fukazawa Y, Nishizaki R, Matano S, Oya S, Maki H. Microemitter-Based IR Spectroscopy and Imaging with Multilayer Graphene Thermal Emission. NANO LETTERS 2022; 22:3236-3244. [PMID: 35435683 DOI: 10.1021/acs.nanolett.1c04857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
IR analyses such as Fourier transform infrared spectroscopy (FTIR) are widely used in many fields; however, the performance of FTIR is limited by the slow speed (∼10 Hz), large footprint (∼ millimeter), and glass bulb structure of IR light sources. Herein, we present IR spectroscopy and imaging based on multilayer-graphene microemitters, which have distinct features: a planar structure, bright intensity, a small footprint (sub-μm2), and high modulation speed of >50 kHz. We developed an IR analysis system based on the multilayer-graphene microemitter and performed IR absorption spectroscopy. We show two-dimensional IR chemical imaging that visualizes the distribution of the chemical information. In addition, we present high-spatial-resolution IR imaging with a spatial resolution of ∼1 μm, far higher than the diffraction limit. The graphene-based IR spectroscopy and imaging can open new routes for IR applications in chemistry, material science, medicine, biology, electronics, and physics.
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Affiliation(s)
- Kenta Nakagawa
- Department of Applied Physics and Physico-Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
- Kanagawa Institute of Industrial Science and Technology (KISTEC), 705-1 Shimoimaizumi, Ebina, Kanagawa 243-0435, Japan
| | - Yui Shimura
- Department of Applied Physics and Physico-Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Yusuke Fukazawa
- Department of Applied Physics and Physico-Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Ryosuke Nishizaki
- Department of Applied Physics and Physico-Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Shinichiro Matano
- Department of Applied Physics and Physico-Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Shuma Oya
- Department of Applied Physics and Physico-Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Hideyuki Maki
- Department of Applied Physics and Physico-Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
- Center for Spintronics Research Network, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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24
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Kviatkovsky I, Chrzanowski HM, Ramelow S. Mid-infrared microscopy via position correlations of undetected photons. OPTICS EXPRESS 2022; 30:5916-5925. [PMID: 35209543 DOI: 10.1364/oe.440534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
Quantum imaging with undetected photons (QIUP) has recently emerged as a new powerful imaging tool. Exploiting the spatial entanglement of photon pairs, it allows decoupling of the sensing and detection wavelengths, facilitating imaging in otherwise challenging spectral regions by leveraging mature silicon-based detection technology. All existing implementations of QIUP have so far utilised the momentum correlations within the biphoton states produced by spontaneous parametric downconversion. Here, for the first time, we implement and examine theoretically and numerically the complementary scenario - utilising the tight position correlations formed within photon pairs at birth. This image plane arrangement facilitates high resolution imaging with comparative experimental ease, and we experimentally show resolutions below 10 μm at a sensing wavelength of 3.7 μm. Moreover, we present a quantitative numerical model predicting the imaging capabilities of QIUP for a wide range of parameters. Finally, by imaging mouse heart tissue at the mid-IR to reveal morphological features on the cellular level, we further demonstrate the viability of this technique for the life sciences. These results offer new perspectives on the capabilities of QIUP for label-free widefield mid-IR microscopy, enabling real-world biomedical as well as industrial imaging applications.
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25
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Sacré PY, Alaoui Mansouri M, De Bleye C, Coïc L, Hubert P, Ziemons E. Evaluation of distributional homogeneity of pharmaceutical formulation using laser direct infrared imaging. Int J Pharm 2022; 612:121373. [PMID: 34906650 DOI: 10.1016/j.ijpharm.2021.121373] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 10/19/2022]
Abstract
The distributional homogeneity of chemicals is a key parameter of solid pharmaceutical formulations. Indeed, it may affect the efficacy of the drug and consequently its safety. Chemical imaging offers a unique insight enabling the visualisation of the different constituents of a pharmaceutical tablet. It allows identifying ingredients poorly distributed offering the possibility to optimize the process parameters or to adapt characteristics of incoming raw materials to increase the final product quality. Among the available chemical imaging tools, Raman imaging is one of the most widely used since it offers a high spatial resolution with well-resolved peaks resulting in a high spectral specificity. However, Raman imaging suffers from sample autofluorescence and long acquisition times. Recently commercialised, laser direct infrared reflectance imaging (LDIR) is a quantum cascade laser (QCL) based imaging technique that offers the opportunity to rapidly analyse samples. In this study, a typical pharmaceutical formulation blend composed of two active pharmaceutical ingredients and three excipients was aliquoted at different mixing timepoints. The collected aliquots were tableted and analysed using both Raman and LDIR imaging. The distributional homogeneity indexes of one active ingredient image were then computed and compared. The results show that both techniques achieved similar conclusions. However, the analysis times were drastically different. While Raman imaging required a total analysis time of 4 h per tablet to obtain the distribution map of acetylsalicylic acid with a step size of 100 µm, it only took 7.5 min to achieve the same result with LDIR. The results obtained in the present study show that LDIR is a promising technique for the analysis of pharmaceutical formulations and that it could be a valuable tool when developing new pharmaceutical formulations.
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Affiliation(s)
- P-Y Sacré
- University of Liege (ULiege), CIRM, Vibra-Santé Hub, Department of Pharmacy, Laboratory of Pharmaceutical Analytical Chemistry, Liege, Belgium.
| | - M Alaoui Mansouri
- University of Liege (ULiege), CIRM, Vibra-Santé Hub, Department of Pharmacy, Laboratory of Pharmaceutical Analytical Chemistry, Liege, Belgium
| | - C De Bleye
- University of Liege (ULiege), CIRM, Vibra-Santé Hub, Department of Pharmacy, Laboratory of Pharmaceutical Analytical Chemistry, Liege, Belgium
| | - L Coïc
- University of Liege (ULiege), CIRM, Vibra-Santé Hub, Department of Pharmacy, Laboratory of Pharmaceutical Analytical Chemistry, Liege, Belgium
| | - Ph Hubert
- University of Liege (ULiege), CIRM, Vibra-Santé Hub, Department of Pharmacy, Laboratory of Pharmaceutical Analytical Chemistry, Liege, Belgium
| | - E Ziemons
- University of Liege (ULiege), CIRM, Vibra-Santé Hub, Department of Pharmacy, Laboratory of Pharmaceutical Analytical Chemistry, Liege, Belgium
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26
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Hong T, Yin JY, Nie SP, Xie MY. Applications of infrared spectroscopy in polysaccharide structural analysis: Progress, challenge and perspective. Food Chem X 2021; 12:100168. [PMID: 34877528 PMCID: PMC8633561 DOI: 10.1016/j.fochx.2021.100168] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/31/2022] Open
Abstract
Functional properties of polysaccharides depend on their structural features. IR spectroscopy is widely used in polysaccharide structural analysis. Classical applications of IR spectroscopy in polysaccharide are reviewed. IR integrating techniques can considerably expand its application scope.
Polysaccharides are important biomacromolecules with numerous beneficial functions and a wide range of industrial applications. Functions and properties of polysaccharides are closely related to their structural features. Infrared (IR) spectroscopy is a well-established technique which has been widely applied in polysaccharide structural analysis. In this paper, the principle of IR and interpretation of polysaccharide IR spectrum are briefly introduced. Classical applications of IR spectroscopy in polysaccharide structural elucidation are reviewed from qualitative and quantitative aspects. Some advanced IR techniques including integrating with mass spectrometry (MS), microscopy and computational chemistry are introduced and their applications are emphasized. These emerging techniques can considerably expand application scope of IR, thus exert a more important effect on carbohydrate characterization. Overall, this review seeks to provide a comprehensive insight to applications of IR spectroscopy in polysaccharide structural analysis and highlights the importance of advanced IR-integrating techniques.
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Affiliation(s)
- Tao Hong
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, People's Republic of China
| | - Jun-Yi Yin
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, People's Republic of China
| | - Shao-Ping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, People's Republic of China
| | - Ming-Yong Xie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang, Jiangxi 330047, People's Republic of China
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Zhang L, Zou X, Huang J, Fan J, Sun X, Zhang B, Zheng B, Guo C, Fu D, Yao L, Ji M. Label-Free Histology and Evaluation of Human Pancreatic Cancer with Coherent Nonlinear Optical Microscopy. Anal Chem 2021; 93:15550-15558. [PMID: 34751027 DOI: 10.1021/acs.analchem.1c03861] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Surgeries achieving maximal tumor resection remain the major effective treatment of pancreatic cancer. Rapid and precise intraoperative diagnosis of pancreatic tissues is critical for optimum surgical outcomes but is challenging for the current staining-based histological methods. We demonstrated that label-free coherent nonlinear optical microscopy with combined stimulated Raman scattering (SRS) and second harmonic generation (SHG) could reveal key diagnostic features of both normal and cancerous human pancreatic tissues. Adjacent pairs of tissue sections from resection margins of 37 patients were imaged by SRS and hematoxylin and eosin staining for direct comparison, demonstrating high diagnostic concordance (Cohen's kappa, κ > 0.97) between them. Fresh unprocessed tissues showed well-preserved histoarchitectures including pancreatic ducts, islets, acini, and nerves. Moreover, the area ratios of collagen fibers were analyzed and found to correlate with the drainage pancreatic amylase level (odds ratio = 28.0, p = 0.0017). Our results indicated that SRS/SHG histology provides potential for rapid intraoperative diagnosis of pancreatic cancer as well as a predictive value of postoperative pancreatic fistula.
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Affiliation(s)
- Lili Zhang
- State Key Laboratory of Surface Physics and Department of Physics, Human Phenome Institute, Academy for Engineering and Technology, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai 200433, China
| | - Xiang Zou
- Department of Pancreatic Surgery, Department of Neurosurgery, Department of Pathology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Jing Huang
- State Key Laboratory of Surface Physics and Department of Physics, Human Phenome Institute, Academy for Engineering and Technology, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai 200433, China
| | - Jie Fan
- Department of Pancreatic Surgery, Department of Neurosurgery, Department of Pathology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xiangjie Sun
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Bohan Zhang
- State Key Laboratory of Surface Physics and Department of Physics, Human Phenome Institute, Academy for Engineering and Technology, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai 200433, China
| | - Bin Zheng
- Department of Otolaryngology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310014, China
| | - Chongyuan Guo
- Shanghai Starriver Bilingual School, Shanghai 201108, China
| | - Deliang Fu
- Department of Pancreatic Surgery, Department of Neurosurgery, Department of Pathology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Lie Yao
- Department of Pancreatic Surgery, Department of Neurosurgery, Department of Pathology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Minbiao Ji
- State Key Laboratory of Surface Physics and Department of Physics, Human Phenome Institute, Academy for Engineering and Technology, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai 200433, China.,Yiwu Research Institute of Fudan University, Chengbei Road, Yiwu City, Zhejiang 322000, China
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Keen AN, Mackrill JJ, Gardner P, Shiels HA. Compliance of the fish outflow tract is altered by thermal acclimation through connective tissue remodelling. J R Soc Interface 2021; 18:20210492. [PMID: 34784777 PMCID: PMC8596013 DOI: 10.1098/rsif.2021.0492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To protect the gill capillaries from high systolic pulse pressure, the fish heart contains a compliant non-contractile chamber called the bulbus arteriosus which is part of the outflow tract (OFT) which extends from the ventricle to the ventral aorta. Thermal acclimation alters the form and function of the fish atria and ventricle to ensure appropriate cardiac output at different temperatures, but its impact on the OFT is unknown. Here we used ex vivo pressure-volume curves to demonstrate remodelling of passive stiffness in the rainbow trout (Oncorhynchus mykiss) bulbus arteriosus following more than eight weeks of thermal acclimation to 5, 10 and 18°C. We then combined novel, non-biased Fourier transform infrared spectroscopy with classic histological staining to show that changes in compliance were achieved by changes in tissue collagen-to-elastin ratio. In situ gelatin zymography and SDS-PAGE zymography revealed that collagen remodelling was underpinned, at least in part, by changes in activity and abundance of collagen degrading matrix metalloproteinases. Collectively, we provide the first indication of bulbus arteriosus thermal remodelling in a fish and suggest this remodelling ensures optimal blood flow and blood pressure in the OFT during temperature change.
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Affiliation(s)
- Adam N Keen
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - John J Mackrill
- Department of Physiology, University College Cork, Cork, County Cork, Ireland
| | - Peter Gardner
- School of Chemical Engineering and Analytical Science, Manchester Institute of Biotechnology, University of Manchester, UK
| | - Holly A Shiels
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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29
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Confer MP, Holcombe BM, Foes AG, Holmquist JM, Walker SC, Deb S, Ghosh A. Label-Free Infrared Spectroscopic Imaging Reveals Heterogeneity of β-Sheet Aggregates in Alzheimer's Disease. J Phys Chem Lett 2021; 12:9662-9671. [PMID: 34590866 PMCID: PMC8933041 DOI: 10.1021/acs.jpclett.1c02306] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The aggregation of the amyloid beta (Aβ) protein into plaques is a pathological feature of Alzheimer's disease (AD). While amyloid aggregates have been extensively studied in vitro, their structural aspects and associated chemistry in the brain are not fully understood. In this report, we demonstrate, using infrared spectroscopic imaging, that Aβ plaques exhibit significant heterogeneities in terms of their secondary structure and phospholipid content. We show that the capabilities of discrete frequency infrared imaging (DFIR) are ideally suited for characterization of amyloid deposits in brain tissues and employ DFIR to identify nonplaque β-sheet aggregates distributed throughout brain tissues. We further demonstrate that phospholipid-rich β-sheet deposits exist outside of plaques in all diseased tissues, indicating their potential clinical significance. This is the very first application of DFIR toward a characterization of protein aggregates in an AD brain and provides a rapid, label-free approach that allows us to uncover β-sheet heterogeneities in the AD, which may be significant for targeted therapeutic strategies in the future.
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30
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Phal Y, Yeh K, Bhargava R. Design Considerations for Discrete Frequency Infrared Microscopy Systems. APPLIED SPECTROSCOPY 2021; 75:1067-1092. [PMID: 33876990 PMCID: PMC9993325 DOI: 10.1177/00037028211013372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Discrete frequency infrared chemical imaging is transforming the practice of microspectroscopy by enabling a diversity of instrumentation and new measurement capabilities. While a variety of hardware implementations have been realized, design considerations that are unique to infrared (IR) microscopes have not yet been compiled in literature. Here, we describe the evolution of IR microscopes, provide rationales for design choices, and catalog some major considerations for each of the optical components in an imaging system. We analyze design choices that use these components to optimize performance, under their particular constraints, while providing illustrative examples. We then summarize a framework to assess the factors that determine an instrument's performance mathematically. Finally, we provide a validation approach by enumerating performance metrics that can be used to evaluate the capabilities of imaging systems or suitability for specific intended applications. Together, the presented concepts and examples should aid in understanding available instrument configurations, while guiding innovations in design of the next generation of IR chemical imaging spectrometers.
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Affiliation(s)
- Yamuna Phal
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Kevin Yeh
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Rohit Bhargava
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, USA
- Departments of Bioengineering, Mechanical Science and Engineering, Chemical and Biomolecular Engineering, and Chemistry, University of Illinois at Urbana-Champaign, Urbana, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, USA
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31
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Dicke SS, Alperstein AM, Schueler KL, Stapleton DS, Simonett SP, Fields CR, Chalyavi F, Keller MP, Attie AD, Zanni MT. Application of 2D IR Bioimaging: Hyperspectral Images of Formalin-Fixed Pancreatic Tissues and Observation of Slow Protein Degradation. J Phys Chem B 2021; 125:9517-9525. [PMID: 34396779 PMCID: PMC8769495 DOI: 10.1021/acs.jpcb.1c05554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We used two-dimensional IR bioimaging to study the structural heterogeneity of formalin-fixed mouse pancreas. Images were generated from the hyperspectral data sets by plotting quantities associated with the amide I vibrational mode, which is created by the backbone carbonyl stretch. Images that measure the fundamental vibrational frequencies, cross peaks, and anharmonic shifts are presented. Histograms are generated for each quantity, providing averaged values and distributions around the mean that serve as metrics for protein structures. Images were generated from tissue that had been stored in a formalin fixation for 3, 8, and 48 weeks. Over this period, all three metrics show that that the β-sheet content of the samples increased, consistent with protein aggregation. Our results indicate that formalin fixation does not entirely arrest the degradation of a protein structure in pancreas tissue.
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Affiliation(s)
- Sidney S Dicke
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Ariel M Alperstein
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Kathryn L Schueler
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Donald S Stapleton
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Shane P Simonett
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Caitlyn R Fields
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Farzaneh Chalyavi
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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32
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POTMA ERICO, KNEZ DAVID, CHEN YONG, DAVYDOVA YULIA, DURKIN AMANDA, FAST ALEXANDER, BALU MIHAELA, NORTON-BAKER BRENNA, MARTIN RACHELW, BALDACCHINI TOMMASO, FISHMAN DMITRYA. Rapid chemically selective 3D imaging in the mid-infrared. OPTICA 2021; 8:995-1002. [PMID: 35233439 PMCID: PMC8884451 DOI: 10.1364/optica.426199] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/16/2021] [Indexed: 05/04/2023]
Abstract
The emerging technique of mid-infrared optical coherence tomography (MIR-OCT) takes advantage of the reduced scattering of MIR light in various materials and devices, enabling tomographic imaging at deeper penetration depths. Because of challenges in MIR detection technology, the image acquisition time is, however, significantly longer than for tomographic imaging methods in the visible/near-infrared. Here we demonstrate an alternative approach to MIR tomography with high-speed imaging capabilities. Through femtosecond nondegenerate two-photon absorption of MIR light in a conventional Si-based CCD camera, we achieve wide-field, high-definition tomographic imaging with chemical selectivity of structured materials and biological samples in mere seconds.
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Affiliation(s)
- ERIC O. POTMA
- Department of Chemistry, University of California Irvine, California 92697, USA
- Beckman Laser Institute, University of California Irvine, California 92697, USA
- e-mail:
| | - DAVID KNEZ
- Department of Chemistry, University of California Irvine, California 92697, USA
| | - YONG CHEN
- Epstein Department of Industrial and Systems Engineering, University of Southern California, Los Angeles, California 90089, USA
| | - YULIA DAVYDOVA
- Department of Chemistry, University of California Irvine, California 92697, USA
| | - AMANDA DURKIN
- Beckman Laser Institute, University of California Irvine, California 92697, USA
| | - ALEXANDER FAST
- Beckman Laser Institute, University of California Irvine, California 92697, USA
| | - MIHAELA BALU
- Beckman Laser Institute, University of California Irvine, California 92697, USA
| | - BRENNA NORTON-BAKER
- Department of Chemistry, University of California Irvine, California 92697, USA
| | - RACHEL W. MARTIN
- Department of Chemistry, University of California Irvine, California 92697, USA
- Department of Molecular Biology & Biochemistry, University of California Irvine, California 92697, USA
| | - TOMMASO BALDACCHINI
- Department of Chemistry, University of California Irvine, California 92697, USA
- Current address: Edwards Life Sciences, Irvine, California 92612, USA
| | - DMITRY A. FISHMAN
- Department of Chemistry, University of California Irvine, California 92697, USA
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33
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Bai Y, Yin J, Cheng JX. Bond-selective imaging by optically sensing the mid-infrared photothermal effect. SCIENCE ADVANCES 2021; 7:eabg1559. [PMID: 33990332 PMCID: PMC8121423 DOI: 10.1126/sciadv.abg1559] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/25/2021] [Indexed: 05/03/2023]
Abstract
Mid-infrared (IR) spectroscopic imaging using inherent vibrational contrast has been broadly used as a powerful analytical tool for sample identification and characterization. However, the low spatial resolution and large water absorption associated with the long IR wavelengths hinder its applications to study subcellular features in living systems. Recently developed mid-infrared photothermal (MIP) microscopy overcomes these limitations by probing the IR absorption-induced photothermal effect using a visible light. MIP microscopy yields submicrometer spatial resolution with high spectral fidelity and reduced water background. In this review, we categorize different photothermal contrast mechanisms and discuss instrumentations for scanning and widefield MIP microscope configurations. We highlight a broad range of applications from life science to materials. We further provide future perspective and potential venues in MIP microscopy field.
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Affiliation(s)
- Yeran Bai
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
| | - Jiaze Yin
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
| | - Ji-Xin Cheng
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA.
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
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34
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Kazarian SG. Perspectives on infrared spectroscopic imaging from cancer diagnostics to process analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 251:119413. [PMID: 33461133 DOI: 10.1016/j.saa.2020.119413] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 05/20/2023]
Abstract
This perspective paper discusses the recent and potential developments in the application of infrared spectroscopic imaging, with a focus on Fourier transform infrared (FTIR) spectroscopic imaging. The current state-of-the-art has been briefly reported, that includes recent trends and advances in applications of FTIR spectroscopic imaging to biomedical systems. Here, some new opportunities for research in the biomedical field, particularly for cancer diagnostics, and also in the engineering field of process analysis; as well as challenges in FTIR spectroscopic imaging are discussed. Current and future prospects that will bring spectroscopic imaging technologies to the frontier of advanced medical diagnostics and to process analytics in engineering applications will be outlined in this opinion paper.
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Affiliation(s)
- Sergei G Kazarian
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom.
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35
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Tai F, Koike K, Kawagoe H, Ando J, Kumamoto Y, Smith NI, Sodeoka M, Fujita K. Detecting nitrile-containing small molecules by infrared photothermal microscopy. Analyst 2021; 146:2307-2312. [PMID: 33620044 DOI: 10.1039/d0an02198a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of infrared (IR) photothermal microscopy (IR-PTM) is emerging for imaging chemical substances in various samples. In this research, we demonstrated the use of a nitrile group as a vibrational tag to image target molecules in the low water-background region. We performed IR photothermal imaging of trifluoromethoxy carbonyl cyanide phenylhydrazone (FCCP) in cells and confirmed the high spatial resolution by photothermal detection using visible light as a probe beam. We imaged FCCP-treated HeLa cells and confirmed that the photothermal signal was indeed produced from the vibrational tag in lipid droplets. We also compared the results with nitrile imaging by stimulated Raman scattering (SRS) microscopy. From both the calculated and experimental results, IR-PTM demonstrated a signal-to-noise ratio (SNR) several tens of times better than that of SRS microscopy on the basis of the same power input.
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Affiliation(s)
- Fangfang Tai
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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36
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The effect of deformation of absorbing scatterers on Mie-type signatures in infrared microspectroscopy. Sci Rep 2021; 11:4675. [PMID: 33633244 PMCID: PMC7907113 DOI: 10.1038/s41598-021-84064-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 01/18/2021] [Indexed: 11/28/2022] Open
Abstract
Mie-type scattering features such as ripples (i.e., sharp shape-resonance peaks) and wiggles (i.e., broad oscillations), are frequently-observed scattering phenomena in infrared microspectroscopy of cells and tissues. They appear in general when the wavelength of electromagnetic radiation is of the same order as the size of the scatterer. By use of approximations to the Mie solutions for spheres, iterative algorithms have been developed to retrieve pure absorbance spectra. However, the question remains to what extent the Mie solutions, and approximations thereof, describe the extinction efficiency in practical situations where the shapes of scatterers deviate considerably from spheres. The aim of the current study is to investigate how deviations from a spherical scatterer can change the extinction properties of the scatterer in the context of chaos in wave systems. For this purpose, we investigate a chaotic scatterer and compare it with an elliptically shaped scatterer, which exhibits only regular scattering. We find that chaotic scattering has an accelerating effect on the disappearance of Mie ripples. We further show that the presence of absorption and the high numerical aperture of infrared microscopes does not explain the absence of ripples in most measurements of biological samples.
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37
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Querido W, Kandel S, Pleshko N. Applications of Vibrational Spectroscopy for Analysis of Connective Tissues. Molecules 2021; 26:922. [PMID: 33572384 PMCID: PMC7916244 DOI: 10.3390/molecules26040922] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/30/2021] [Accepted: 02/04/2021] [Indexed: 02/07/2023] Open
Abstract
Advances in vibrational spectroscopy have propelled new insights into the molecular composition and structure of biological tissues. In this review, we discuss common modalities and techniques of vibrational spectroscopy, and present key examples to illustrate how they have been applied to enrich the assessment of connective tissues. In particular, we focus on applications of Fourier transform infrared (FTIR), near infrared (NIR) and Raman spectroscopy to assess cartilage and bone properties. We present strengths and limitations of each approach and discuss how the combination of spectrometers with microscopes (hyperspectral imaging) and fiber optic probes have greatly advanced their biomedical applications. We show how these modalities may be used to evaluate virtually any type of sample (ex vivo, in situ or in vivo) and how "spectral fingerprints" can be interpreted to quantify outcomes related to tissue composition and quality. We highlight the unparalleled advantage of vibrational spectroscopy as a label-free and often nondestructive approach to assess properties of the extracellular matrix (ECM) associated with normal, developing, aging, pathological and treated tissues. We believe this review will assist readers not only in better understanding applications of FTIR, NIR and Raman spectroscopy, but also in implementing these approaches for their own research projects.
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Affiliation(s)
| | | | - Nancy Pleshko
- Department of Bioengineering, Temple University, Philadelphia, PA 19122, USA; (W.Q.); (S.K.)
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38
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Tiwari S, Kajdacsy-Balla A, Whiteley J, Cheng G, Hewitt SM, Bhargava R. INFORM: INFrared-based ORganizational Measurements of tumor and its microenvironment to predict patient survival. SCIENCE ADVANCES 2021; 7:7/6/eabb8292. [PMID: 33536203 PMCID: PMC7857685 DOI: 10.1126/sciadv.abb8292] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 12/11/2020] [Indexed: 05/14/2023]
Abstract
The structure and organization of a tumor and its microenvironment are often associated with cancer outcomes due to spatially varying molecular composition and signaling. A persistent challenge is to use this physical and chemical spatial organization to understand cancer progression. Here, we present a high-definition infrared imaging-based organizational measurement framework (INFORM) that leverages intrinsic chemical contrast of tissue to label unique components of the tumor and its microenvironment. Using objective and automated computational methods, further, we determine organization characteristics important for prediction. We show that the tumor spatial organization assessed with this framework is predictive of overall survival in colon cancer that adds to capability from clinical variables such as stage and grade, approximately doubling the risk of death in high-risk individuals. Our results open an all-digital avenue for measuring and studying the association between tumor spatial organization and disease progression.
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Affiliation(s)
- Saumya Tiwari
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andre Kajdacsy-Balla
- Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Joshua Whiteley
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Rohit Bhargava
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Departments of Electrical and Computer Engineering, Mechanical Science and Engineering, Chemical and Biomolecular Engineering and Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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39
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Afara IO, Shaikh R, Nippolainen E, Querido W, Torniainen J, Sarin JK, Kandel S, Pleshko N, Töyräs J. Characterization of connective tissues using near-infrared spectroscopy and imaging. Nat Protoc 2021; 16:1297-1329. [PMID: 33462441 DOI: 10.1038/s41596-020-00468-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023]
Abstract
Near-infrared (NIR) spectroscopy is a powerful analytical method for rapid, non-destructive and label-free assessment of biological materials. Compared to mid-infrared spectroscopy, NIR spectroscopy excels in penetration depth, allowing intact biological tissue assessment, albeit at the cost of reduced molecular specificity. Furthermore, it is relatively safe compared to Raman spectroscopy, with no risk of laser-induced photothermal damage. A typical NIR spectroscopy workflow for biological tissue characterization involves sample preparation, spectral acquisition, pre-processing and analysis. The resulting spectrum embeds intrinsic information on the tissue's biomolecular, structural and functional properties. Here we demonstrate the analytical power of NIR spectroscopy for exploratory and diagnostic applications by providing instructions for acquiring NIR spectra, maps and images in biological tissues. By adapting and extending this protocol from the demonstrated application in connective tissues to other biological tissues, we expect that a typical NIR spectroscopic study can be performed by a non-specialist user to characterize biological tissues in basic research or clinical settings. We also describe how to use this protocol for exploratory study on connective tissues, including differentiating among ligament types, non-destructively monitoring changes in matrix formation during engineered cartilage development, mapping articular cartilage proteoglycan content across bovine patella and spectral imaging across the depth-wise zones of articular cartilage and subchondral bone. Depending on acquisition mode and experiment objectives, a typical exploratory study can be completed within 6 h, including sample preparation and data analysis.
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Affiliation(s)
- Isaac O Afara
- Department of Applied Physics, University of Eastern Finland, Kuopio, Finland.
- School of Information Technology and Electrical Engineering, The University of Queensland, Brisbane, Queensland, Australia.
| | - Rubina Shaikh
- Department of Applied Physics, University of Eastern Finland, Kuopio, Finland
- Diagnostic Imaging Centre, Kuopio University Hospital, Kuopio, Finland
| | - Ervin Nippolainen
- Department of Applied Physics, University of Eastern Finland, Kuopio, Finland
| | - William Querido
- Department of Bioengineering, Temple University, Philadelphia, PA, USA
| | - Jari Torniainen
- Department of Applied Physics, University of Eastern Finland, Kuopio, Finland
| | - Jaakko K Sarin
- Diagnostic Imaging Centre, Kuopio University Hospital, Kuopio, Finland
| | - Shital Kandel
- Department of Bioengineering, Temple University, Philadelphia, PA, USA
| | - Nancy Pleshko
- Department of Bioengineering, Temple University, Philadelphia, PA, USA
| | - Juha Töyräs
- Department of Applied Physics, University of Eastern Finland, Kuopio, Finland
- School of Information Technology and Electrical Engineering, The University of Queensland, Brisbane, Queensland, Australia
- Diagnostic Imaging Centre, Kuopio University Hospital, Kuopio, Finland
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40
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Zhang B, Xu H, Chen J, Zhu X, Xue Y, Yang Y, Ao J, Hua Y, Ji M. Highly specific and label-free histological identification of microcrystals in fresh human gout tissues with stimulated Raman scattering. Theranostics 2021; 11:3074-3088. [PMID: 33537075 PMCID: PMC7847673 DOI: 10.7150/thno.53755] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/17/2020] [Indexed: 12/16/2022] Open
Abstract
Gout is a common metabolic disease with growing burden, caused by monosodium urate (MSU) microcrystal deposition. In situ and chemical-specific histological identification of MSU is crucial in the diagnosis and management of gout, yet it remains inaccessible for current histological methods. Methods: Stimulated Raman scattering (SRS) microscopy was utilized to image MSU based on its fingerprint Raman spectra. We first tested SRS for the diagnosis capability of gout and the differentiation power from pseudogout with rat models of acute gout arthritis, calcium pyrophosphate deposition disease (CPDD) and comorbidity. Then, human synovial fluid and surgical specimens (n=120) were were imaged with SRS to obtain the histopathology of MSU and collagen fibers. Finally, quantitative SRS analysis was performed in gout tissue of different physiological phases (n=120) to correlate with traditional histopathology including H&E and immunohistochemistry staining. Results: We demonstrated that SRS is capable of early diagnosis of gout, rapid detection of MSU in synovial fluid and fresh unprocessed surgical tissues, and accurate differentiation of gout from pseudogout in various pathophysiological conditions. Furthermore, quantitative SRS analysis revealed the optical characteristics of MSU deposition at different pathophysiological stages, which were found to matched well with corresponding immunofluorescence histochemistry features. Conclusion: Our work demonstrated the potential of SRS microscopy for rapid intraoperative diagnosis of gout and may facilitate future fundamental researches of MSU-based diseases.
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Marschall M, Hornemann A, Wübbeler G, Hoehl A, Rühl E, Kästner B, Elster C. Compressed FTIR spectroscopy using low-rank matrix reconstruction. OPTICS EXPRESS 2020; 28:38762-38772. [PMID: 33379438 DOI: 10.1364/oe.404959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
Fourier transform infrared (FTIR) spectroscopy is a powerful technique in analytical chemistry. Typically, spatially distributed spectra of the substance of interest are conducted simultaneously using FTIR spectrometers equipped with array detectors. Scanning-based methods such as near-field FTIR spectroscopy, on the other hand, are a promising alternative providing higher spatial resolution. However, serial recording severely limits their application due to the long acquisition times involved and the resulting stability issues. We demonstrate that it is possible to significantly reduce the measurement time of scanning methods by applying the mathematical technique of low-rank matrix reconstruction. Data from a previous pilot study of Leishmania strains are analyzed by randomly selecting 5% of the interferometer samples. The results obtained for bioanalytical fingerprinting using the proposed approach are shown to be essentially the same as those obtained from the full set of data. This finding can significantly foster the practical applicability of high-resolution serial scanning techniques in analytical chemistry and is also expected to improve other applications of FTIR spectroscopy and spectromicroscopy.
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Shi X, Chen C, Liu S, Li G. Nonvolatile, Reconfigurable and Narrowband Mid-Infrared Filter Based on Surface Lattice Resonance in Phase-Change Ge 2Sb 2Te 5. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2530. [PMID: 33339400 PMCID: PMC7766875 DOI: 10.3390/nano10122530] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 12/27/2022]
Abstract
We propose a nonvolatile, reconfigurable, and narrowband mid-infrared bandpass filter based on surface lattice resonance in phase-change material Ge2Sb2Te5. The proposed filter is composed of a two-dimensional gold nanorod array embedded in a thick Ge2Sb2Te5 film. Results show that when Ge2Sb2Te5 transits from the amorphous state to the crystalline state, the narrowband reflection spectrum of the proposed filter is tuned from 3.197 μm to 4.795 μm, covering the majority of the mid-infrared regime, the peak reflectance decreases from 72.6% to 25.8%, and the corresponding quality factor decreases from 19.6 to 10.3. We show that the spectral tuning range can be adjusted by varying the incidence angle or the lattice period. By properly designing the gold nanorod sizes, we also show that the quality factor can be greatly increased to 70 at the cost of relatively smaller peak reflection efficiencies, and that the peak reflection efficiency can be further increased to 80% at the cost of relatively smaller quality factors. We expect that this work will advance the engineering of Ge2Sb2Te5-based nonvalatile tunable surface lattice resonances and will promote their applications especially in reconfigurable narrowband filters.
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Affiliation(s)
- Xingzhe Shi
- Guangdong Provincial Key Laboratory of Nanophotonic Functional Materials and Devices, School of Information Optoelectronic Science and Engineering, South China Normal University, Guangzhou 510006, China; (X.S.); (C.C.); (S.L.)
- CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Chinese Academy of Sciences, Shenzhen Institutes of Advanced Technology, Shenzhen 518055, China
| | - Changshui Chen
- Guangdong Provincial Key Laboratory of Nanophotonic Functional Materials and Devices, School of Information Optoelectronic Science and Engineering, South China Normal University, Guangzhou 510006, China; (X.S.); (C.C.); (S.L.)
| | - Songhao Liu
- Guangdong Provincial Key Laboratory of Nanophotonic Functional Materials and Devices, School of Information Optoelectronic Science and Engineering, South China Normal University, Guangzhou 510006, China; (X.S.); (C.C.); (S.L.)
| | - Guangyuan Li
- CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Chinese Academy of Sciences, Shenzhen Institutes of Advanced Technology, Shenzhen 518055, China
- Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen 518055, China
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43
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Magnussen EA, Solheim JH, Blazhko U, Tafintseva V, Tøndel K, Liland KH, Dzurendova S, Shapaval V, Sandt C, Borondics F, Kohler A. Deep convolutional neural network recovers pure absorbance spectra from highly scatter-distorted spectra of cells. JOURNAL OF BIOPHOTONICS 2020; 13:e202000204. [PMID: 32844585 DOI: 10.1002/jbio.202000204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/21/2020] [Accepted: 08/21/2020] [Indexed: 06/11/2023]
Abstract
Infrared spectroscopy of cells and tissues is prone to Mie scattering distortions, which grossly obscure the relevant chemical signals. The state-of-the-art Mie extinction extended multiplicative signal correction (ME-EMSC) algorithm is a powerful tool for the recovery of pure absorbance spectra from highly scatter-distorted spectra. However, the algorithm is computationally expensive and the correction of large infrared imaging datasets requires weeks of computations. In this paper, we present a deep convolutional descattering autoencoder (DSAE) which was trained on a set of ME-EMSC corrected infrared spectra and which can massively reduce the computation time for scatter correction. Since the raw spectra showed large variability in chemical features, different reference spectra matching the chemical signals of the spectra were used to initialize the ME-EMSC algorithm, which is beneficial for the quality of the correction and the speed of the algorithm. One DSAE was trained on the spectra, which were corrected with different reference spectra and validated on independent test data. The DSAE outperformed the ME-EMSC correction in terms of speed, robustness, and noise levels. We confirm that the same chemical information is contained in the DSAE corrected spectra as in the spectra corrected with ME-EMSC.
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Affiliation(s)
| | | | - Uladzislau Blazhko
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Valeria Tafintseva
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Kristin Tøndel
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Kristian Hovde Liland
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Simona Dzurendova
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | | | | | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
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44
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Kviatkovsky I, Chrzanowski HM, Avery EG, Bartolomaeus H, Ramelow S. Microscopy with undetected photons in the mid-infrared. SCIENCE ADVANCES 2020; 6:eabd0264. [PMID: 33055168 PMCID: PMC10763735 DOI: 10.1126/sciadv.abd0264] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
Owing to its capacity for unique (bio)-chemical specificity, microscopy with mid-infrared (IR) illumination holds tremendous promise for a wide range of biomedical and industrial applications. The primary limitation, however, remains detection, with current mid-IR detection technology often marrying inferior technical capabilities with prohibitive costs. Here, we experimentally show how nonlinear interferometry with entangled light can provide a powerful tool for mid-IR microscopy while only requiring near-IR detection with a silicon-based camera. In this proof-of-principle implementation, we demonstrate widefield imaging over a broad wavelength range covering 3.4 to 4.3 μm and demonstrate a spatial resolution of 35 μm for images containing 650 resolved elements. Moreover, we demonstrate that our technique is suitable for acquiring microscopic images of biological tissue samples in the mid-IR. These results form a fresh perspective for potential relevance of quantum imaging techniques in the life sciences.
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Affiliation(s)
- Inna Kviatkovsky
- Institut für Physik, Humboldt-Universität zu Berlin, Berlin, Germany.
| | | | - Ellen G Avery
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Freie Universität Berlin, Berlin, Germany
| | - Hendrik Bartolomaeus
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Sven Ramelow
- Institut für Physik, Humboldt-Universität zu Berlin, Berlin, Germany
- IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany
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45
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Paterova AV, Maniam SM, Yang H, Grenci G, Krivitsky LA. Hyperspectral infrared microscopy with visible light. SCIENCE ADVANCES 2020; 6:eabd0460. [PMID: 33127685 PMCID: PMC7608807 DOI: 10.1126/sciadv.abd0460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/16/2020] [Indexed: 05/08/2023]
Abstract
Hyperspectral microscopy is an imaging technique that provides spectroscopic information with high spatial resolution. When applied in the relevant wavelength region, such as in the infrared (IR), it can reveal a rich spectral fingerprint across different regions of a sample. Challenges associated with low efficiency and high cost of IR light sources and detector arrays have limited its broad adoption. Here, we introduce a new approach to IR hyperspectral microscopy, where the IR spectral map is obtained with off-the-shelf components built for visible light. The method is based on the nonlinear interference of correlated photons generated via parametric down-conversion. In this proof-of-concept we demonstrate the chemical mapping of a patterned sample, where different areas have distinctive IR spectroscopic fingerprints. The method provides a wide field of view, fast readout, and negligible heat delivered to the sample, which opens prospects for its further development for applications in material and biological studies.
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Affiliation(s)
- Anna V Paterova
- Institute of Materials Research and Engineering (IMRE), Agency for Science Technology and Research (A*STAR), Singapore 138634, Singapore
| | - Sivakumar M Maniam
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
- National Institute of Education, Nanyang Technological University, Singapore 637616, Singapore
| | - Hongzhi Yang
- Institute of Materials Research and Engineering (IMRE), Agency for Science Technology and Research (A*STAR), Singapore 138634, Singapore
| | - Gianluca Grenci
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore.
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
| | - Leonid A Krivitsky
- Institute of Materials Research and Engineering (IMRE), Agency for Science Technology and Research (A*STAR), Singapore 138634, Singapore.
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46
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Trukhan S, Tafintseva V, Tøndel K, Großerueschkamp F, Mosig A, Kovalev V, Gerwert K, Kohler A. Grayscale representation of infrared microscopy images by extended multiplicative signal correction for registration with histological images. JOURNAL OF BIOPHOTONICS 2020; 13:e201960223. [PMID: 32352634 DOI: 10.1002/jbio.201960223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
Fourier-transform infrared (FTIR) microspectroscopy is rounding the corner to become a label-free routine method for cancer diagnosis. In order to build infrared-spectral based classifiers, infrared images need to be registered with Hematoxylin and Eosin (H&E) stained histological images. While FTIR images have a deep spectral domain with thousands of channels carrying chemical and scatter information, the H&E images have only three color channels for each pixel and carry mainly morphological information. Therefore, image representations of infrared images are needed that match the morphological information in H&E images. In this paper, we propose a novel approach for representation of FTIR images based on extended multiplicative signal correction highlighting morphological features that showed to correlate well with morphological information in H&E images. Based on the obtained representations, we developed a strategy for global-to-local image registration for FTIR images and H&E stained histological images of parallel tissue sections.
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Affiliation(s)
- Stanislau Trukhan
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
- Department of Biomedical Image Analysis, United Institute of Informatics Problems, Minsk, Belarus
| | - Valeria Tafintseva
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Kristin Tøndel
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Frederik Großerueschkamp
- Departament of Biophysics, Ruhr University Bochum, Bochum, Germany
- Center for Protein Diagnostics (ProDi), Ruhr University Bochum, Bochum, Germany
| | - Axel Mosig
- Departament of Biophysics, Ruhr University Bochum, Bochum, Germany
- Center for Protein Diagnostics (ProDi), Ruhr University Bochum, Bochum, Germany
| | - Vassili Kovalev
- Department of Biomedical Image Analysis, United Institute of Informatics Problems, Minsk, Belarus
| | - Klaus Gerwert
- Departament of Biophysics, Ruhr University Bochum, Bochum, Germany
- Center for Protein Diagnostics (ProDi), Ruhr University Bochum, Bochum, Germany
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
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47
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Knez D, Hanninen AM, Prince RC, Potma EO, Fishman DA. Infrared chemical imaging through non-degenerate two-photon absorption in silicon-based cameras. LIGHT, SCIENCE & APPLICATIONS 2020; 9:125. [PMID: 32704358 PMCID: PMC7371741 DOI: 10.1038/s41377-020-00369-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/30/2020] [Accepted: 07/08/2020] [Indexed: 05/08/2023]
Abstract
Chemical imaging based on mid-infrared (MIR) spectroscopic contrast is an important technique with a myriad of applications, including biomedical imaging and environmental monitoring. Current MIR cameras, however, lack performance and are much less affordable than mature Si-based devices, which operate in the visible and near-infrared regions. Here, we demonstrate fast MIR chemical imaging through non-degenerate two-photon absorption (NTA) in a standard Si-based charge-coupled device (CCD). We show that wide-field MIR images can be obtained at 100 ms exposure times using picosecond pulse energies of only a few femtojoules per pixel through NTA directly on the CCD chip. Because this on-chip approach does not rely on phase matching, it is alignment-free and does not necessitate complex postprocessing of the images. We emphasize the utility of this technique through chemically selective MIR imaging of polymers and biological samples, including MIR videos of moving targets, physical processes and live nematodes.
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Affiliation(s)
- David Knez
- Department of Chemistry, University of California, Irvine, CA 92697 USA
| | - Adam M. Hanninen
- Department of Chemistry, University of California, Irvine, CA 92697 USA
| | - Richard C. Prince
- Department of Biomedical Engineering, University of California, Irvine, CA 92697 USA
| | - Eric O. Potma
- Department of Chemistry, University of California, Irvine, CA 92697 USA
- Department of Biomedical Engineering, University of California, Irvine, CA 92697 USA
| | - Dmitry A. Fishman
- Department of Chemistry, University of California, Irvine, CA 92697 USA
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48
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Kenkel S, Mittal S, Bhargava R. Closed-loop atomic force microscopy-infrared spectroscopic imaging for nanoscale molecular characterization. Nat Commun 2020; 11:3225. [PMID: 32591515 PMCID: PMC7320136 DOI: 10.1038/s41467-020-17043-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 05/28/2020] [Indexed: 01/15/2023] Open
Abstract
Atomic force microscopy-infrared (AFM-IR) spectroscopic imaging offers non-perturbative, molecular contrast for nanoscale characterization. The need to mitigate measurement artifacts and enhance sensitivity, however, requires narrowly-defined and strict sample preparation protocols. This limits reliable and facile characterization; for example, when using common substrates such as Silicon or glass. Here, we demonstrate a closed-loop (CL) piezo controller design for responsivity-corrected AFM-IR imaging. Instead of the usual mode of recording cantilever deflection driven by sample expansion, the principle of our approach is to maintain a zero amplitude harmonic cantilever deflection by CL control of a subsample piezo. We show that the piezo voltage used to maintain a null deflection provides a reliable measure of the local IR absorption with significantly reduced noise. A complete analytical description of the CL operation and characterization of the controller for achieving robust performance are presented. Accurate measurement of IR absorption of nanothin PMMA films on glass and Silicon validates the robust capability of CL AFM-IR in routine mapping of nanoscale molecular information.
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Affiliation(s)
- Seth Kenkel
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana Champaign, Urbana, IL, 61801, USA.,Department of Mechanical Engineering, University of Illinois at Urbana Champaign, Urbana, IL, 61801, USA
| | - Shachi Mittal
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana Champaign, Urbana, IL, 61801, USA
| | - Rohit Bhargava
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana Champaign, Urbana, IL, 61801, USA. .,Department of Mechanical Engineering, University of Illinois at Urbana Champaign, Urbana, IL, 61801, USA. .,Cancer Center at Illinois and the Departments Chemical and Biomolecular Engineering, Bioengineering, Electrical and Computer Engineering, and Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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49
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Fellner L, Kraus M, Gebert F, Walter A, Duschek F. Multispectral LIF-Based Standoff Detection System for the Classification of CBE Hazards by Spectral and Temporal Features. SENSORS 2020; 20:s20092524. [PMID: 32365598 PMCID: PMC7249005 DOI: 10.3390/s20092524] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/20/2020] [Accepted: 04/27/2020] [Indexed: 12/16/2022]
Abstract
Laser-induced fluorescence (LIF) is a well-established technique for monitoring chemical processes and for the standoff detection of biological substances because of its simple technical implementation and high sensitivity. Frequently, standoff LIF spectra from large molecules and bio-agents are only slightly structured and a gain of deeper information, such as classification, let alone identification, might become challenging. Improving the LIF technology by recording spectral and additionally time-resolved fluorescence emission, a significant gain of information can be achieved. This work presents results from a LIF based detection system and an analysis of the influence of time-resolved data on the classification accuracy. A multi-wavelength sub-nanosecond laser source is used to acquire spectral and time-resolved data from a standoff distance of 3.5 m. The data set contains data from seven different bacterial species and six types of oil. Classification is performed with a decision tree algorithm separately for spectral data, time-resolved data and the combination of both. The first findings show a valuable contribution of time-resolved fluorescence data to the classification of the investigated chemical and biological agents to their species level. Temporal and spectral data have been proven as partly complementary. The classification accuracy is increased from 86% for spectral data only to more than 92%.
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50
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Lind AJ, Kowligy A, Timmers H, Cruz FC, Nader N, Silfies MC, Allison TK, Diddams SA. Mid-Infrared Frequency Comb Generation and Spectroscopy with Few-Cycle Pulses and χ^{(2)} Nonlinear Optics. PHYSICAL REVIEW LETTERS 2020; 124:133904. [PMID: 32302192 DOI: 10.1103/physrevlett.124.133904] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 01/22/2020] [Accepted: 03/09/2020] [Indexed: 06/11/2023]
Abstract
The mid-infrared atmospheric window of 3-5.5 μm holds valuable information regarding molecular composition and function for fundamental and applied spectroscopy. Using a robust, mode-locked fiber-laser source of <11 fs pulses in the near infrared, we explore quadratic (χ^{(2)}) nonlinear optical processes leading to frequency comb generation across this entire mid-infrared atmospheric window. With experiments and modeling, we demonstrate intrapulse difference frequency generation that yields few-cycle mid-infrared pulses in a single pass through periodically poled lithium niobate. Harmonic and cascaded χ^{(2)} nonlinearities further provide direct access to the carrier-envelope offset frequency of the near infrared driving pulse train. The high frequency stability of the mid-infrared frequency comb is exploited for spectroscopy of acetone and carbonyl sulfide with simultaneous bandwidths exceeding 11 THz and with spectral resolution as high as 0.003 cm^{-1}. The combination of low noise and broad spectral coverage enables detection of trace gases with concentrations in the part-per-billion range.
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Affiliation(s)
- Alexander J Lind
- Time and Frequency Division, National Institute of Standards and Technology, 325 Broadway, Boulder, Colorado 80305, USA
- Department of Physics, University of Colorado, 2000 Colorado Avenue, Boulder, Colorado 80309, USA
| | - Abijith Kowligy
- Time and Frequency Division, National Institute of Standards and Technology, 325 Broadway, Boulder, Colorado 80305, USA
- Department of Physics, University of Colorado, 2000 Colorado Avenue, Boulder, Colorado 80309, USA
| | - Henry Timmers
- Time and Frequency Division, National Institute of Standards and Technology, 325 Broadway, Boulder, Colorado 80305, USA
| | - Flavio C Cruz
- Time and Frequency Division, National Institute of Standards and Technology, 325 Broadway, Boulder, Colorado 80305, USA
- Instituto de Fisica Gleb Wataghin, Universidade Estadual de Campinas, Campinas, SP 13083-859, Brazil
| | - Nima Nader
- Applied Physics Division, National Institute of Standards and Technology, 325 Broadway, Boulder, Colorado 80305, USA
| | - Myles C Silfies
- Department of Chemistry and Physics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Thomas K Allison
- Department of Chemistry and Physics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Scott A Diddams
- Time and Frequency Division, National Institute of Standards and Technology, 325 Broadway, Boulder, Colorado 80305, USA
- Department of Physics, University of Colorado, 2000 Colorado Avenue, Boulder, Colorado 80309, USA
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