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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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2
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Laurino A, Franceschini A, Pesce L, Cinci L, Montalbano A, Mazzamuto G, Sancataldo G, Nesi G, Costantini I, Silvestri L, Pavone FS. A Guide to Perform 3D Histology of Biological Tissues with Fluorescence Microscopy. Int J Mol Sci 2023; 24:ijms24076747. [PMID: 37047724 PMCID: PMC10094801 DOI: 10.3390/ijms24076747] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/09/2023] Open
Abstract
The analysis of histological alterations in all types of tissue is of primary importance in pathology for highly accurate and robust diagnosis. Recent advances in tissue clearing and fluorescence microscopy made the study of the anatomy of biological tissue possible in three dimensions. The combination of these techniques with classical hematoxylin and eosin (H&E) staining has led to the birth of three-dimensional (3D) histology. Here, we present an overview of the state-of-the-art methods, highlighting the optimal combinations of different clearing methods and advanced fluorescence microscopy techniques for the investigation of all types of biological tissues. We employed fluorescence nuclear and eosin Y staining that enabled us to obtain hematoxylin and eosin pseudo-coloring comparable with the gold standard H&E analysis. The computational reconstructions obtained with 3D optical imaging can be analyzed by a pathologist without any specific training in volumetric microscopy, paving the way for new biomedical applications in clinical pathology.
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Affiliation(s)
- Annunziatina Laurino
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, 50019 Florence, Italy
| | - Alessandra Franceschini
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, 50019 Florence, Italy
| | - Luca Pesce
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, 50019 Florence, Italy
| | - Lorenzo Cinci
- Department of Experimental and Clinical Biomedical Sciences, Radiodiagnostic Unit n. 2, Careggi University Hospital, 50134 Florence, Italy
| | - Alberto Montalbano
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- Department of Neurofarba Section of Pharmacology and Toxicology, University of Florence, 50139 Florence, Italy
| | - Giacomo Mazzamuto
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, 50019 Florence, Italy
- National Research Council—National Institute of Optics (CNR-INO), 50125 Sesto Fiorentino, Italy
| | - Giuseppe Sancataldo
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, 50019 Florence, Italy
| | - Gabriella Nesi
- Department of Health Sciences, University of Florence, 50139 Florence, Italy
| | - Irene Costantini
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- National Research Council—National Institute of Optics (CNR-INO), 50125 Sesto Fiorentino, Italy
- Department of Biology, University of Florence, 50019 Florence, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, 50019 Florence, Italy
- National Research Council—National Institute of Optics (CNR-INO), 50125 Sesto Fiorentino, Italy
| | - Francesco Saverio Pavone
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, 50019 Florence, Italy
- National Research Council—National Institute of Optics (CNR-INO), 50125 Sesto Fiorentino, Italy
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Touil M, Idlahcen S, Becheker R, Lebrun D, Rozé C, Hideur A, Godin T. Acousto-optically driven lensless single-shot ultrafast optical imaging. LIGHT, SCIENCE & APPLICATIONS 2022; 11:66. [PMID: 35318313 PMCID: PMC8940908 DOI: 10.1038/s41377-022-00759-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/14/2022] [Accepted: 03/01/2022] [Indexed: 05/02/2023]
Abstract
Driven by many applications in a wide span of scientific fields, a myriad of advanced ultrafast imaging techniques have emerged in the last decade, featuring record-high imaging speeds above a trillion-frame-per-second with long sequence depths. Although bringing remarkable insights into various ultrafast phenomena, their application out of a laboratory environment is however limited in most cases, either by the cost, complexity of the operation or by heavy data processing. We then report a versatile single-shot imaging technique combining sequentially timed all-optical mapping photography (STAMP) with acousto-optics programmable dispersive filtering (AOPDF) and digital in-line holography (DIH). On the one hand, a high degree of simplicity is reached through the AOPDF, which enables full control over the acquisition parameters via an electrically driven phase and amplitude spectro-temporal tailoring of the imaging pulses. Here, contrary to most single-shot techniques, the frame rate, exposure time, and frame intensities can be independently adjusted in a wide range of pulse durations and chirp values without resorting to complex shaping stages, making the system remarkably agile and user-friendly. On the other hand, the use of DIH, which does not require any reference beam, allows to achieve an even higher technical simplicity by allowing its lensless operation but also for reconstructing the object on a wide depth of field, contrary to classical techniques that only provide images in a single plane. The imaging speed of the system as well as its flexibility are demonstrated by visualizing ultrashort events on both the picosecond and nanosecond timescales. The virtues and limitations as well as the potential improvements of this on-demand ultrafast imaging method are critically discussed.
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Affiliation(s)
- Mohamed Touil
- CORIA, CNRS UMR6614-Université de Rouen Normandie-INSA Rouen, 76800, Saint Etienne du Rouvray, France
| | - Saïd Idlahcen
- CORIA, CNRS UMR6614-Université de Rouen Normandie-INSA Rouen, 76800, Saint Etienne du Rouvray, France
| | - Rezki Becheker
- CORIA, CNRS UMR6614-Université de Rouen Normandie-INSA Rouen, 76800, Saint Etienne du Rouvray, France
| | - Denis Lebrun
- CORIA, CNRS UMR6614-Université de Rouen Normandie-INSA Rouen, 76800, Saint Etienne du Rouvray, France
| | - Claude Rozé
- CORIA, CNRS UMR6614-Université de Rouen Normandie-INSA Rouen, 76800, Saint Etienne du Rouvray, France
| | - Ammar Hideur
- CORIA, CNRS UMR6614-Université de Rouen Normandie-INSA Rouen, 76800, Saint Etienne du Rouvray, France
| | - Thomas Godin
- CORIA, CNRS UMR6614-Université de Rouen Normandie-INSA Rouen, 76800, Saint Etienne du Rouvray, France.
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Würthwein T, Wallmeier K, Brinkmann M, Hellwig T, Lüpken NM, Lemberger NS, Fallnich C. Multi-color stimulated Raman scattering with a frame-to-frame wavelength-tunable fiber-based light source. BIOMEDICAL OPTICS EXPRESS 2021; 12:6228-6236. [PMID: 34745731 PMCID: PMC8547978 DOI: 10.1364/boe.436299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
We present multi-color imaging by stimulated Raman scattering (SRS) enabled by an ultrafast fiber-based light source with integrated amplitude modulation and frame-to-frame wavelength tuning. With a relative intensity noise level of -153.7 dBc/Hz at 20.25 MHz the light source is well suited for SRS imaging and outperforms other fiber-based light source concepts for SRS imaging. The light source is tunable in under 5 ms per arbitrary wavelength step between 700 cm-1 and 3200 cm-1, which allows for addressing Raman resonances from the fingerprint to the CH-stretch region. Moreover, the compact and environmentally stable system is predestined for fast multi-color assessments of medical or rapidly evolving samples with high chemical specificity, paving the way for diagnostics and sensing outside of specialized laser laboratories.
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Affiliation(s)
- Thomas Würthwein
- Institute of Applied Physics, University of Münster, Corrensstraße 2, 48149 Münster, Germany
| | - Kristin Wallmeier
- Institute of Applied Physics, University of Münster, Corrensstraße 2, 48149 Münster, Germany
| | | | - Tim Hellwig
- Refined Laser Systems GmbH, Mendelstraße 11, 48149 Münster, Germany
| | - Niklas M. Lüpken
- Institute of Applied Physics, University of Münster, Corrensstraße 2, 48149 Münster, Germany
| | - Nick S. Lemberger
- Institute of Applied Physics, University of Münster, Corrensstraße 2, 48149 Münster, Germany
| | - Carsten Fallnich
- Institute of Applied Physics, University of Münster, Corrensstraße 2, 48149 Münster, Germany
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, Enschede 7500 AE, The Netherlands
- Cells in Motion Interfaculty Centre, University of Münster, Münster, Germany
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Prince RC, Potma EO. Coherent Raman scattering microscopy: capable solution in search of a larger audience. JOURNAL OF BIOMEDICAL OPTICS 2021; 26:JBO-210102-PER. [PMID: 34085436 PMCID: PMC8174578 DOI: 10.1117/1.jbo.26.6.060601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/20/2021] [Indexed: 05/18/2023]
Abstract
SIGNIFICANCE Coherent Raman scattering (CRS) microscopy is an optical imaging technique with capabilities that could benefit a broad range of biomedical research studies. AIM We reflect on the birth, rapid rise, and inescapable growing pains of the technique and look back on nearly four decades of developments to examine where the CRS imaging approach might be headed in the next decade to come. APPROACH We provide a brief historical account of CRS microscopy, followed by a discussion of the challenges to disseminate the technique to a larger audience. We then highlight recent progress in expanding the capabilities of the CRS microscope and assess its current appeal as a practical imaging tool. RESULTS New developments in Raman tagging have improved the specificity and sensitivity of the CRS technique. In addition, technical advances have led to CRS microscopes that can capture hyperspectral data cubes at practical acquisition times. These improvements have broadened the application space of the technique. CONCLUSION The technical performance of the CRS microscope has improved dramatically since its inception, but these advances have not yet translated into a substantial user base beyond a strong core of enthusiasts. Nonetheless, new developments are poised to move the unique capabilities of the technique into the hands of more users.
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Affiliation(s)
- Richard C. Prince
- University of California, Irvine, Department of Biomedical Engineering, Irvine, California, United States
| | - Eric O. Potma
- University of California, Irvine, Department of Biomedical Engineering, Irvine, California, United States
- University of California, Irvine, Department of Chemistry, Irvine, California, United States
- Address all correspondence to Eric O. Potma,
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Shi L, Fung AA, Zhou A. Advances in stimulated Raman scattering imaging for tissues and animals. Quant Imaging Med Surg 2021; 11:1078-1101. [PMID: 33654679 PMCID: PMC7829158 DOI: 10.21037/qims-20-712] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022]
Abstract
Stimulated Raman scattering (SRS) microscopy has emerged in the last decade as a powerful optical imaging technology with high chemical selectivity, speed, and subcellular resolution. Since the invention of SRS microscopy, it has been extensively employed in life science to study composition, structure, metabolism, development, and disease in biological systems. Applications of SRS in research and the clinic have generated new insights in many fields including neurobiology, tumor biology, developmental biology, metabolomics, pharmacokinetics, and more. Herein we review the advances and applications of SRS microscopy imaging in tissues and animals, as well as envision future applications and development of SRS imaging in life science and medicine.
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Affiliation(s)
- Lingyan Shi
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Anthony A Fung
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Andy Zhou
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
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Lee M, Herrington CS, Ravindra M, Sepp K, Davies A, Hulme AN, Brunton VG. Recent advances in the use of stimulated Raman scattering in histopathology. Analyst 2021; 146:789-802. [PMID: 33393954 DOI: 10.1039/d0an01972k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Stimulated Raman histopathology (SRH) utilises the intrinsic vibrational properties of lipids, proteins and nucleic acids to generate contrast providing rapid image acquisition that allows visualisation of histopathological features. It is currently being trialled in the intraoperative setting, where the ability to image unprocessed samples rapidly and with high resolution offers several potential advantages over the use of conventional haematoxylin and eosin stained images. Here we review recent advances in the field including new updates in instrumentation and computer aided diagnosis. We also discuss how other non-linear modalities can be used to provide additional diagnostic contrast which together pave the way for enhanced histopathology and open up possibilities for in vivo pathology.
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Affiliation(s)
- Martin Lee
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XR, UK.
| | - C Simon Herrington
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XR, UK.
| | - Manasa Ravindra
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Kristel Sepp
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XR, UK. and EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Amy Davies
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XR, UK.
| | - Alison N Hulme
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Valerie G Brunton
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XR, UK.
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Li Y, Shen B, Li S, Zhao Y, Qu J, Liu L. Review of Stimulated Raman Scattering Microscopy Techniques and Applications in the Biosciences. Adv Biol (Weinh) 2020; 5:e2000184. [PMID: 33724734 DOI: 10.1002/adbi.202000184] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/17/2020] [Indexed: 01/10/2023]
Abstract
Stimulated Raman scattering (SRS) microscopy is a nonlinear optical imaging method for visualizing chemical content based on molecular vibrational bonds. Featuring high speed, high resolution, high sensitivity, high accuracy, and 3D sectioning, SRS microscopy has made tremendous progress toward biochemical information acquisition, cellular function investigation, and label-free medical diagnosis in the biosciences. In this review, the principle of SRS, system design, and data analysis are introduced, and the current innovations of the SRS system are reviewed. In particular, combined with various bio-orthogonal Raman tags, the applications of SRS microscopy in cell metabolism, tumor diagnosis, neuroscience, drug tracking, and microbial detection are briefly examined. The future prospects for SRS microscopy are also shared.
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Affiliation(s)
- Yanping Li
- Key Laboratory of Optoelectronic Devices and Systems of Guangdong Province and Ministry of Education, College of Physics and Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Avenue, Shenzhen, 518060, China
| | - Binglin Shen
- Key Laboratory of Optoelectronic Devices and Systems of Guangdong Province and Ministry of Education, College of Physics and Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Avenue, Shenzhen, 518060, China
| | - Shaowei Li
- Key Laboratory of Optoelectronic Devices and Systems of Guangdong Province and Ministry of Education, College of Physics and Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Avenue, Shenzhen, 518060, China
| | - Yihua Zhao
- Key Laboratory of Optoelectronic Devices and Systems of Guangdong Province and Ministry of Education, College of Physics and Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Avenue, Shenzhen, 518060, China
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Guangdong Province and Ministry of Education, College of Physics and Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Avenue, Shenzhen, 518060, China
| | - Liwei Liu
- Key Laboratory of Optoelectronic Devices and Systems of Guangdong Province and Ministry of Education, College of Physics and Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Avenue, Shenzhen, 518060, China
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