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Aghigh A, Preston SEJ, Jargot G, Ibrahim H, Del Rincón SV, Légaré F. Nonlinear microscopy and deep learning classification for mammary gland microenvironment studies. BIOMEDICAL OPTICS EXPRESS 2023; 14:2181-2195. [PMID: 37206132 PMCID: PMC10191635 DOI: 10.1364/boe.487087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/26/2023] [Accepted: 03/29/2023] [Indexed: 05/21/2023]
Abstract
Tumors, their microenvironment, and the mechanisms by which collagen morphology changes throughout cancer progression have recently been a topic of interest. Second harmonic generation (SHG) and polarization second harmonic (P-SHG) microscopy are label-free, hallmark methods that can highlight this alteration in the extracellular matrix (ECM). This article uses automated sample scanning SHG and P-SHG microscopy to investigate ECM deposition associated with tumors residing in the mammary gland. We show two different analysis approaches using the acquired images to distinguish collagen fibrillar orientation changes in the ECM. Lastly, we apply a supervised deep-learning model to classify naïve and tumor-bearing mammary gland SHG images. We benchmark the trained model using transfer learning with the well-known MobileNetV2 architecture. By fine-tuning the different parameters of these models, we show a trained deep-learning model that suits such a small dataset with 73% accuracy.
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Affiliation(s)
- Arash Aghigh
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, Varennes, Québec, Canada
| | - Samuel E. J. Preston
- Department of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, Québec, Canada
- Gerald Bronfman Department of Oncology, Segal Cancer Centre, Lady Davis Institute and Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Gaëtan Jargot
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, Varennes, Québec, Canada
| | - Heide Ibrahim
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, Varennes, Québec, Canada
| | - Sonia V Del Rincón
- Department of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, Québec, Canada
- Gerald Bronfman Department of Oncology, Segal Cancer Centre, Lady Davis Institute and Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - François Légaré
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, Varennes, Québec, Canada
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Al-Rekabi Z, Dondi C, Faruqui N, Siddiqui NS, Elowsson L, Rissler J, Kåredal M, Mudway I, Larsson-Callerfelt AK, Shaw M. Uncovering the cytotoxic effects of air pollution with multi-modal imaging of in vitro respiratory models. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221426. [PMID: 37063998 PMCID: PMC10090883 DOI: 10.1098/rsos.221426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Annually, an estimated seven million deaths are linked to exposure to airborne pollutants. Despite extensive epidemiological evidence supporting clear associations between poor air quality and a range of short- and long-term health effects, there are considerable gaps in our understanding of the specific mechanisms by which pollutant exposure induces adverse biological responses at the cellular and tissue levels. The development of more complex, predictive, in vitro respiratory models, including two- and three-dimensional cell cultures, spheroids, organoids and tissue cultures, along with more realistic aerosol exposure systems, offers new opportunities to investigate the cytotoxic effects of airborne particulates under controlled laboratory conditions. Parallel advances in high-resolution microscopy have resulted in a range of in vitro imaging tools capable of visualizing and analysing biological systems across unprecedented scales of length, time and complexity. This article considers state-of-the-art in vitro respiratory models and aerosol exposure systems and how they can be interrogated using high-resolution microscopy techniques to investigate cell-pollutant interactions, from the uptake and trafficking of particles to structural and functional modification of subcellular organelles and cells. These data can provide a mechanistic basis from which to advance our understanding of the health effects of airborne particulate pollution and develop improved mitigation measures.
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Affiliation(s)
- Zeinab Al-Rekabi
- Department of Chemical and Biological Sciences, National Physical Laboratory, Teddington, UK
| | - Camilla Dondi
- Department of Chemical and Biological Sciences, National Physical Laboratory, Teddington, UK
| | - Nilofar Faruqui
- Department of Chemical and Biological Sciences, National Physical Laboratory, Teddington, UK
| | - Nazia S. Siddiqui
- Faculty of Medical Sciences, University College London, London, UK
- Kingston Hospital NHS Foundation Trust, Kingston upon Thames, UK
| | - Linda Elowsson
- Lung Biology, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Jenny Rissler
- Bioeconomy and Health, RISE Research Institutes of Sweden, Lund, Sweden
- Ergonomics and Aerosol Technology, Lund University, Lund, Sweden
| | - Monica Kåredal
- Occupational and Environmental Medicine, Lund University, Lund, Sweden
| | - Ian Mudway
- MRC Centre for Environment and Health, Imperial College London, London, UK
- National Institute of Health Protection Research Unit in Environmental Exposures and Health, London, UK
- Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK
| | | | - Michael Shaw
- Department of Chemical and Biological Sciences, National Physical Laboratory, Teddington, UK
- Department of Computer Science, University College London, London, UK
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Meah A, Boodram V, Bucinca-Cupallari F, Lim H. Axonal architecture of the mouse inner retina revealed by second harmonic generation. PNAS NEXUS 2022; 1:pgac160. [PMID: 36106183 PMCID: PMC9463061 DOI: 10.1093/pnasnexus/pgac160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/11/2022] [Indexed: 01/29/2023]
Abstract
We describe a novel method for visualizing the network of axons in the unlabeled fresh wholemount retina. The intrinsic radiation of second harmonic generation (SHG) was utilized to visualize single axons of all major retinal neurons, i.e., photoreceptors, horizontal cells, bipolar cells, amacrine cells, and the retinal ganglion cells. The cell types of SHG+ axons were determined using transgenic GFP/YFP mice. New findings were obtained with retinal SHG imaging: Müller cells do not maintain uniformly polarized microtubules in the processes; SHG+ axons of bipolar cells terminate in the inner plexiform layer (IPL) in a subtype-specific manner; a subset of amacrine cells, presumably the axon-bearing types, emits SHG; and the axon-like neurites of amacrine cells provide a cytoskeletal scaffolding for the IPL stratification. To demonstrate the utility, retinal SHG imaging was applied to testing whether the inner retina is preserved in glaucoma, using DBA/2 mice as a model of glaucoma and DBA/2-Gpnmb+ as the nonglaucomatous control. It was found that the morphology of the inner retina was largely intact in glaucoma and the presynaptic compartments to the retinal ganglion cells were uncompromised. It proves retinal SHG imaging as a promising technology for studying the physiological and diseased retinas in 3D.
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Affiliation(s)
- Arafat Meah
- Department of Physics and Astronomy, Hunter College, New York, NY 10065, USA
| | - Vinessia Boodram
- Department of Physics and Astronomy, Hunter College, New York, NY 10065, USA
| | - Festa Bucinca-Cupallari
- Department of Physics and Astronomy, Hunter College, New York, NY 10065, USA,The Graduate Centre of the City University of New York, New York, NY 10065, USA
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PSHG-TISS: A collection of polarization-resolved second harmonic generation microscopy images of fixed tissues. Sci Data 2022; 9:376. [PMID: 35780180 PMCID: PMC9250519 DOI: 10.1038/s41597-022-01477-1] [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: 01/14/2022] [Accepted: 06/13/2022] [Indexed: 11/23/2022] Open
Abstract
Second harmonic generation (SHG) microscopy is acknowledged as an established imaging technique capable to provide information on the collagen architecture in tissues that is highly valuable for the diagnostics of various pathologies. The polarization-resolved extension of SHG (PSHG) microscopy, together with associated image processing methods, retrieves extensive image sets under different input polarization settings, which are not fully exploited in clinical settings. To facilitate this, we introduce PSHG-TISS, a collection of PSHG images, accompanied by additional computationally generated images which can be used to complement the subjective qualitative analysis of SHG images. These latter have been calculated using the single-axis molecule model for collagen and provide 2D representations of different specific PSHG parameters known to account for the collagen structure and distribution. PSHG-TISS can aid refining existing PSHG image analysis methods, while also supporting the development of novel image processing and analysis methods capable to extract meaningful quantitative data from the raw PSHG image sets. PSHG-TISS can facilitate the breadth and widespread of PSHG applications in tissue analysis and diagnostics. Measurement(s) | Type I Collagen | Technology Type(s) | multi-photon laser scanning microscopy | Factor Type(s) | second order susceptibility tensor elements | Sample Characteristic - Organism | Homo sapiens | Sample Characteristic - Environment | laboratory environment | Sample Characteristic - Location | Romania |
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Hilzenrat G, Gill ET, McArthur SL. Imaging approaches for monitoring three-dimensional cell and tissue culture systems. JOURNAL OF BIOPHOTONICS 2022; 15:e202100380. [PMID: 35357086 DOI: 10.1002/jbio.202100380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
The past decade has seen an increasing demand for more complex, reproducible and physiologically relevant tissue cultures that can mimic the structural and biological features of living tissues. Monitoring the viability, development and responses of such tissues in real-time are challenging due to the complexities of cell culture physical characteristics and the environments in which these cultures need to be maintained in. Significant developments in optics, such as optical manipulation, improved detection and data analysis, have made optical imaging a preferred choice for many three-dimensional (3D) cell culture monitoring applications. The aim of this review is to discuss the challenges associated with imaging and monitoring 3D tissues and cell culture, and highlight topical label-free imaging tools that enable bioengineers and biophysicists to non-invasively characterise engineered living tissues.
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Affiliation(s)
- Geva Hilzenrat
- Bioengineering Engineering Group, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, Victoria, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Clayton, Victoria, Australia
| | - Emma T Gill
- Bioengineering Engineering Group, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, Victoria, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Clayton, Victoria, Australia
| | - Sally L McArthur
- Bioengineering Engineering Group, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, Victoria, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Clayton, Victoria, Australia
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Liu K, Li J, Raghunathan R, Zhao H, Li X, Wong STC. The Progress of Label-Free Optical Imaging in Alzheimer's Disease Screening and Diagnosis. Front Aging Neurosci 2021; 13:699024. [PMID: 34366828 PMCID: PMC8341907 DOI: 10.3389/fnagi.2021.699024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/02/2021] [Indexed: 01/13/2023] Open
Abstract
As the major neurodegenerative disease of dementia, Alzheimer's disease (AD) has caused an enormous social and economic burden on society. Currently, AD has neither clear pathogenesis nor effective treatments. Positron emission tomography (PET) and magnetic resonance imaging (MRI) have been verified as potential tools for diagnosing and monitoring Alzheimer's disease. However, the high costs, low spatial resolution, and long acquisition time limit their broad clinical utilization. The gold standard of AD diagnosis routinely used in research is imaging AD biomarkers with dyes or other reagents, which are unsuitable for in vivo studies owing to their potential toxicity and prolonged and costly process of the U.S. Food and Drug Administration (FDA) approval for human use. Furthermore, these exogenous reagents might bring unwarranted interference to mechanistic studies, causing unreliable results. Several label-free optical imaging techniques, such as infrared spectroscopic imaging (IRSI), Raman spectroscopic imaging (RSI), optical coherence tomography (OCT), autofluorescence imaging (AFI), optical harmonic generation imaging (OHGI), etc., have been developed to circumvent this issue and made it possible to offer an accurate and detailed analysis of AD biomarkers. In this review, we present the emerging label-free optical imaging techniques and their applications in AD, along with their potential and challenges in AD diagnosis.
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Affiliation(s)
- Kai Liu
- Translational Biophotonics Laboratory, Systems Medicine and Bioengineering Department, Houston Methodist Cancer Center, Houston, TX, United States
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Jiasong Li
- Translational Biophotonics Laboratory, Systems Medicine and Bioengineering Department, Houston Methodist Cancer Center, Houston, TX, United States
- T. T. and W. F. Chao Center for BRAIN, Houston Methodist Hospital, Houston, TX, United States
| | - Raksha Raghunathan
- Translational Biophotonics Laboratory, Systems Medicine and Bioengineering Department, Houston Methodist Cancer Center, Houston, TX, United States
- T. T. and W. F. Chao Center for BRAIN, Houston Methodist Hospital, Houston, TX, United States
| | - Hong Zhao
- Translational Biophotonics Laboratory, Systems Medicine and Bioengineering Department, Houston Methodist Cancer Center, Houston, TX, United States
| | - Xuping Li
- T. T. and W. F. Chao Center for BRAIN, Houston Methodist Hospital, Houston, TX, United States
| | - Stephen T. C. Wong
- Translational Biophotonics Laboratory, Systems Medicine and Bioengineering Department, Houston Methodist Cancer Center, Houston, TX, United States
- T. T. and W. F. Chao Center for BRAIN, Houston Methodist Hospital, Houston, TX, United States
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May MA, Barré N, Kummer KK, Kress M, Ritsch-Marte M, Jesacher A. Fast holographic scattering compensation for deep tissue biological imaging. Nat Commun 2021; 12:4340. [PMID: 34267207 PMCID: PMC8282637 DOI: 10.1038/s41467-021-24666-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/11/2021] [Indexed: 12/03/2022] Open
Abstract
Scattering in biological tissues is a major barrier for in vivo optical imaging of all but the most superficial structures. Progress toward overcoming the distortions caused by scattering in turbid media has been made by shaping the excitation wavefront to redirect power into a single point in the imaging plane. However, fast, non-invasive determination of the required wavefront compensation remains challenging. Here, we introduce a quickly converging algorithm for non-invasive scattering compensation, termed DASH, in which holographic phase stepping interferometry enables new phase information to be updated after each measurement. This leads to rapid improvement of the wavefront correction, forming a focus after just one measurement iteration and achieving an order of magnitude higher signal enhancement at this stage than the previous state-of-the-art. Using DASH, we demonstrate two-photon fluorescence imaging of microglia cells in highly turbid mouse hippocampal tissue down to a depth of 530 μm.
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Affiliation(s)
- Molly A May
- Institute of Biomedical Physics, Medical University of Innsbruck, Innsbruck, Austria.
| | - Nicolas Barré
- Institute of Biomedical Physics, Medical University of Innsbruck, Innsbruck, Austria
| | - Kai K Kummer
- Institute of Physiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Michaela Kress
- Institute of Physiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Monika Ritsch-Marte
- Institute of Biomedical Physics, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexander Jesacher
- Institute of Biomedical Physics, Medical University of Innsbruck, Innsbruck, Austria
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An Optical Frequency Domain Angle Measurement Method Based on Second Harmonic Generation. SENSORS 2021; 21:s21020670. [PMID: 33477976 PMCID: PMC7835813 DOI: 10.3390/s21020670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/15/2021] [Accepted: 01/17/2021] [Indexed: 11/22/2022]
Abstract
This paper proposes a new optical angle measurement method in the optical frequency domain based on second harmonic generation with a mode-locked femtosecond laser source by making use of the unique characteristic of the high peak power and wide spectral range of the femtosecond laser pulses. To get a wide measurable range of angle measurement, a theoretical calculation for several nonlinear optical crystals is performed. As a result, LiNbO3 crystal is employed in the proposed method. In the experiment, the validity of the use of a parabolic mirror is also demonstrated, where the chromatic aberration of the focusing beam caused the localization of second harmonic generation in our previous research. Moreover, an experimental demonstration is also carried out for the proposed angle measurement method. The measurable range of 10,000 arc-seconds is achieved.
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