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Pham DL, Gillette AA, Riendeau J, Wiech K, Guzman EC, Datta R, Skala MC. Perspectives on label-free microscopy of heterogeneous and dynamic biological systems. JOURNAL OF BIOMEDICAL OPTICS 2025; 29:S22702. [PMID: 38434231 PMCID: PMC10903072 DOI: 10.1117/1.jbo.29.s2.s22702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/22/2023] [Accepted: 12/14/2023] [Indexed: 03/05/2024]
Abstract
Significance Advancements in label-free microscopy could provide real-time, non-invasive imaging with unique sources of contrast and automated standardized analysis to characterize heterogeneous and dynamic biological processes. These tools would overcome challenges with widely used methods that are destructive (e.g., histology, flow cytometry) or lack cellular resolution (e.g., plate-based assays, whole animal bioluminescence imaging). Aim This perspective aims to (1) justify the need for label-free microscopy to track heterogeneous cellular functions over time and space within unperturbed systems and (2) recommend improvements regarding instrumentation, image analysis, and image interpretation to address these needs. Approach Three key research areas (cancer research, autoimmune disease, and tissue and cell engineering) are considered to support the need for label-free microscopy to characterize heterogeneity and dynamics within biological systems. Based on the strengths (e.g., multiple sources of molecular contrast, non-invasive monitoring) and weaknesses (e.g., imaging depth, image interpretation) of several label-free microscopy modalities, improvements for future imaging systems are recommended. Conclusion Improvements in instrumentation including strategies that increase resolution and imaging speed, standardization and centralization of image analysis tools, and robust data validation and interpretation will expand the applications of label-free microscopy to study heterogeneous and dynamic biological systems.
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Affiliation(s)
- Dan L. Pham
- University of Wisconsin—Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | | | | | - Kasia Wiech
- University of Wisconsin—Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | | | - Rupsa Datta
- Morgridge Institute for Research, Madison, Wisconsin, United States
| | - Melissa C. Skala
- University of Wisconsin—Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
- Morgridge Institute for Research, Madison, Wisconsin, United States
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2
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Zhang J, Sheng X, Ding Q, Wang Y, Zhao J, Zhang J. Subretinal fibrosis secondary to neovascular age-related macular degeneration: mechanisms and potential therapeutic targets. Neural Regen Res 2025; 20:378-393. [PMID: 38819041 PMCID: PMC11317958 DOI: 10.4103/nrr.nrr-d-23-01642] [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: 09/30/2023] [Revised: 12/19/2023] [Accepted: 01/15/2024] [Indexed: 06/01/2024] Open
Abstract
Subretinal fibrosis is the end-stage sequelae of neovascular age-related macular degeneration. It causes local damage to photoreceptors, retinal pigment epithelium, and choroidal vessels, which leads to permanent central vision loss of patients with neovascular age-related macular degeneration. The pathogenesis of subretinal fibrosis is complex, and the underlying mechanisms are largely unknown. Therefore, there are no effective treatment options. A thorough understanding of the pathogenesis of subretinal fibrosis and its related mechanisms is important to elucidate its complications and explore potential treatments. The current article reviews several aspects of subretinal fibrosis, including the current understanding on the relationship between neovascular age-related macular degeneration and subretinal fibrosis; multimodal imaging techniques for subretinal fibrosis; animal models for studying subretinal fibrosis; cellular and non-cellular constituents of subretinal fibrosis; pathophysiological mechanisms involved in subretinal fibrosis, such as aging, infiltration of macrophages, different sources of mesenchymal transition to myofibroblast, and activation of complement system and immune cells; and several key molecules and signaling pathways participating in the pathogenesis of subretinal fibrosis, such as vascular endothelial growth factor, connective tissue growth factor, fibroblast growth factor 2, platelet-derived growth factor and platelet-derived growth factor receptor-β, transforming growth factor-β signaling pathway, Wnt signaling pathway, and the axis of heat shock protein 70-Toll-like receptors 2/4-interleukin-10. This review will improve the understanding of the pathogenesis of subretinal fibrosis, allow the discovery of molecular targets, and explore potential treatments for the management of subretinal fibrosis.
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Affiliation(s)
- Jingxiang Zhang
- Department of Ophthalmology, People’s Hospital of Huangdao District, Qingdao, Shandong Province, China
| | - Xia Sheng
- Department of Ophthalmology, People’s Hospital of Huangdao District, Qingdao, Shandong Province, China
| | - Quanju Ding
- Department of Ophthalmology, People’s Hospital of Huangdao District, Qingdao, Shandong Province, China
| | - Yujun Wang
- Department of Urology, People’s Hospital of Huangdao District, Qingdao, Shandong Province, China
| | - Jiwei Zhao
- Department of Ophthalmology, People’s Hospital of Huangdao District, Qingdao, Shandong Province, China
| | - Jingfa Zhang
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People’s Hospital), Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, China
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3
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Ravan A, Procopio S, Chemla YR, Gruebele M. Temperature-jump microscopy and interaction of Hsp70 heat shock protein with a client protein in vivo. Methods 2024; 231:154-164. [PMID: 39362572 DOI: 10.1016/j.ymeth.2024.09.019] [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: 07/05/2024] [Revised: 09/28/2024] [Accepted: 09/30/2024] [Indexed: 10/05/2024] Open
Abstract
Biomolecular processes such as protein-protein interactions can depend strongly on cell type and even vary within a single cell type. Here we develop a microscope with a Peltier-controlled temperature stage, a laser temperature jump to induce heat stress, and an autofocusing feature to mitigate temperature drift during experiments, to study a protein-protein interaction in a selected cell type within a live organism, the zebrafish larva. As an application of the instrument, we show that there is considerable cell-to-cell variation of the heat shock protein Hsp70 binding to one of its clients, phosphoglycerate kinase in vivo. We adapt a key feature from our previous folding study, rare transformation of cells within the larva, so that individual cells can be imaged and differentiated for cell-to-cell response. Our approach can be extended to other organisms and cell types than the ones demonstrated in this work.
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Affiliation(s)
- Aniket Ravan
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana Champaign, Urbana 61801, USA
| | - Samuel Procopio
- Department of Physics, University of Illinois Urbana Champaign, Urbana 61801, USA
| | - Yann R Chemla
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana Champaign, Urbana 61801, USA; Department of Physics, University of Illinois Urbana Champaign, Urbana 61801, USA
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana Champaign, Urbana 61801, USA; Department of Physics, University of Illinois Urbana Champaign, Urbana 61801, USA; Department of Chemistry and Carle-Illinois College of Medicine, University of Illinois Urbana Champaign, Urbana 61801, USA.
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4
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Marte ME, Kurokawa K, Jung H, Liu Y, Bernucci MT, King BJ, Miller DT. Characterizing Presumed Displaced Retinal Ganglion Cells in the Living Human Retina of Healthy and Glaucomatous Eyes. Invest Ophthalmol Vis Sci 2024; 65:20. [PMID: 39259176 PMCID: PMC11401130 DOI: 10.1167/iovs.65.11.20] [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: 09/12/2024] Open
Abstract
Purpose The purpose of this study was to investigate the large somas presumed to be displaced retinal ganglion cells (dRGCs) located in the inner nuclear layer (INL) of the living human retina. Whereas dRGCs have previously been studied in mammals and human donor tissue, they have never been investigated in the living human retina. Methods Five young, healthy subjects and three subjects with varying types of glaucoma were imaged at multiple locations in the macula using adaptive optics optical coherence tomography. In the acquired volumes, bright large somas at the INL border with the inner plexiform layer were identified, and the morphometric biomarkers of soma density, en face diameter, and spatial distribution were measured at up to 13 degrees retinal eccentricity. Susceptibility to glaucoma was assessed. Results In the young, healthy individuals, mean density of the bright, large somas was greatest foveally (550 and 543 cells/mm2 at 2 degrees temporal and nasal, respectively) and decreased with increasing retinal eccentricity (38 cells/mm2 at 13 degrees temporal, the farthest we measured). Soma size distribution showed the opposite trend with diameters and size variation increasing with retinal eccentricity, from 12.7 ± 1.8 µm at 2 degrees to 15.7 ± 3.5 µm at 13 degrees temporal, and showed evidence of a bimodal distribution in more peripheral locations. Within and adjacent to the arcuate defects of the subjects with glaucoma, density of the bright large somas was significantly lower than found in the young, healthy individuals. Conclusions Our results suggest that the bright, large somas at the INL border are likely comprised of dRGCs but amacrine cells may contribute too. These somas appear highly susceptible to glaucomatous damage.
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Affiliation(s)
- Mary E Marte
- Indiana University School of Optometry, Bloomington, Indiana, United States
| | - Kazuhiro Kurokawa
- Indiana University School of Optometry, Bloomington, Indiana, United States
| | - HaeWon Jung
- Indiana University School of Optometry, Bloomington, Indiana, United States
| | - Yan Liu
- Indiana University School of Optometry, Bloomington, Indiana, United States
| | - Marcel T Bernucci
- Indiana University School of Optometry, Bloomington, Indiana, United States
| | - Brett J King
- Indiana University School of Optometry, Bloomington, Indiana, United States
| | - Donald T Miller
- Indiana University School of Optometry, Bloomington, Indiana, United States
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5
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Popescu CC, Aryana K, Garud P, Dao KP, Vitale S, Liberman V, Bae HB, Lee TW, Kang M, Richardson KA, Julian M, Ocampo CAR, Zhang Y, Gu T, Hu J, Kim HJ. Electrically Reconfigurable Phase-Change Transmissive Metasurface. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2400627. [PMID: 38724020 DOI: 10.1002/adma.202400627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/25/2024] [Indexed: 07/23/2024]
Abstract
Programmable and reconfigurable optics hold significant potential for transforming a broad spectrum of applications, spanning space explorations to biomedical imaging, gas sensing, and optical cloaking. The ability to adjust the optical properties of components like filters, lenses, and beam steering devices could result in dramatic reductions in size, weight, and power consumption in future optoelectronic devices. Among the potential candidates for reconfigurable optics, chalcogenide-based phase change materials (PCMs) offer great promise due to their non-volatile and analogue switching characteristics. Although PCM have found widespread use in electronic data storage, these memory devices are deeply sub-micron-sized. To incorporate phase change materials into free-space optical components, it is essential to scale them up to beyond several hundreds of microns while maintaining reliable switching characteristics. This study demonstrated a non-mechanical, non-volatile transmissive filter based on low-loss PCMs with a 200 × 200 µm2 switching area. The device/metafilter can be consistently switched between low- and high-transmission states using electrical pulses with a switching contrast ratio of 5.5 dB. The device was reversibly switched for 1250 cycles before accelerated degradation took place. The work represents an important step toward realizing free-space reconfigurable optics based on PCMs.
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Affiliation(s)
- Cosmin Constantin Popescu
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | - Parth Garud
- NASA Langley Research Center, Hampton, VA, 23666, USA
| | - Khoi Phuong Dao
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Steven Vitale
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, 02421, USA
| | - Vladimir Liberman
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, 02421, USA
| | - Hyung-Bin Bae
- KAIST Analysis Center, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, 34141, South Korea
| | - Tae-Woo Lee
- KAIST Analysis Center, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, 34141, South Korea
| | - Myungkoo Kang
- CREOL, The College of Optics & Photonics University of Central Florida Orlando, Orlando, FL, 32816, USA
| | - Kathleen A Richardson
- CREOL, The College of Optics & Photonics University of Central Florida Orlando, Orlando, FL, 32816, USA
| | | | - Carlos A Ríos Ocampo
- Department of Materials Science & Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Yifei Zhang
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tian Gu
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Materials Research Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Juejun Hu
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Materials Research Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Hyun Jung Kim
- NASA Langley Research Center, Hampton, VA, 23666, USA
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6
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Xu C, Nedergaard M, Fowell DJ, Friedl P, Ji N. Multiphoton fluorescence microscopy for in vivo imaging. Cell 2024; 187:4458-4487. [PMID: 39178829 PMCID: PMC11373887 DOI: 10.1016/j.cell.2024.07.036] [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: 04/23/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 08/26/2024]
Abstract
Multiphoton fluorescence microscopy (MPFM) has been a game-changer for optical imaging, particularly for studying biological tissues deep within living organisms. MPFM overcomes the strong scattering of light in heterogeneous tissue by utilizing nonlinear excitation that confines fluorescence emission mostly to the microscope focal volume. This enables high-resolution imaging deep within intact tissue and has opened new avenues for structural and functional studies. MPFM has found widespread applications and has led to numerous scientific discoveries and insights into complex biological processes. Today, MPFM is an indispensable tool in many research communities. Its versatility and effectiveness make it a go-to technique for researchers investigating biological phenomena at the cellular and subcellular levels in their native environments. In this Review, the principles, implementations, capabilities, and limitations of MPFM are presented. Three application areas of MPFM, neuroscience, cancer biology, and immunology, are reviewed in detail and serve as examples for applying MPFM to biological research.
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Affiliation(s)
- Chris Xu
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14850, USA
| | - Maiken Nedergaard
- Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 3B, 2200 Copenhagen, Denmark; University of Rochester Medical School, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Deborah J Fowell
- Department of Microbiology & Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Peter Friedl
- Department of Medical BioSciences, Radboud University Medical Centre, Geert Grooteplein 26-28, Nijmegen HB 6500, the Netherlands
| | - Na Ji
- Department of Neuroscience, Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA.
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7
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Ahmed S, Son T, Yao X. Polarization-resolved analysis of outer retinal bands: investigating ballistic and multiply scattered photons using full-field swept-source optical coherence tomography. BIOMEDICAL OPTICS EXPRESS 2024; 15:4749-4763. [PMID: 39346986 PMCID: PMC11427207 DOI: 10.1364/boe.523202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/08/2024] [Accepted: 07/10/2024] [Indexed: 10/01/2024]
Abstract
Precise interpretation of the anatomical origins of outer retinal optical coherence tomography (OCT) presents technical challenges owing to the delicate nature of the retina. To address this challenge, our study introduces a novel polarization-sensitive full-field swept-source OCT (FF-SS-OCT) that provides parallel-polarization and cross-polarization OCT measurements, predominantly capturing ballistically reflected photons and multiply scattered photons, respectively. Notably, parallel-polarization OCT unveils layer-like structures more effectively, including the inner plexiform layer (IPL) sub-layers, outer plexiform layer (OPL) sub-layers (in rod-dominant regions), and rod/cone outer segment (OS) tips, compared to cross-polarization OCT, where such sub-layers are not visible. Through a comparative analysis of parallel-polarization and cross-polarization OCT images of the outer retina, we discovered that the 2nd outer retinal OCT band results from contributions from both the ellipsoid zone (EZ) and the inner segment/outer segment (IS/OS) junction. Similarly, the 3rd outer retinal OCT band appears to reflect contributions from both the interdigitation zone (IZ) and photoreceptor OS tips. This polarization-sensitive approach advances our understanding of the origins of outer retinal OCT signals and proposes potential new biomarkers for assessing retinal health and diseases.
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Affiliation(s)
- Shaiban Ahmed
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Taeyoon Son
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Xincheng Yao
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL 60607, USA
- Department of Ophthalmology and Visual Sciences, University of Illinois Chicago, Chicago, IL 60612, USA
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8
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Mcfadden C, Marin Z, Chen B, Daetwyler S, Wang X, Rajendran D, Dean KM, Fiolka R. Adaptive optics in an oblique plane microscope. BIOMEDICAL OPTICS EXPRESS 2024; 15:4498-4512. [PMID: 39346993 PMCID: PMC11427218 DOI: 10.1364/boe.524013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 10/01/2024]
Abstract
Adaptive optics (AO) can restore diffraction-limited performance when imaging beyond superficial cell layers in vivo and in vitro, and as such, is of interest for advanced 3D microscopy methods such as light-sheet fluorescence microscopy (LSFM). In a typical LSFM system, the illumination and detection paths are separate and subject to different optical aberrations. To achieve optimal microscope performance, it is necessary to sense and correct these aberrations in both light paths, resulting in a complex microscope system. Here, we show that in an oblique plane microscope (OPM), a type of LSFM with a single primary objective lens, the same deformable mirror can correct both illumination and fluorescence detection. Besides reducing the complexity, we show that AO in OPM also restores the relative alignment of the light-sheet and focal plane, and that a projection imaging mode can stabilize and improve the wavefront correction in a sensorless AO format. We demonstrate OPM with AO on fluorescent nanospheres and by imaging the vasculature and cancer cells in zebrafish embryos embedded in a glass capillary, restoring diffraction limited resolution and improving the signal strength twofold.
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Affiliation(s)
- Conor Mcfadden
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Zach Marin
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Max Perutz Labs, Department of Structural and Computational Biology, University of Vienna, Dr.Bohr-Gasse 9, 1030 Vienna, Austria
| | - Bingying Chen
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Stephan Daetwyler
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Xiaoding Wang
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Divya Rajendran
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Kevin M Dean
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Reto Fiolka
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
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9
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Rodríguez C, Pan D, Natan RG, Mohr MA, Miao M, Chen X, Northen TR, Vogel JP, Ji N. Adaptive optical third-harmonic generation microscopy for in vivo imaging of tissues. BIOMEDICAL OPTICS EXPRESS 2024; 15:4513-4524. [PMID: 39347005 PMCID: PMC11427202 DOI: 10.1364/boe.527357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/12/2024] [Accepted: 06/17/2024] [Indexed: 10/01/2024]
Abstract
Third-harmonic generation microscopy is a powerful label-free nonlinear imaging technique, providing essential information about structural characteristics of cells and tissues without requiring external labelling agents. In this work, we integrated a recently developed compact adaptive optics module into a third-harmonic generation microscope, to measure and correct for optical aberrations in complex tissues. Taking advantage of the high sensitivity of the third-harmonic generation process to material interfaces and thin membranes, along with the 1,300-nm excitation wavelength used here, our adaptive optical third-harmonic generation microscope enabled high-resolution in vivo imaging within highly scattering biological model systems. Examples include imaging of myelinated axons and vascular structures within the mouse spinal cord and deep cortical layers of the mouse brain, along with imaging of key anatomical features in the roots of the model plant Brachypodium distachyon. In all instances, aberration correction led to enhancements in image quality.
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Affiliation(s)
- Cristina Rodríguez
- Department of Physics, University of California, Berkeley, CA, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Present address: Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Daisong Pan
- Department of Physics, University of California, Berkeley, CA, USA
| | - Ryan G Natan
- Department of Physics, University of California, Berkeley, CA, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Manuel A Mohr
- Department of Biology, Stanford University, Stanford, CA, USA
- Present address: Yale Ventures, Yale University, New Haven, CT, USA
| | - Max Miao
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xiaoke Chen
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John P Vogel
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Na Ji
- Department of Physics, University of California, Berkeley, CA, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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10
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Liu J, Li Y, Chen T, Zhang F, Xu F. Machine Learning for Single-Molecule Localization Microscopy: From Data Analysis to Quantification. Anal Chem 2024; 96:11103-11114. [PMID: 38946062 DOI: 10.1021/acs.analchem.3c05857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Single-molecule localization microscopy (SMLM) is a versatile tool for realizing nanoscale imaging with visible light and providing unprecedented opportunities to observe bioprocesses. The integration of machine learning with SMLM enhances data analysis by improving efficiency and accuracy. This tutorial aims to provide a comprehensive overview of the data analysis process and theoretical aspects of SMLM, while also highlighting the typical applications of machine learning in this field. By leveraging advanced analytical techniques, SMLM is becoming a powerful quantitative analysis tool for biological research.
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Affiliation(s)
- Jianli Liu
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Yumian Li
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Tailong Chen
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Fa Zhang
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Fan Xu
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
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11
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Li D, Shi T, Xiao Y, Wu C. Sensorless adaptive optics in the second near-infrared window for deep vascular imaging in vivo. OPTICS LETTERS 2024; 49:4002-4005. [PMID: 39008762 DOI: 10.1364/ol.528634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/22/2024] [Indexed: 07/17/2024]
Abstract
We have experimentally validated the use of sensorless adaptive optics (AO) to enhance laser scanning confocal microscopy in the second near-infrared (NIR II) spectral range, termed as AO-NIR II confocal microscopy. This approach harnesses a NIR II fluorophore, excited by an 808 nm wavelength and emitting beyond 1000 nm, to visualize intricate structures in deep brain tissues with the intact skull. By leveraging the reduced scattering and aberrations in the NIR II spectrum, we successfully captured a three-dimensional (3D) vascular structure map extending 310 µm beneath the skull. AO typically boosts the fluorescence signal by approximately 2-3 times, leading to a superior contrast and diminished smearing effects. Consequently, small blood vessels at various depths can be clearly visualized, which might otherwise remain undetectable without AO corrections.
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12
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Būtaitė UG, Sharp C, Horodynski M, Gibson GM, Padgett MJ, Rotter S, Taylor JM, Phillips DB. Photon-efficient optical tweezers via wavefront shaping. SCIENCE ADVANCES 2024; 10:eadi7792. [PMID: 38968347 PMCID: PMC11225778 DOI: 10.1126/sciadv.adi7792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 05/31/2024] [Indexed: 07/07/2024]
Abstract
Optical tweezers enable noncontact trapping of microscale objects using light. It is not known how tightly it is possible to three-dimensionally (3D) trap microparticles with a given photon budget. Reaching this elusive limit would enable maximally stiff particle trapping for precision measurements on the nanoscale and photon-efficient tweezing of light-sensitive objects. Here, we customize the shape of light fields to suit specific particles, with the aim of optimizing trapping stiffness in 3D. We show, theoretically, that the confinement volume of microspheres held in sculpted optical traps can be reduced by one to two orders of magnitude. Experimentally, we use a wavefront shaping-inspired strategy to passively suppress the Brownian fluctuations of microspheres in every direction concurrently, demonstrating order-of-magnitude reductions in their confinement volumes. Our work paves the way toward the fundamental limits of optical control over the mesoscopic realm.
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Affiliation(s)
- Unė G. Būtaitė
- School of Physics and Astronomy, University of Exeter, Exeter EX4 4QL, UK
| | - Christina Sharp
- School of Physics and Astronomy, University of Exeter, Exeter EX4 4QL, UK
| | - Michael Horodynski
- Institute for Theoretical Physics, Vienna University of Technology (TU Wien), A-1040 Vienna, Austria, EU
| | - Graham M. Gibson
- School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, UK
| | - Miles J. Padgett
- School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, UK
| | - Stefan Rotter
- Institute for Theoretical Physics, Vienna University of Technology (TU Wien), A-1040 Vienna, Austria, EU
| | - Jonathan M. Taylor
- School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, UK
| | - David B. Phillips
- School of Physics and Astronomy, University of Exeter, Exeter EX4 4QL, UK
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13
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Aizik D, Levin A. Non-invasive and noise-robust light focusing using confocal wavefront shaping. Nat Commun 2024; 15:5575. [PMID: 38956030 PMCID: PMC11219997 DOI: 10.1038/s41467-024-49697-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 06/11/2024] [Indexed: 07/04/2024] Open
Abstract
Wavefront-shaping is a promising approach for imaging fluorescent targets deep inside scattering tissue despite strong aberrations. It enables focusing an incoming illumination into a single spot inside tissue, as well as correcting the outgoing light scattered from the tissue. Previously, wavefront shaping modulations have been successively estimated using feedback from strong fluorescent beads, which have been manually added to a sample. However, such algorithms do not generalize to neurons whose emission is orders of magnitude weaker. We suggest a wavefront shaping approach that works with a confocal modulation of both the illumination and imaging arms. Since the aberrations are corrected in the optics before the detector, the low photon budget is directed into a single sensor spot and detected with high signal-noise ratio. We derive a score function for modulation evaluation from mathematical principles, and successfully use it to image fluorescence neurons, despite scattering through thick tissue.
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Affiliation(s)
- Dror Aizik
- Department of Electrical and Computer Engineering, Technion, Haifa, Israel.
| | - Anat Levin
- Department of Electrical and Computer Engineering, Technion, Haifa, Israel
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14
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Hira R. Closed-loop experiments and brain machine interfaces with multiphoton microscopy. NEUROPHOTONICS 2024; 11:033405. [PMID: 38375331 PMCID: PMC10876015 DOI: 10.1117/1.nph.11.3.033405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024]
Abstract
In the field of neuroscience, the importance of constructing closed-loop experimental systems has increased in conjunction with technological advances in measuring and controlling neural activity in live animals. We provide an overview of recent technological advances in the field, focusing on closed-loop experimental systems where multiphoton microscopy-the only method capable of recording and controlling targeted population activity of neurons at a single-cell resolution in vivo-works through real-time feedback. Specifically, we present some examples of brain machine interfaces (BMIs) using in vivo two-photon calcium imaging and discuss applications of two-photon optogenetic stimulation and adaptive optics to real-time BMIs. We also consider conditions for realizing future optical BMIs at the synaptic level, and their possible roles in understanding the computational principles of the brain.
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Affiliation(s)
- Riichiro Hira
- Tokyo Medical and Dental University, Graduate School of Medical and Dental Sciences, Department of Physiology and Cell Biology, Tokyo, Japan
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15
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Shroff H, Testa I, Jug F, Manley S. Live-cell imaging powered by computation. Nat Rev Mol Cell Biol 2024; 25:443-463. [PMID: 38378991 DOI: 10.1038/s41580-024-00702-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 02/22/2024]
Abstract
The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. The prevailing challenge in live-cell fluorescence microscopy is capturing intra-cellular dynamics while preserving cell viability. Computational methods can help to address this challenge and are now shifting the boundaries of what is possible to capture in living systems. In this Review, we discuss these computational methods focusing on artificial intelligence-based approaches that can be layered on top of commonly used existing microscopies as well as hybrid methods that integrate computation and microscope hardware. We specifically discuss how computational approaches can improve the signal-to-noise ratio, spatial resolution, temporal resolution and multi-colour capacity of live-cell imaging.
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Affiliation(s)
- Hari Shroff
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Florian Jug
- Fondazione Human Technopole (HT), Milan, Italy
| | - Suliana Manley
- Institute of Physics, School of Basic Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
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16
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Chen L, Hu Y, Nie J, Xue T, Gu J. Learning-based lens wavefront aberration recovery. OPTICS EXPRESS 2024; 32:18931-18943. [PMID: 38859039 DOI: 10.1364/oe.521125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/22/2024] [Indexed: 06/12/2024]
Abstract
Wavefront aberration describes the deviation of a wavefront in an imaging system from a desired perfect shape, such as a plane or a sphere, which may be caused by a variety of factors, such as imperfections in optical equipment, atmospheric turbulence, and the physical properties of imaging subjects and medium. Measuring the wavefront aberration of an imaging system is a crucial part of modern optics and optical engineering, with a variety of applications such as adaptive optics, optical testing, microscopy, laser system design, and ophthalmology. While there are dedicated wavefront sensors that aim to measure the phase of light, they often exhibit some drawbacks, such as higher cost and limited spatial resolution compared to regular intensity measurement. In this paper, we introduce a lightweight and practical learning-based method, named LWNet, to recover the wavefront aberration for an imaging system from a single intensity measurement. Specifically, LWNet takes a measured point spread function (PSF) as input and recovers the wavefront aberration with a two-stage network. The first stage network estimates an initial wavefront aberration via supervised learning, and the second stage network further optimizes the wavefront aberration via self-supervised learning by enforcing the statistical priors and physical constraints of wavefront aberrations via Zernike decomposition. For supervised learning, we created a synthetic PSF-wavefront aberration dataset via ray tracing of 88 lenses. Experimental results show that even trained with simulated data, LWNet works well for wavefront aberration estimation of real imaging systems and consistently outperforms prior learning-based methods.
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17
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Rodríguez C, Pan D, Natan RG, Mohr MA, Miao M, Chen X, Northen TR, Vogel JP, Ji N. Adaptive optical third-harmonic generation microscopy for in vivo imaging of tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592275. [PMID: 38746456 PMCID: PMC11092640 DOI: 10.1101/2024.05.02.592275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Third-harmonic generation microscopy is a powerful label-free nonlinear imaging technique, providing essential information about structural characteristics of cells and tissues without requiring external labelling agents. In this work, we integrated a recently developed compact adaptive optics module into a third-harmonic generation microscope, to measure and correct for optical aberrations in complex tissues. Taking advantage of the high sensitivity of the third-harmonic generation process to material interfaces and thin membranes, along with the 1,300-nm excitation wavelength used here, our adaptive optical third-harmonic generation microscope enabled high-resolution in vivo imaging within highly scattering biological model systems. Examples include imaging of myelinated axons and vascular structures within the mouse spinal cord and deep cortical layers of the mouse brain, along with imaging of key anatomical features in the roots of the model plant Brachypodium distachyon. In all instances, aberration correction led to significant enhancements in image quality.
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Affiliation(s)
- Cristina Rodríguez
- Department of Physics, University of California, Berkeley, CA, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Present address: Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Daisong Pan
- Department of Physics, University of California, Berkeley, CA, USA
| | - Ryan G. Natan
- Department of Physics, University of California, Berkeley, CA, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Manuel A. Mohr
- Department of Biology, Stanford University, Stanford, CA, USA
- Present address: Yale Ventures, Yale University, New Haven, CT, USA
| | - Max Miao
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xiaoke Chen
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Trent R. Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John P. Vogel
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Na Ji
- Department of Physics, University of California, Berkeley, CA, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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18
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Das V, Zhang F, Bower AJ, Li J, Liu T, Aguilera N, Alvisio B, Liu Z, Hammer DX, Tam J. Revealing speckle obscured living human retinal cells with artificial intelligence assisted adaptive optics optical coherence tomography. COMMUNICATIONS MEDICINE 2024; 4:68. [PMID: 38600290 PMCID: PMC11006674 DOI: 10.1038/s43856-024-00483-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 03/13/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND In vivo imaging of the human retina using adaptive optics optical coherence tomography (AO-OCT) has transformed medical imaging by enabling visualization of 3D retinal structures at cellular-scale resolution, including the retinal pigment epithelial (RPE) cells, which are essential for maintaining visual function. However, because noise inherent to the imaging process (e.g., speckle) makes it difficult to visualize RPE cells from a single volume acquisition, a large number of 3D volumes are typically averaged to improve contrast, substantially increasing the acquisition duration and reducing the overall imaging throughput. METHODS Here, we introduce parallel discriminator generative adversarial network (P-GAN), an artificial intelligence (AI) method designed to recover speckle-obscured cellular features from a single AO-OCT volume, circumventing the need for acquiring a large number of volumes for averaging. The combination of two parallel discriminators in P-GAN provides additional feedback to the generator to more faithfully recover both local and global cellular structures. Imaging data from 8 eyes of 7 participants were used in this study. RESULTS We show that P-GAN not only improves RPE cell contrast by 3.5-fold, but also improves the end-to-end time required to visualize RPE cells by 99-fold, thereby enabling large-scale imaging of cells in the living human eye. RPE cell spacing measured across a large set of AI recovered images from 3 participants were in agreement with expected normative ranges. CONCLUSIONS The results demonstrate the potential of AI assisted imaging in overcoming a key limitation of RPE imaging and making it more accessible in a routine clinical setting.
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Affiliation(s)
- Vineeta Das
- National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Furu Zhang
- National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Andrew J Bower
- National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Joanne Li
- National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tao Liu
- National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nancy Aguilera
- National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bruno Alvisio
- National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Zhuolin Liu
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Daniel X Hammer
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Johnny Tam
- National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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19
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McFadden C, Marin Z, Chen B, Daetwyler S, Wang X, Rajendran D, Dean KM, Fiolka R. Adaptive Optics in an Oblique Plane Microscope. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586191. [PMID: 38562744 PMCID: PMC10983975 DOI: 10.1101/2024.03.21.586191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Adaptive optics (AO) can restore diffraction limited performance when imaging beyond superficial cell layers in vivo and in vitro, and as such is of interest for advanced 3D microscopy methods such as light-sheet fluorescence microscopy (LSFM). In a typical LSFM system, the illumination and detection paths are separate and subject to different optical aberrations. To achieve optimal microscope performance, it is necessary to sense and correct these aberrations in both light paths, resulting in a complex microscope system. Here, we show that in an oblique plane microscope (OPM), a type of LSFM with a single primary objective lens, the same deformable mirror can correct both the illumination and fluorescence detection. Besides reducing the complexity, we show that AO in OPM also restores the relative alignment of the light-sheet and focal plane, and that a projection imaging mode can stabilize and improve the wavefront correction in a sensorless AO format. We demonstrate OPM with AO on fluorescent nanospheres and by imaging the vasculature and cancer cells in zebrafish embryos embedded in a glass capillary, restoring diffraction limited resolution and improving the signal strength twofold.
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Affiliation(s)
- Conor McFadden
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Zach Marin
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Bingying Chen
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Stephan Daetwyler
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Xiaoding Wang
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Divya Rajendran
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Kevin M. Dean
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Reto Fiolka
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
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20
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Daich Varela M, Dixit M, Kalitzeos A, Michaelides M. Adaptive Optics Retinal Imaging in RDH12-Associated Early Onset Severe Retinal Dystrophy. Invest Ophthalmol Vis Sci 2024; 65:9. [PMID: 38466282 PMCID: PMC10929749 DOI: 10.1167/iovs.65.3.9] [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: 10/11/2023] [Accepted: 12/03/2023] [Indexed: 03/12/2024] Open
Abstract
Purpose RDH12 is among the most common genes found in individuals with early-onset severe retinal (EOSRD). Adaptive optics scanning light ophthalmoscopy (AOSLO) enables resolution of individual rod and cone photoreceptors in the retina. This study presents the first AOSLO imaging of individuals with RDH12-associated EOSRD. Methods Case series of patients who attended Moorfields Eye Hospital (London, UK). Spectral-domain optical coherence tomography, near-infrared reflectance (NIR), and blue autofluorescence imaging were analyzed. En face image sequences of photoreceptors were recorded using either of two AOSLO modalities. Cross-sectional analysis was undertaken for seven patients and longitudinal analysis for one patient. Results Nine eyes from eight patients are presented in this case series. The mean age at the time of the assessment was 11.2 ± 6.5 years of age (range 7-29). A subfoveal continuous ellipsoid zone (EZ) line was present in eight eyes. Posterior pole AOSLO revealed patches of cone mosaics. Average cone densities at regions of interest 0.5° to the fovea ranged from 12,620 to 23,660 cells/mm2, whereas intercell spacing ranged from 7.0 to 9.7 µm. Conclusions This study demonstrates that AOSLO can provide useful high-quality images in patients with EOSRD, even during childhood, with nystagmus, and early macular atrophy. Cones at the posterior pole can appear as scattered islands or, possibly later in life, as a single subfoveal conglomerate. Detailed image analysis suggests that retinal pigment epithelial stress and dysfunction may be the initial step toward degeneration, with NIR being a useful tool to assess retinal well-being in RDH12-associated EOSRD.
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Affiliation(s)
- Malena Daich Varela
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Mira Dixit
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Angelos Kalitzeos
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Michel Michaelides
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
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21
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Tanaka M, Ando T, Horiuchi T. Automatic MTF Conversion between Different Characteristics Caused by Imaging Devices. J Imaging 2024; 10:49. [PMID: 38392097 PMCID: PMC10889508 DOI: 10.3390/jimaging10020049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 01/26/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
Depending on various design conditions, including optics and circuit design, the image-forming characteristics of the modulated transfer function (MTF), which affect the spatial resolution of a digital image, may vary among image channels within or between imaging devices. In this study, we propose a method for automatically converting the MTF to the target MTF, focusing on adjusting the MTF characteristics that affect the signals of different image channels within and between different image devices. The experimental results of MTF conversion using the proposed method for multiple image channels with different MTF characteristics indicated that the proposed method could produce sharper images by moving the source MTF of each channel closer to a target MTF with a higher MTF value. This study is expected to contribute to technological advancements in various imaging devices as follows: (1) Even if the imaging characteristics of the hardware are unknown, the MTF can be converted to the target MTF using the image after it is captured. (2) As any MTF can be converted into a target, image simulation for conversion to a different MTF is possible. (3) It is possible to generate high-definition images, thereby meeting the requirements of various industrial and research fields in which high-definition images are required.
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Affiliation(s)
- Midori Tanaka
- Graduate School of Global and Transdisciplinary Studies, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba 263-8522, Japan
- Graduate School of Science and Engineering, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba 263-8522, Japan
| | - Tsubasa Ando
- Graduate School of Science and Engineering, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba 263-8522, Japan
| | - Takahiko Horiuchi
- Graduate School of Science and Engineering, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba 263-8522, Japan
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22
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Alido J, Greene J, Xue Y, Hu G, Gilmore M, Monk KJ, DiBenedictis BT, Davison IG, Tian L, Li Y. Robust single-shot 3D fluorescence imaging in scattering media with a simulator-trained neural network. OPTICS EXPRESS 2024; 32:6241-6257. [PMID: 38439332 PMCID: PMC11018337 DOI: 10.1364/oe.514072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 03/06/2024]
Abstract
Imaging through scattering is a pervasive and difficult problem in many biological applications. The high background and the exponentially attenuated target signals due to scattering fundamentally limits the imaging depth of fluorescence microscopy. Light-field systems are favorable for high-speed volumetric imaging, but the 2D-to-3D reconstruction is fundamentally ill-posed, and scattering exacerbates the condition of the inverse problem. Here, we develop a scattering simulator that models low-contrast target signals buried in heterogeneous strong background. We then train a deep neural network solely on synthetic data to descatter and reconstruct a 3D volume from a single-shot light-field measurement with low signal-to-background ratio (SBR). We apply this network to our previously developed computational miniature mesoscope and demonstrate the robustness of our deep learning algorithm on scattering phantoms with different scattering conditions. The network can robustly reconstruct emitters in 3D with a 2D measurement of SBR as low as 1.05 and as deep as a scattering length. We analyze fundamental tradeoffs based on network design factors and out-of-distribution data that affect the deep learning model's generalizability to real experimental data. Broadly, we believe that our simulator-based deep learning approach can be applied to a wide range of imaging through scattering techniques where experimental paired training data is lacking.
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Affiliation(s)
- Jeffrey Alido
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, 02215, USA
| | - Joseph Greene
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, 02215, USA
| | - Yujia Xue
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, 02215, USA
| | - Guorong Hu
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, 02215, USA
| | - Mitchell Gilmore
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, 02215, USA
| | - Kevin J. Monk
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
| | - Brett T. DiBenedictis
- Department of Psychology and Brain Sciences, Boston University, Boston, Massachusetts 02215, USA
| | - Ian G. Davison
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
| | - Lei Tian
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, USA
| | - Yunzhe Li
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, 02215, USA
- Current address: Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, 94720, USA
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23
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Huang L, Yao K, Chen L, Wang J, Liu Y. Daytime HyWFS approach for daylight adaptive optics wavefront sensing. OPTICS EXPRESS 2024; 32:5996-6010. [PMID: 38439313 DOI: 10.1364/oe.514790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/25/2024] [Indexed: 03/06/2024]
Abstract
Bright daylight photon noise and the saturation of wavefront sensors pose challenges to high-resolution daytime imaging. In this paper, a daytime hybrid wavefront sensor (HyWFS) approach for real-time wavefront sensing in daylight adaptive optics (AO) is described. The Shack-Hartmann wavefront sensor (SHWFS) algorithm is used to efficiently compensate large-scale wavefronts, while the pyramid wavefront sensor (PyWFS) algorithm offers highly sensitive correction of small wavefronts. Daylight closed-loop AO experiments were performed using the daytime HyWFS approach with both algorithms, respectively. The experiment results indicate that the proposed approach provides accurate daylight AO correction and allows for a simple switch between the two algorithms without increasing system complexity. The daytime HyWFS approach can serve as an alternative for daylight natural guide star AO, enabling high-resolution observation of resident space objects no longer limited to dawn and dusk.
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24
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Kurokawa K, Nemeth M. Multifunctional adaptive optics optical coherence tomography allows cellular scale reflectometry, polarimetry, and angiography in the living human eye. BIOMEDICAL OPTICS EXPRESS 2024; 15:1331-1354. [PMID: 38404344 PMCID: PMC10890865 DOI: 10.1364/boe.505395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/27/2024]
Abstract
Clinicians are unable to detect glaucoma until substantial loss or dysfunction of retinal ganglion cells occurs. To this end, novel measures are needed. We have developed an optical imaging solution based on adaptive optics optical coherence tomography (AO-OCT) to discern key clinical features of glaucoma and other neurodegenerative diseases at the cellular scale in the living eye. Here, we test the feasibility of measuring AO-OCT-based reflectance, retardance, optic axis orientation, and angiogram at specifically targeted locations in the living human retina and optic nerve head. Multifunctional imaging, combined with focus stacking and global image registration algorithms, allows us to visualize cellular details of retinal nerve fiber bundles, ganglion cell layer somas, glial septa, superior vascular complex capillaries, and connective tissues. These are key histologic features of neurodegenerative diseases, including glaucoma, that are now measurable in vivo with excellent repeatability and reproducibility. Incorporating this noninvasive cellular-scale imaging with objective measurements will significantly enhance existing clinical assessments, which is pivotal in facilitating the early detection of eye disease and understanding the mechanisms of neurodegeneration.
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Affiliation(s)
- Kazuhiro Kurokawa
- Discoveries in Sight Research Laboratories, Devers Eye Institute, Legacy Research Institute, Legacy Health, Portland, OR 97232, USA
| | - Morgan Nemeth
- Discoveries in Sight Research Laboratories, Devers Eye Institute, Legacy Research Institute, Legacy Health, Portland, OR 97232, USA
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25
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Nam K, Park JH. Reference-free in situ rapid regional calibration of phase-only spatial light modulators. OPTICS LETTERS 2024; 49:522-525. [PMID: 38300049 DOI: 10.1364/ol.506749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/20/2023] [Indexed: 02/02/2024]
Abstract
Spatial light modulators (SLMs) have become an indispensable element in modern optics for their versatile performance in many applications. Among various types of SLMs, such as digital micromirror devices (DMD), liquid crystal-based phase-only spatial light modulators (LC-SLMs), and deformable mirrors (DM), LC-SLMs are often the method of choice due to their high efficiency, precise phase modulation, and abundant number of effective pixels. In general, for research grade applications, an additional SLM calibration step is required due to fabrication imperfection resulting in non-flat liquid crystal panels and varying phase responses over the SLM area. Here, we demonstrate a straightforward approach for reference-free orthogonal calibration of an arbitrary number of SLM subregions which only requires the same measurement time as global calibration. The proposed method requires minimal optical elements and can be applied to any optical setup as is. As a benchmark performance test, we achieved a 2.2-fold enhancement in correction efficiency for wavefront shaping through scattering media utilizing the calibrated 2160 subregions of the SLM, in comparison with a single global look-up table (LUT).
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Dai X, Yu Y, Ye T, Deng J, Bu Y, Shi M, Wang R, Zhou J, Sun L, Chen X, Shen X. Dynamically Reconfigurable on-Chip Polarimeters Based on Nanoantenna Enabled Polarization Dependent Optoelectronic Computing. NANO LETTERS 2024; 24:983-992. [PMID: 38206182 DOI: 10.1021/acs.nanolett.3c04454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
On-chip polarization detectors have attracted extensive research interest due to their filterless and ultracompact architecture. However, their polarization-dependent photoresponses cannot be dynamically adjusted, hindering the development toward intelligence. Here, we propose dynamically reconfigurable polarimetry based on in-sensor differentiation of two self-powered photoresponses with orthogonal polarization dependences and tunable responsivities. Such a device can be electrostatically configured in an ultrahigh polarization extinction ratio (PER) mode, where the PER tends to infinity, a Stokes parameter direct sensing mode, where the photoresponse is proportional to S1 or S2 with high accuracy (RMSES1 = 1.5%, RMSES2 = 2.0%), or a background suppressing mode, where the target-background polarization contrast is singularly enhanced. Moreover, the device achieves a polarization angle sensitivity of 0.51 mA·W-1·degree-1 and a specific polarization angle detectivity of 2.8 × 105 cm·Hz1/2·W·degree-1. This scheme is demonstrated throughout the near-to-long-wavelength infrared range, and it will bring a leap for next-generation on-chip polarimeters.
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Affiliation(s)
- Xu Dai
- State Key Laboratory of Infrared Science and Technology, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yu Tian Road, Shanghai 200083, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yu Yu
- State Key Laboratory of Infrared Science and Technology, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yu Tian Road, Shanghai 200083, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tao Ye
- State Key Laboratory of Infrared Science and Technology, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yu Tian Road, Shanghai 200083, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jie Deng
- State Key Laboratory of Infrared Science and Technology, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yu Tian Road, Shanghai 200083, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yonghao Bu
- State Key Laboratory of Infrared Science and Technology, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yu Tian Road, Shanghai 200083, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Mengdie Shi
- State Key Laboratory of Infrared Science and Technology, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yu Tian Road, Shanghai 200083, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Ruowen Wang
- State Key Laboratory of Infrared Science and Technology, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yu Tian Road, Shanghai 200083, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jing Zhou
- State Key Laboratory of Infrared Science and Technology, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yu Tian Road, Shanghai 200083, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Liaoxin Sun
- State Key Laboratory of Infrared Science and Technology, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yu Tian Road, Shanghai 200083, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Xiaoshuang Chen
- State Key Laboratory of Infrared Science and Technology, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yu Tian Road, Shanghai 200083, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Xuechu Shen
- State Key Laboratory of Infrared Science and Technology, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yu Tian Road, Shanghai 200083, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
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27
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Wu T, Zhang Y, Blochet B, Arjmand P, Berto P, Guillon M. Single-shot digital optical fluorescence phase conjugation through forward multiple-scattering samples. SCIENCE ADVANCES 2024; 10:eadi1120. [PMID: 38241370 PMCID: PMC10798569 DOI: 10.1126/sciadv.adi1120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024]
Abstract
Aberrations and multiple scattering in biological tissues critically distort light beams into highly complex speckle patterns. In this regard, digital optical phase conjugation (DOPC) is a promising technique enabling in-depth focusing. However, DOPC becomes challenging when using fluorescent guide stars for four main reasons: the low photon budget available, the large spectral bandwidth of the fluorescent signal, the Stokes shift between the emission and the excitation wavelength, and the absence of reference beam preventing holographic measurement. Here, we demonstrate the possibility to focus a laser beam through multiple-scattering samples by measuring speckle fields in a single acquisition step with a reference-free, high-resolution wavefront sensor. By taking advantage of the large spectral bandwidth of forward multiply scattering samples, digital fluorescence phase conjugation is achieved to focus a laser beam at the excitation wavelength while measuring the broadband speckle field arising from a micrometer-sized fluorescent bead.
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Affiliation(s)
- Tengfei Wu
- Saints-Pères Paris Institute for the Neurosciences, CNRS UMR 8003, Université Paris Cité, 45 rue des Saints-Pères, Paris 75006, France
| | - Yixuan Zhang
- Saints-Pères Paris Institute for the Neurosciences, CNRS UMR 8003, Université Paris Cité, 45 rue des Saints-Pères, Paris 75006, France
| | - Baptiste Blochet
- Saints-Pères Paris Institute for the Neurosciences, CNRS UMR 8003, Université Paris Cité, 45 rue des Saints-Pères, Paris 75006, France
| | - Payvand Arjmand
- Saints-Pères Paris Institute for the Neurosciences, CNRS UMR 8003, Université Paris Cité, 45 rue des Saints-Pères, Paris 75006, France
| | - Pascal Berto
- Saints-Pères Paris Institute for the Neurosciences, CNRS UMR 8003, Université Paris Cité, 45 rue des Saints-Pères, Paris 75006, France
- Sorbonne Université, CNRS, INSERM, Institut de la Vision, 17 Rue Moreau, Paris 75012, France
- Institut Universitaire de France (IUF), Paris 75007, France
| | - Marc Guillon
- Saints-Pères Paris Institute for the Neurosciences, CNRS UMR 8003, Université Paris Cité, 45 rue des Saints-Pères, Paris 75006, France
- Institut Universitaire de France (IUF), Paris 75007, France
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28
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Phillips TA, Marcotti S, Cox S, Parsons M. Imaging actin organisation and dynamics in 3D. J Cell Sci 2024; 137:jcs261389. [PMID: 38236161 PMCID: PMC10906668 DOI: 10.1242/jcs.261389] [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: 01/19/2024] Open
Abstract
The actin cytoskeleton plays a critical role in cell architecture and the control of fundamental processes including cell division, migration and survival. The dynamics and organisation of F-actin have been widely studied in a breadth of cell types on classical two-dimensional (2D) surfaces. Recent advances in optical microscopy have enabled interrogation of these cytoskeletal networks in cells within three-dimensional (3D) scaffolds, tissues and in vivo. Emerging studies indicate that the dimensionality experienced by cells has a profound impact on the structure and function of the cytoskeleton, with cells in 3D environments exhibiting cytoskeletal arrangements that differ to cells in 2D environments. However, the addition of a third (and fourth, with time) dimension leads to challenges in sample preparation, imaging and analysis, necessitating additional considerations to achieve the required signal-to-noise ratio and spatial and temporal resolution. Here, we summarise the current tools for imaging actin in a 3D context and highlight examples of the importance of this in understanding cytoskeletal biology and the challenges and opportunities in this domain.
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Affiliation(s)
- Thomas A. Phillips
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunts House, Guys Campus, London SE1 1UL, UK
| | - Stefania Marcotti
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunts House, Guys Campus, London SE1 1UL, UK
- Microscopy Innovation Centre, King's College London, Guys Campus, London SE1 1UL, UK
| | - Susan Cox
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunts House, Guys Campus, London SE1 1UL, UK
| | - Maddy Parsons
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunts House, Guys Campus, London SE1 1UL, UK
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29
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Gao Y, Xiang F, Yu J, Wu T, Liao J, Li H, Ye S, Zheng W. Accurate piecewise centroid calculation algorithm for wavefront measurement in adaptive optics. OPTICS EXPRESS 2024; 32:301-312. [PMID: 38175057 DOI: 10.1364/oe.510881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024]
Abstract
Adaptive optics using direct wavefront sensing (direct AO) is widely used in two-photon microscopy to correct sample-induced aberrations and restore diffraction-limited performance at high speeds. In general, the direct AO method employs a Sharked-Hartman wavefront sensor (SHWS) to directly measure the aberrations through a spot array. However, the signal-to-noise ratio (SNR) of spots in SHWS varies significantly within deep tissues, presenting challenges for accurately locating spot centroids over a large SNR range, particularly under extremely low SNR conditions. To address this issue, we propose a piecewise centroid calculation algorithm called GCP, which integrates three optimal algorithms for accurate spot centroid calculations under high-, medium-, and low-SNR conditions. Simulations and experiments demonstrate that the GCP can accurately measure aberrations over a large SNR range and exhibits robustness under extremely low-SNR conditions. Importantly, GCP improves the AO working depth by 150 µm compared to the conventional algorithm.
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30
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Alido J, Greene J, Xue Y, Hu G, Li Y, Gilmore M, Monk KJ, Dibenedictis BT, Davison IG, Tian L. Robust single-shot 3D fluorescence imaging in scattering media with a simulator-trained neural network. ARXIV 2023:arXiv:2303.12573v2. [PMID: 36994164 PMCID: PMC10055497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Imaging through scattering is a pervasive and difficult problem in many biological applications. The high background and the exponentially attenuated target signals due to scattering fundamentally limits the imaging depth of fluorescence microscopy. Light-field systems are favorable for high-speed volumetric imaging, but the 2D-to-3D reconstruction is fundamentally ill-posed, and scattering exacerbates the condition of the inverse problem. Here, we develop a scattering simulator that models low-contrast target signals buried in heterogeneous strong background. We then train a deep neural network solely on synthetic data to descatter and reconstruct a 3D volume from a single-shot light-field measurement with low signal-to-background ratio (SBR). We apply this network to our previously developed Computational Miniature Mesoscope and demonstrate the robustness of our deep learning algorithm on scattering phantoms with different scattering conditions. The network can robustly reconstruct emitters in 3D with a 2D measurement of SBR as low as 1.05 and as deep as a scattering length. We analyze fundamental tradeoffs based on network design factors and out-of-distribution data that affect the deep learning model's generalizability to real experimental data. Broadly, we believe that our simulator-based deep learning approach can be applied to a wide range of imaging through scattering techniques where experimental paired training data is lacking.
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Affiliation(s)
- Jeffrey Alido
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - Joseph Greene
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - Yujia Xue
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - Guorong Hu
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - Yunzhe Li
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - Mitchell Gilmore
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - Kevin J. Monk
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Brett T. Dibenedictis
- Department of Psychology and Brain Sciences, Boston University, Boston, MA 02215, USA
| | - Ian G. Davison
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Lei Tian
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
- Department of Psychology and Brain Sciences, Boston University, Boston, MA 02215, USA
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31
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Fang L, Huang F. Measurement precision bounds on aberrated single molecule emission patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569462. [PMID: 38076960 PMCID: PMC10705439 DOI: 10.1101/2023.11.30.569462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Single-Molecule Localization Microscopy (SMLM) has revolutionized the study of biological phenomena by providing exquisite nanoscale spatial resolution. However, optical aberrations induced by sample and system imperfections distort the single molecule emission patterns (i.e. PSFs), leading to reduced precision and resolution of SMLM, particularly in three-dimensional (3D) applications. While various methods, both analytical and instrumental, have been employed to mitigate these aberrations, a comprehensive analysis of how different types of commonly encountered aberrations affect single molecule experiments and their image formation remains missing. In this study, we addressed this gap by conducting a quantitative study of the theoretical precision limit for position and wavefront distortion measurements in the presence of aberrations. Leveraging Fisher information and Cramér-Rao lower bound (CRLB), we quantitively analyzed and compared the effects of different aberration types, including index mismatch aberrations, on localization precision in both biplane and astigmatism 3D modalities as well as 2D SMLM imaging. Furthermore, we studied the achievable wavefront estimation precision from aberrated single molecule emission patterns, a pivot step for successful adaptive optics in SMLM through thick specimens. This analysis lays a quantitative foundation for the development and application of SMLM in whole-cells, tissues and with large field of view, providing in-depth insights into the behavior of different aberration types in single molecule imaging and thus generating theoretical guidelines for developing highly efficient aberration correction strategies and enhancing the precision and reliability of 3D SMLM.
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Affiliation(s)
- Li Fang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
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32
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Gong D, Scherer NF. Tandem aberration correction optics (TACO) in wide-field structured illumination microscopy. BIOMEDICAL OPTICS EXPRESS 2023; 14:6381-6396. [PMID: 38420301 PMCID: PMC10898552 DOI: 10.1364/boe.503801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 03/02/2024]
Abstract
Structured illumination microscopy (SIM) is a powerful super-resolution imaging technique that uses patterned illumination to down-modulate high spatial-frequency information of samples. However, the presence of spatially-dependent aberrations can severely disrupt the illumination pattern, limiting the quality of SIM imaging. Conventional adaptive optics (AO) techniques that employ wavefront correctors at the pupil plane are not capable of effectively correcting these spatially-dependent aberrations. We introduce the Tandem Aberration Correction Optics (TACO) approach that combines both pupil AO and conjugate AO for aberration correction in SIM. TACO incorporates a deformable mirror (DM) for pupil AO in the detection path to correct for global aberrations, while a spatial light modulator (SLM) is placed at the plane conjugate to the aberration source near the sample plane, termed conjugate AO, to compensate spatially-varying aberrations in the illumination path. Our numerical simulations and experimental results show that the TACO approach can recover the illumination pattern close to an ideal condition, even when severely misshaped by aberrations, resulting in high-quality super-resolution SIM reconstruction. The TACO approach resolves a critical traditional shortcoming of aberration correction for structured illumination. This advance significantly expands the application of SIM imaging in the study of complex, particularly biological, samples and should be effective in other wide-field microscopies.
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Affiliation(s)
- Daozheng Gong
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Norbert F. Scherer
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
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33
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Yao P, Liu R, Broggini T, Thunemann M, Kleinfeld D. Construction and use of an adaptive optics two-photon microscope with direct wavefront sensing. Nat Protoc 2023; 18:3732-3766. [PMID: 37914781 PMCID: PMC11033548 DOI: 10.1038/s41596-023-00893-w] [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: 02/08/2023] [Accepted: 07/24/2023] [Indexed: 11/03/2023]
Abstract
Two-photon microscopy, combined with the appropriate optical labelling, enables the measurement and tracking of submicrometer structures within brain cells, as well as the spatiotemporal mapping of spikes in individual neurons and of neurotransmitter release in individual synapses. Yet, the spatial resolution of two-photon microscopy rapidly degrades as imaging is attempted at depths of more than a few scattering lengths into tissue, i.e., below the superficial layers that constitute the top 300-400 µm of the neocortex. To obviate this limitation, we shape the focal volume, generated by the excitation beam, by modulating the incident wavefront via guidestar-assisted adaptive optics. Here, we describe the construction, calibration and operation of a two-photon microscope that incorporates adaptive optics to restore diffraction-limited resolution at depths close to 900 µm in the mouse cortex. Our setup detects a guidestar formed by the excitation of a red-shifted dye in blood serum, used to directly measure the wavefront. We incorporate predominantly commercially available optical, optomechanical, mechanical and electronic components, and supply computer-aided design models of other customized components. The resulting adaptive optics two-photon microscope is modular and allows for expanded imaging and optical excitation capabilities. We demonstrate our methodology in the mouse neocortex by imaging the morphology of somatostatin-expressing neurons that lie 700 µm beneath the pia, calcium dynamics of layer 5b projection neurons and thalamocortical glutamate transmission to L4 neurons. The protocol requires ~30 d to complete and is suitable for users with graduate-level expertise in optics.
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Affiliation(s)
- Pantong Yao
- Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Rui Liu
- Department of Physics, University of California San Diego, La Jolla, CA, USA
| | - Thomas Broggini
- Department of Physics, University of California San Diego, La Jolla, CA, USA
| | - Martin Thunemann
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - David Kleinfeld
- Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, USA.
- Department of Physics, University of California San Diego, La Jolla, CA, USA.
- Department of Neurobiology, University of California San Diego, La Jolla, CA, USA.
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34
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Hu Q, Hailstone M, Wang J, Wincott M, Stoychev D, Atilgan H, Gala D, Chaiamarit T, Parton RM, Antonello J, Packer AM, Davis I, Booth MJ. Universal adaptive optics for microscopy through embedded neural network control. LIGHT, SCIENCE & APPLICATIONS 2023; 12:270. [PMID: 37953294 PMCID: PMC10641083 DOI: 10.1038/s41377-023-01297-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 09/24/2023] [Accepted: 10/01/2023] [Indexed: 11/14/2023]
Abstract
The resolution and contrast of microscope imaging is often affected by aberrations introduced by imperfect optical systems and inhomogeneous refractive structures in specimens. Adaptive optics (AO) compensates these aberrations and restores diffraction limited performance. A wide range of AO solutions have been introduced, often tailored to a specific microscope type or application. Until now, a universal AO solution - one that can be readily transferred between microscope modalities - has not been deployed. We propose versatile and fast aberration correction using a physics-based machine learning assisted wavefront-sensorless AO control (MLAO) method. Unlike previous ML methods, we used a specially constructed neural network (NN) architecture, designed using physical understanding of the general microscope image formation, that was embedded in the control loop of different microscope systems. The approach means that not only is the resulting NN orders of magnitude simpler than previous NN methods, but the concept is translatable across microscope modalities. We demonstrated the method on a two-photon, a three-photon and a widefield three-dimensional (3D) structured illumination microscope. Results showed that the method outperformed commonly-used modal-based sensorless AO methods. We also showed that our ML-based method was robust in a range of challenging imaging conditions, such as 3D sample structures, specimen motion, low signal to noise ratio and activity-induced fluorescence fluctuations. Moreover, as the bespoke architecture encapsulated physical understanding of the imaging process, the internal NN configuration was no-longer a "black box", but provided physical insights on internal workings, which could influence future designs.
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Affiliation(s)
- Qi Hu
- Department of Engineering Science, University of Oxford, Oxford, UK
| | | | - Jingyu Wang
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Matthew Wincott
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Danail Stoychev
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Huriye Atilgan
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, UK
| | - Dalia Gala
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Tai Chaiamarit
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Jacopo Antonello
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Adam M Packer
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, UK
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Martin J Booth
- Department of Engineering Science, University of Oxford, Oxford, UK.
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35
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Yu Y, Hou M, Hou C, Shi Z, Zhao J, Cui G. Self-Modulated Ghost Imaging in Dynamic Scattering Media. SENSORS (BASEL, SWITZERLAND) 2023; 23:9002. [PMID: 37960701 PMCID: PMC10648716 DOI: 10.3390/s23219002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/19/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023]
Abstract
In this paper, self-modulated ghost imaging (SMGI) in a surrounded scattering medium is proposed. Different from traditional ghost imaging, SMGI can take advantage of the dynamic scattering medium that originally affects the imaging quality and generate pseudo-thermal light through the dynamic scattering of free particles' Brownian motion in the scattering environment for imaging. Theoretical analysis and simulation were used to establish the relationship between imaging quality and particle concentration. An experimental setup was also built to verify the feasibility of the SMGI. Compared with the reconstructed image quality and evaluation indexes of traditional ghost imaging, SMGI has better image quality, which demonstrates a promising future in dynamic high-scattering media such as dense fog and turbid water.
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Affiliation(s)
- Ying Yu
- Institute of Carbon Neutrality and New Energy, School of Electronics and Information, Hangzhou Dianzi University, Hangzhou 310018, China; (Y.Y.); (M.H.); (Z.S.); (J.Z.); (G.C.)
- Zhejiang Province Key Laboratory of Equipment Electronics, Hangzhou 310018, China
| | - Mingxuan Hou
- Institute of Carbon Neutrality and New Energy, School of Electronics and Information, Hangzhou Dianzi University, Hangzhou 310018, China; (Y.Y.); (M.H.); (Z.S.); (J.Z.); (G.C.)
- Zhejiang Province Key Laboratory of Equipment Electronics, Hangzhou 310018, China
| | - Changlun Hou
- Institute of Carbon Neutrality and New Energy, School of Electronics and Information, Hangzhou Dianzi University, Hangzhou 310018, China; (Y.Y.); (M.H.); (Z.S.); (J.Z.); (G.C.)
- Zhejiang Province Key Laboratory of Equipment Electronics, Hangzhou 310018, China
| | - Zhen Shi
- Institute of Carbon Neutrality and New Energy, School of Electronics and Information, Hangzhou Dianzi University, Hangzhou 310018, China; (Y.Y.); (M.H.); (Z.S.); (J.Z.); (G.C.)
- Zhejiang Province Key Laboratory of Equipment Electronics, Hangzhou 310018, China
| | - Jufeng Zhao
- Institute of Carbon Neutrality and New Energy, School of Electronics and Information, Hangzhou Dianzi University, Hangzhou 310018, China; (Y.Y.); (M.H.); (Z.S.); (J.Z.); (G.C.)
- Zhejiang Province Key Laboratory of Equipment Electronics, Hangzhou 310018, China
| | - Guangmang Cui
- Institute of Carbon Neutrality and New Energy, School of Electronics and Information, Hangzhou Dianzi University, Hangzhou 310018, China; (Y.Y.); (M.H.); (Z.S.); (J.Z.); (G.C.)
- Zhejiang Province Key Laboratory of Equipment Electronics, Hangzhou 310018, China
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36
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Wu X, Huang L, Gu N. Enhanced-resolution Shack-Hartmann wavefront sensing for extended objects. OPTICS LETTERS 2023; 48:5691-5694. [PMID: 37910735 DOI: 10.1364/ol.504057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/07/2023] [Indexed: 11/03/2023]
Abstract
Adaptive optics systems for large-aperture solar telescopes, especially multiconjugate adaptive optics systems, suffer from a fundamental trade-off between wavefront sampling rate and sub-aperture resolution. We introduce an enhanced-resolution Shack-Hartmann wavefront sensing method that decouples sub-aperture resolution from the desired wavefront sampling rate. We experimentally verified the validity of this method. Results show that by synthesizing multiple low-spatial samplings, this method is capable to sense higher-frequency aberrations beyond any low-spatial sampling involved in the synthesis, and it allows higher sub-aperture resolution and higher operating bandwidths, which can better fulfill the needs of solar adaptive optics.
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37
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Zhang P, Ma D, Cheng X, Tsai AP, Tang Y, Gao HC, Fang L, Bi C, Landreth GE, Chubykin AA, Huang F. Deep learning-driven adaptive optics for single-molecule localization microscopy. Nat Methods 2023; 20:1748-1758. [PMID: 37770712 PMCID: PMC10630144 DOI: 10.1038/s41592-023-02029-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/23/2023] [Indexed: 09/30/2023]
Abstract
The inhomogeneous refractive indices of biological tissues blur and distort single-molecule emission patterns generating image artifacts and decreasing the achievable resolution of single-molecule localization microscopy (SMLM). Conventional sensorless adaptive optics methods rely on iterative mirror changes and image-quality metrics. However, these metrics result in inconsistent metric responses and thus fundamentally limit their efficacy for aberration correction in tissues. To bypass iterative trial-then-evaluate processes, we developed deep learning-driven adaptive optics for SMLM to allow direct inference of wavefront distortion and near real-time compensation. Our trained deep neural network monitors the individual emission patterns from single-molecule experiments, infers their shared wavefront distortion, feeds the estimates through a dynamic filter and drives a deformable mirror to compensate sample-induced aberrations. We demonstrated that our method simultaneously estimates and compensates 28 wavefront deformation shapes and improves the resolution and fidelity of three-dimensional SMLM through >130-µm-thick brain tissue specimens.
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Affiliation(s)
- Peiyi Zhang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Donghan Ma
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
| | - Xi Cheng
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA
| | - Andy P Tsai
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yu Tang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA
| | - Hao-Cheng Gao
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Li Fang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Cheng Bi
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Gary E Landreth
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Alexander A Chubykin
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA.
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA.
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.
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38
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Clare RM, Weddell SJ, Engler BE. Direct wavefront reconstruction with the cone wavefront sensor using the inverse radon transform. APPLIED OPTICS 2023; 62:8052-8059. [PMID: 38038100 DOI: 10.1364/ao.497707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/01/2023] [Indexed: 12/02/2023]
Abstract
The cone wavefront sensor consists of a cone (or axicon) placed at the focal plane of the imaging system, from which an annular intensity image is formed. Typically, the wavefront phase is estimated using inversion of an interaction matrix relating the intensity image to different aberration modes. In this paper, we show that the intensity image for the cone wavefront sensor is related to the radon transform of the wavefront phase. A reconstruction method using the inverse radon transform (filtered back-projection) is shown to be able to directly approximate the wavefront phase without the need for an interaction matrix for small wavefront aberrations.
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39
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Xu A, Nourshargh C, Salter PS, He C, Elston SJ, Booth MJ, Morris SM. Laser-Written Tunable Liquid Crystal Aberration Correctors. ACS PHOTONICS 2023; 10:3401-3408. [PMID: 37743939 PMCID: PMC10515613 DOI: 10.1021/acsphotonics.3c00907] [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: 06/30/2023] [Indexed: 09/26/2023]
Abstract
In this Article, we present a series of novel laser-written liquid crystal (LC) devices for aberration control for applications in beam shaping or aberration correction through adaptive optics. Each transparent LC device can correct for a chosen aberration mode with continuous greyscale tuning up to a total magnitude of more than 2π radians phase difference peak to peak at a wavelength of λ = 660 nm. For the purpose of demonstration, we present five different devices for the correction of five independent Zernike polynomial modes (although the technique could readily be used to manufacture devices based on other modes). Each device is operated by a single electrode pair tuned between 0 and 10 V. These devices have potential as a low-cost alternative to spatial light modulators for applications where a low-order aberration correction is sufficient and transmissive geometries are required.
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Affiliation(s)
- Alec Xu
- Department of Engineering
Science, University of Oxford, Parks Road, Oxford, OX3 1PJ, United Kingdom
| | - Camron Nourshargh
- Department of Engineering
Science, University of Oxford, Parks Road, Oxford, OX3 1PJ, United Kingdom
| | - Patrick S. Salter
- Department of Engineering
Science, University of Oxford, Parks Road, Oxford, OX3 1PJ, United Kingdom
| | - Chao He
- Department of Engineering
Science, University of Oxford, Parks Road, Oxford, OX3 1PJ, United Kingdom
| | - Steve J. Elston
- Department of Engineering
Science, University of Oxford, Parks Road, Oxford, OX3 1PJ, United Kingdom
| | - Martin J. Booth
- Department of Engineering
Science, University of Oxford, Parks Road, Oxford, OX3 1PJ, United Kingdom
| | - Stephen M. Morris
- Department of Engineering
Science, University of Oxford, Parks Road, Oxford, OX3 1PJ, United Kingdom
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40
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Samanta R, Mujumdar S. Controlling the transmission of broadband light through scattering media using a digital micromirror device. OPTICS LETTERS 2023; 48:4241-4244. [PMID: 37582002 DOI: 10.1364/ol.495297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/11/2023] [Indexed: 08/17/2023]
Abstract
Wavefront shaping has emerged as a valuable technique in complex photonics, wherein the various eigenmodes of the disordered medium are selectively excited to control the overall transmission through the medium. The process utilizes active optical devices such as liquid crystal-based spatial light modulators (LC-SLM), deformable mirrors (DM), and digital micromirror devices (DMD). Among these, the latter is preferred for imaging through dynamic scattering media such as living biological tissues due to their high-speed refresh rate and increased resolution. This study employs a genetic algorithm along with binary amplitude modulation generated by a digital micromirror device to spatially and spectrally control the large spectral bandwidth through a scattering medium. We illustrate spatial single-point focusing of broadband light, multipoint focusing of broadband light, and programmable spectral filtering of the same through disordered samples.
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41
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Feng BY, Guo H, Xie M, Boominathan V, Sharma MK, Veeraraghavan A, Metzler CA. NeuWS: Neural wavefront shaping for guidestar-free imaging through static and dynamic scattering media. SCIENCE ADVANCES 2023; 9:eadg4671. [PMID: 37379386 DOI: 10.1126/sciadv.adg4671] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/23/2023] [Indexed: 06/30/2023]
Abstract
Diffraction-limited optical imaging through scattering media has the potential to transform many applications such as airborne and space-based imaging (through the atmosphere), bioimaging (through skin and human tissue), and fiber-based imaging (through fiber bundles). Existing wavefront shaping methods can image through scattering media and other obscurants by optically correcting wavefront aberrations using high-resolution spatial light modulators-but these methods generally require (i) guidestars, (ii) controlled illumination, (iii) point scanning, and/or (iv) statics scenes and aberrations. We propose neural wavefront shaping (NeuWS), a scanning-free wavefront shaping technique that integrates maximum likelihood estimation, measurement modulation, and neural signal representations to reconstruct diffraction-limited images through strong static and dynamic scattering media without guidestars, sparse targets, controlled illumination, nor specialized image sensors. We experimentally demonstrate guidestar-free, wide field-of-view, high-resolution, diffraction-limited imaging of extended, nonsparse, and static/dynamic scenes captured through static/dynamic aberrations.
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Affiliation(s)
- Brandon Y Feng
- Department of Computer Science, The University of Maryland, College Park, College Park, MD 20742, USA
| | - Haiyun Guo
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Mingyang Xie
- Department of Computer Science, The University of Maryland, College Park, College Park, MD 20742, USA
| | - Vivek Boominathan
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Manoj K Sharma
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Ashok Veeraraghavan
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Christopher A Metzler
- Department of Computer Science, The University of Maryland, College Park, College Park, MD 20742, USA
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42
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Zhu Z, Wen Y, Li J, Chen Y, Peng Z, Li J, Zhu L, Wu Y, Zhou L, Liu L, Zong L, Yu S. Metasurface-enabled polarization-independent LCoS spatial light modulator for 4K resolution and beyond. LIGHT, SCIENCE & APPLICATIONS 2023; 12:151. [PMID: 37331984 DOI: 10.1038/s41377-023-01202-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 05/17/2023] [Accepted: 06/03/2023] [Indexed: 06/20/2023]
Abstract
With the distinct advantages of high resolution, small pixel size, and multi-level pure phase modulation, liquid crystal on silicon (LCoS) devices afford precise and reconfigurable spatial light modulation that enables versatile applications ranging from micro-displays to optical communications. However, LCoS devices suffer from a long-standing problem of polarization-dependent response in that they only perform phase modulation on one linear polarization of light, and polarization-independent phase modulation-essential for most applications-have had to use complicated polarization-diversity optics. We propose and demonstrate, for the first time, an LCoS device that directly achieves high-performance polarization-independent phase modulation at telecommunication wavelengths with 4K resolution and beyond by embedding a polarization-rotating metasurface between the LCoS backplane and the liquid crystal phase-modulating layer. We verify the device with a number of typical polarization-independent application functions including beam steering, holographical display, and in a key optical switching element - wavelength selective switch (WSS), demonstrating the significant benefits in terms of both configuration simplification and performance improvement.
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Affiliation(s)
- Zhaoxiang Zhu
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yuanhui Wen
- Huawei Technologies Co., Ltd., Bantian, Longgang District, Shenzhen, 518129, China
| | - Jiaqi Li
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yujie Chen
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Zenghui Peng
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China
| | - Jianxiong Li
- Huawei Technologies Co., Ltd., Bantian, Longgang District, Shenzhen, 518129, China
| | - Lei Zhu
- Huawei Technologies Co., Ltd., Bantian, Longgang District, Shenzhen, 518129, China
| | - Yunfei Wu
- Huawei Technologies Co., Ltd., Bantian, Longgang District, Shenzhen, 518129, China
| | - Lidan Zhou
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Lin Liu
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Liangjia Zong
- Huawei Technologies Co., Ltd., Bantian, Longgang District, Shenzhen, 518129, China.
| | - Siyuan Yu
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, 510275, China
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43
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Daetwyler S, Fiolka RP. Light-sheets and smart microscopy, an exciting future is dawning. Commun Biol 2023; 6:502. [PMID: 37161000 PMCID: PMC10169780 DOI: 10.1038/s42003-023-04857-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 04/20/2023] [Indexed: 05/11/2023] Open
Abstract
Light-sheet fluorescence microscopy has transformed our ability to visualize and quantitatively measure biological processes rapidly and over long time periods. In this review, we discuss current and future developments in light-sheet fluorescence microscopy that we expect to further expand its capabilities. This includes smart and adaptive imaging schemes to overcome traditional imaging trade-offs, i.e., spatiotemporal resolution, field of view and sample health. In smart microscopy, a microscope will autonomously decide where, when, what and how to image. We further assess how image restoration techniques provide avenues to overcome these tradeoffs and how "open top" light-sheet microscopes may enable multi-modal imaging with high throughput. As such, we predict that light-sheet microscopy will fulfill an important role in biomedical and clinical imaging in the future.
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Affiliation(s)
- Stephan Daetwyler
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Reto Paul Fiolka
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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44
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Zhao Z, Zhou Y, Liu B, He J, Zhao J, Cai Y, Fan J, Li X, Wang Z, Lu Z, Wu J, Qi H, Dai Q. Two-photon synthetic aperture microscopy for minimally invasive fast 3D imaging of native subcellular behaviors in deep tissue. Cell 2023; 186:2475-2491.e22. [PMID: 37178688 DOI: 10.1016/j.cell.2023.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/21/2023] [Accepted: 04/10/2023] [Indexed: 05/15/2023]
Abstract
Holistic understanding of physio-pathological processes requires noninvasive 3D imaging in deep tissue across multiple spatial and temporal scales to link diverse transient subcellular behaviors with long-term physiogenesis. Despite broad applications of two-photon microscopy (TPM), there remains an inevitable tradeoff among spatiotemporal resolution, imaging volumes, and durations due to the point-scanning scheme, accumulated phototoxicity, and optical aberrations. Here, we harnessed the concept of synthetic aperture radar in TPM to achieve aberration-corrected 3D imaging of subcellular dynamics at a millisecond scale for over 100,000 large volumes in deep tissue, with three orders of magnitude reduction in photobleaching. With its advantages, we identified direct intercellular communications through migrasome generation following traumatic brain injury, visualized the formation process of germinal center in the mouse lymph node, and characterized heterogeneous cellular states in the mouse visual cortex, opening up a horizon for intravital imaging to understand the organizations and functions of biological systems at a holistic level.
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Affiliation(s)
- Zhifeng Zhao
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou 311100, China
| | - Yiliang Zhou
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou 311100, China
| | - Bo Liu
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Laboratory of Dynamic Immunobiology, Institute for Immunology, Tsinghua University, Beijing 100084, China; Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jing He
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Jiayin Zhao
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518071, China
| | - Yeyi Cai
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Jingtao Fan
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China
| | - Xinyang Li
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou 311100, China; Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518071, China
| | - Zilin Wang
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Department of Anesthesiology, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Zhi Lu
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou 311100, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China.
| | - Hai Qi
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Laboratory of Dynamic Immunobiology, Institute for Immunology, Tsinghua University, Beijing 100084, China; Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua University, Beijing 100084, China; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China.
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45
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Ranasinghesagara JC, Potma EO, Venugopalan V. Modeling nonlinear optical microscopy in scattering media, part I. Propagation from lens to focal volume: tutorial. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2023; 40:867-882. [PMID: 37133184 PMCID: PMC10607893 DOI: 10.1364/josaa.478712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/11/2023] [Indexed: 05/04/2023]
Abstract
The development and application of nonlinear optical (NLO) microscopy methods in biomedical research have experienced rapid growth over the past three decades. Despite the compelling power of these methods, optical scattering limits their practical use in biological tissues. This tutorial offers a model-based approach illustrating how analytical methods from classical electromagnetism can be employed to comprehensively model NLO microscopy in scattering media. In Part I, we quantitatively model focused beam propagation in non-scattering and scattering media from the lens to focal volume. In Part II, we model signal generation, radiation, and far-field detection. Moreover, we detail modeling approaches for major optical microscopy modalities including classical fluorescence, multi-photon fluorescence, second harmonic generation, and coherent anti-Stokes Raman microscopy.
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Affiliation(s)
- Janaka C. Ranasinghesagara
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, USA
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, California 92697, USA
| | - Eric O. Potma
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, California 92697, USA
- Department of Chemistry, University of California, Irvine, California 92697, USA
| | - Vasan Venugopalan
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, USA
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, California 92697, USA
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46
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Zhang Q, Yang Y, Cao KJ, Chen W, Paidi S, Xia CH, Kramer RH, Gong X, Ji N. Retinal microvascular and neuronal pathologies probed in vivo by adaptive optical two-photon fluorescence microscopy. eLife 2023; 12:84853. [PMID: 37039777 PMCID: PMC10089658 DOI: 10.7554/elife.84853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/19/2023] [Indexed: 04/12/2023] Open
Abstract
The retina, behind the transparent optics of the eye, is the only neural tissue whose physiology and pathology can be non-invasively probed by optical microscopy. The aberrations intrinsic to the mouse eye, however, prevent high-resolution investigation of retinal structure and function in vivo. Optimizing the design of a two-photon fluorescence microscope (2PFM) and sample preparation procedure, we found that adaptive optics (AO), by measuring and correcting ocular aberrations, is essential for resolving putative synaptic structures and achieving three-dimensional cellular resolution in the mouse retina in vivo. Applying AO-2PFM to longitudinal retinal imaging in transgenic models of retinal pathology, we characterized microvascular lesions with sub-capillary details in a proliferative vascular retinopathy model, and found Lidocaine to effectively suppress retinal ganglion cell hyperactivity in a retinal degeneration model. Tracking structural and functional changes at high-resolution longitudinally, AO-2PFM enables microscopic investigations of retinal pathology and pharmacology for disease diagnosis and treatment in vivo.
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Affiliation(s)
- Qinrong Zhang
- Department of Physics, University of California, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Yuhan Yang
- Department of Physics, University of California, Berkeley, United States
| | - Kevin J Cao
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- Helen Wills Neuroscience Institute, University of California, Berkeley, United States
| | - Wei Chen
- Department of Physics, University of California, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Santosh Paidi
- School of Optometry, University of California, Berkeley, United States
| | - Chun-Hong Xia
- School of Optometry, University of California, Berkeley, United States
- Vision Science Program, University of California, Berkeley, United States
| | - Richard H Kramer
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- Helen Wills Neuroscience Institute, University of California, Berkeley, United States
- Vision Science Program, University of California, Berkeley, United States
| | - Xiaohua Gong
- School of Optometry, University of California, Berkeley, United States
- Vision Science Program, University of California, Berkeley, United States
| | - Na Ji
- Department of Physics, University of California, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- Helen Wills Neuroscience Institute, University of California, Berkeley, United States
- Vision Science Program, University of California, Berkeley, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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47
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Zhang Q, Hu Q, Berlage C, Kner P, Judkewitz B, Booth M, Ji N. Adaptive optics for optical microscopy [Invited]. BIOMEDICAL OPTICS EXPRESS 2023; 14:1732-1756. [PMID: 37078027 PMCID: PMC10110298 DOI: 10.1364/boe.479886] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 05/03/2023]
Abstract
Optical microscopy is widely used to visualize fine structures. When applied to bioimaging, its performance is often degraded by sample-induced aberrations. In recent years, adaptive optics (AO), originally developed to correct for atmosphere-associated aberrations, has been applied to a wide range of microscopy modalities, enabling high- or super-resolution imaging of biological structure and function in complex tissues. Here, we review classic and recently developed AO techniques and their applications in optical microscopy.
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Affiliation(s)
- Qinrong Zhang
- Department of Physics, Department of Molecular & Cellular Biology, University of California, Berkeley, CA 94720, USA
| | - Qi Hu
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Caroline Berlage
- Charité - Universitätsmedizin Berlin, Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, 10117 Berlin, Germany
- Humboldt-Universität zu Berlin, Institute for Biology, 10099 Berlin, Germany
| | - Peter Kner
- School of Electrical and Computer Engineering, University of Georgia, Athens, GA 30602, USA
| | - Benjamin Judkewitz
- Charité - Universitätsmedizin Berlin, Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, 10117 Berlin, Germany
| | - Martin Booth
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Na Ji
- Department of Physics, Department of Molecular & Cellular Biology, University of California, Berkeley, CA 94720, USA
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48
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Czymmek KJ, Duncan KE, Berg H. Realizing the Full Potential of Advanced Microscopy Approaches for Interrogating Plant-Microbe Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:245-255. [PMID: 36947723 DOI: 10.1094/mpmi-10-22-0208-fi] [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: 06/18/2023]
Abstract
Microscopy has served as a fundamental tool for insight and discovery in plant-microbe interactions for centuries. From classical light and electron microscopy to corresponding specialized methods for sample preparation and cellular contrasting agents, these approaches have become routine components in the toolkit of plant and microbiology scientists alike to visualize, probe and understand the nature of host-microbe relationships. Over the last three decades, three-dimensional perspectives led by the development of electron tomography, and especially, confocal techniques continue to provide remarkable clarity and spatial detail of tissue and cellular phenomena. Confocal and electron microscopy provide novel revelations that are now commonplace in medium and large institutions. However, many other cutting-edge technologies and sample preparation workflows are relatively unexploited yet offer tremendous potential for unprecedented advancement in our understanding of the inner workings of pathogenic, beneficial, and symbiotic plant-microbe interactions. Here, we highlight key applications, benefits, and challenges of contemporary advanced imaging platforms for plant-microbe systems with special emphasis on several recently developed approaches, such as light-sheet, single molecule, super-resolution, and adaptive optics microscopy, as well as ambient and cryo-volume electron microscopy, X-ray microscopy, and cryo-electron tomography. Furthermore, the potential for complementary sample preparation methodologies, such as optical clearing, expansion microscopy, and multiplex imaging, will be reviewed. Our ultimate goal is to stimulate awareness of these powerful cutting-edge technologies and facilitate their appropriate application and adoption to solve important and unresolved biological questions in the field. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Kirk J Czymmek
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
- Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
| | - Keith E Duncan
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
| | - Howard Berg
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
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49
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Siu DMD, Lee KCM, Chung BMF, Wong JSJ, Zheng G, Tsia KK. Optofluidic imaging meets deep learning: from merging to emerging. LAB ON A CHIP 2023; 23:1011-1033. [PMID: 36601812 DOI: 10.1039/d2lc00813k] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Propelled by the striking advances in optical microscopy and deep learning (DL), the role of imaging in lab-on-a-chip has dramatically been transformed from a silo inspection tool to a quantitative "smart" engine. A suite of advanced optical microscopes now enables imaging over a range of spatial scales (from molecules to organisms) and temporal window (from microseconds to hours). On the other hand, the staggering diversity of DL algorithms has revolutionized image processing and analysis at the scale and complexity that were once inconceivable. Recognizing these exciting but overwhelming developments, we provide a timely review of their latest trends in the context of lab-on-a-chip imaging, or coined optofluidic imaging. More importantly, here we discuss the strengths and caveats of how to adopt, reinvent, and integrate these imaging techniques and DL algorithms in order to tailor different lab-on-a-chip applications. In particular, we highlight three areas where the latest advances in lab-on-a-chip imaging and DL can form unique synergisms: image formation, image analytics and intelligent image-guided autonomous lab-on-a-chip. Despite the on-going challenges, we anticipate that they will represent the next frontiers in lab-on-a-chip imaging that will spearhead new capabilities in advancing analytical chemistry research, accelerating biological discovery, and empowering new intelligent clinical applications.
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Affiliation(s)
- Dickson M D Siu
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, Hong Kong.
| | - Kelvin C M Lee
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, Hong Kong.
| | - Bob M F Chung
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong
| | - Justin S J Wong
- Conzeb Limited, Hong Kong Science Park, Shatin, New Territories, Hong Kong
| | - Guoan Zheng
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA
| | - Kevin K Tsia
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, Hong Kong.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong
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Cecconi V, Kumar V, Pasquazi A, Totero Gongora JS, Peccianti M. Nonlinear field-control of terahertz waves in random media for spatiotemporal focusing. OPEN RESEARCH EUROPE 2023; 2:32. [PMID: 37645307 PMCID: PMC10445851 DOI: 10.12688/openreseurope.14508.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/30/2023] [Indexed: 09/15/2023]
Abstract
Controlling the transmission of broadband optical pulses in scattering media is a critical open challenge in photonics. To date, wavefront shaping techniques at optical frequencies have been successfully applied to control the spatial properties of multiple-scattered light. However, a fundamental restriction in achieving an equivalent degree of control over the temporal properties of a broadband pulse is the limited availability of experimental techniques to detect the coherent properties (i.e., the spectral amplitude and absolute phase) of the transmitted field. Terahertz experimental frameworks, on the contrary, enable measuring the field dynamics of broadband pulses at ultrafast (sub-cycle) time scales directly. In this work, we provide a theoretical/numerical demonstration that, within this context, complex scattering can be used to achieve spatio-temporal control of instantaneous fields and manipulate the temporal properties of single-cycle pulses by solely acting on spatial degrees of freedom of the illuminating field. As direct application scenarios, we demonstrate spatio-temporal focusing, chirp compensation, and control of the carrier-envelope-phase (CEP) of a CP-stable, transform-limited THz pulse.
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Affiliation(s)
- Vittorio Cecconi
- Emergent Photonics (EPic) Lab, Department of Physics and Astronomy, University of Sussex, Brighton, BN19QH, UK
- Emergent Photonics Research Centre and Dept. of Physics, Loughborough University, Loughborough, LE11 3TU, UK
| | - Vivek Kumar
- Emergent Photonics (EPic) Lab, Department of Physics and Astronomy, University of Sussex, Brighton, BN19QH, UK
| | - Alessia Pasquazi
- Emergent Photonics (EPic) Lab, Department of Physics and Astronomy, University of Sussex, Brighton, BN19QH, UK
- Emergent Photonics Research Centre and Dept. of Physics, Loughborough University, Loughborough, LE11 3TU, UK
| | - Juan Sebastian Totero Gongora
- Emergent Photonics (EPic) Lab, Department of Physics and Astronomy, University of Sussex, Brighton, BN19QH, UK
- Emergent Photonics Research Centre and Dept. of Physics, Loughborough University, Loughborough, LE11 3TU, UK
| | - Marco Peccianti
- Emergent Photonics (EPic) Lab, Department of Physics and Astronomy, University of Sussex, Brighton, BN19QH, UK
- Emergent Photonics Research Centre and Dept. of Physics, Loughborough University, Loughborough, LE11 3TU, UK
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