1
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Kramer SN, Antarasen J, Reinholt CR, Kisley L. A practical guide to light-sheet microscopy for nanoscale imaging: Looking beyond the cell. JOURNAL OF APPLIED PHYSICS 2024; 136:091101. [PMID: 39247785 PMCID: PMC11380115 DOI: 10.1063/5.0218262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 08/12/2024] [Indexed: 09/10/2024]
Abstract
We present a comprehensive guide to light-sheet microscopy (LSM) to assist scientists in navigating the practical implementation of this microscopy technique. Emphasizing the applicability of LSM to image both static microscale and nanoscale features, as well as diffusion dynamics, we present the fundamental concepts of microscopy, progressing through beam profile considerations, to image reconstruction. We outline key practical decisions in constructing a home-built system and provide insight into the alignment and calibration processes. We briefly discuss the conditions necessary for constructing a continuous 3D image and introduce our home-built code for data analysis. By providing this guide, we aim to alleviate the challenges associated with designing and constructing LSM systems and offer scientists new to LSM a valuable resource in navigating this complex field.
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Affiliation(s)
- Stephanie N Kramer
- Department of Physics, Case Western Reserve University, Rockefeller Building, 2076 Adelbert Road, Cleveland, Ohio 44106, USA
| | - Jeanpun Antarasen
- Department of Physics, Case Western Reserve University, Rockefeller Building, 2076 Adelbert Road, Cleveland, Ohio 44106, USA
| | - Cole R Reinholt
- Department of Physics, Case Western Reserve University, Rockefeller Building, 2076 Adelbert Road, Cleveland, Ohio 44106, USA
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2
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Chen Y, Chauhan S, Gong C, Dayton H, Xu C, De La Cruz ED, Tsai YYW, Datta MS, Rosoklija GB, Dwork AJ, Mann JJ, Boldrini M, Leong KW, Dietrich LEP, Tomer R. Low-cost and scalable projected light-sheet microscopy for the high-resolution imaging of cleared tissue and living samples. Nat Biomed Eng 2024; 8:1109-1123. [PMID: 39209948 DOI: 10.1038/s41551-024-01249-9] [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: 08/06/2023] [Accepted: 08/02/2024] [Indexed: 09/04/2024]
Abstract
Light-sheet fluorescence microscopy (LSFM) is a widely used technique for imaging cleared tissue and living samples. However, high-performance LSFM systems are typically expensive and not easily scalable. Here we introduce a low-cost, scalable and versatile LSFM framework, which we named 'projected light-sheet microscopy' (pLSM), with high imaging performance and small device and computational footprints. We characterized the capabilities of pLSM, which repurposes readily available consumer-grade components, optimized optics, over-network control architecture and software-driven light-sheet modulation, by performing high-resolution mapping of cleared mouse brains and of post-mortem pathological human brain samples, and via the molecular phenotyping of brain and blood-vessel organoids derived from human induced pluripotent stem cells. We also report a method that leverages pLSM for the live imaging of the dynamics of sparsely labelled multi-layered bacterial pellicle biofilms at an air-liquid interface. pLSM can make high-resolution LSFM for biomedical applications more accessible, affordable and scalable.
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Affiliation(s)
- Yannan Chen
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Shradha Chauhan
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Cheng Gong
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Hannah Dayton
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Cong Xu
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | | | - Yu-Young Wesley Tsai
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, USA
| | - Malika S Datta
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, USA
| | - Gorazd B Rosoklija
- Department of Psychiatry, Columbia University Irving Medical Center, New York State Psychiatric Institute, New York, NY, USA
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University Irving Medical Center, New York State Psychiatric Institute, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - J John Mann
- Department of Psychiatry, Columbia University Irving Medical Center, New York State Psychiatric Institute, New York, NY, USA
| | - Maura Boldrini
- Department of Psychiatry, Columbia University Irving Medical Center, New York State Psychiatric Institute, New York, NY, USA
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Raju Tomer
- Department of Biological Sciences, Columbia University, New York, NY, USA.
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
- Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, USA.
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3
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Li C, Rai MR, Cai Y, Ghashghaei HT, Greenbaum A. Intelligent Beam Optimization for Light-Sheet Fluorescence Microscopy through Deep Learning. INTELLIGENT COMPUTING (WASHINGTON, D.C.) 2024; 3:0095. [PMID: 39099879 PMCID: PMC11298055 DOI: 10.34133/icomputing.0095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/22/2024] [Indexed: 08/06/2024]
Abstract
Light-sheet fluorescence microscopy (LSFM) provides the benefit of optical sectioning coupled with rapid acquisition times, enabling high-resolution 3-dimensional imaging of large tissue-cleared samples. Inherent to LSFM, the quality of the imaging heavily relies on the characteristics of the illumination beam, which only illuminates a thin section of the sample. Therefore, substantial efforts are dedicated to identifying slender, nondiffracting beam profiles that yield uniform and high-contrast images. An ongoing debate concerns the identification of optimal illumination beams for different samples: Gaussian, Bessel, Airy patterns, and/or others. However, comparisons among different beam profiles are challenging as their optimization objectives are often different. Given that our large imaging datasets (approximately 0.5 TB of images per sample) are already analyzed using deep learning models, we envisioned a different approach to the problem by designing an illumination beam tailored to boost the performance of the deep learning model. We hypothesized that integrating the physical LSFM illumination model (after passing it through a variable phase mask) into the training of a cell detection network would achieve this goal. Here, we report that joint optimization continuously updates the phase mask and results in improved image quality for better cell detection. The efficacy of our method is demonstrated through both simulations and experiments that reveal substantial enhancements in imaging quality compared to the traditional Gaussian light sheet. We discuss how designing microscopy systems through a computational approach provides novel insights for advancing optical design that relies on deep learning models for the analysis of imaging datasets.
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Affiliation(s)
- Chen Li
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
| | - Mani Ratnam Rai
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
| | - Yuheng Cai
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
| | - H. Troy Ghashghaei
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Alon Greenbaum
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
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4
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Sui X, Kuang D, Liu G, Ding Y, Meng M, Xi R. Highly focused beam generated with a height tuned micro-optical structure for high contrast microscopic imaging. OPTICS EXPRESS 2024; 32:19308-19318. [PMID: 38859068 DOI: 10.1364/oe.523606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/04/2024] [Indexed: 06/12/2024]
Abstract
Light sheet illumination technology improves the signal-to-noise ratio, resolution, and reduces scattered backgrounds for biological microscopic detection system. Here, we developed a novel micro-optical structure to produce a focused and uniform beam for the enhancement of imaging contrast. The beam intensity and working distance can be modified by adjusting the height and period of the structure. Our experiments successfully recorded structured light illumination, demonstrating the ability of the structure to capture high-contrast imaging data. We compared the light fields generated with and without the structure to assess the imaging quality, revealing a maximum 4.78-fold improvement in the signal-to-noise ratio. This work provides a potential method for high-resolution and high-contrast light sheet fluorescence microscopic detection.
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5
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Sirinakis G, Allgeyer ES, Nashchekin D, St Johnston D. User-friendly oblique plane microscopy on a fully functional commercially available microscope base. BIOMEDICAL OPTICS EXPRESS 2024; 15:2358-2376. [PMID: 38633100 PMCID: PMC11019673 DOI: 10.1364/boe.518856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 04/19/2024]
Abstract
In this work we present an oblique plane microscope designed to work seamlessly with a commercially available microscope base. To support all the functionality offered by the microscope base, where the position of the objective lens is not fixed, we adopted a two-mirror scanning geometry that can compensate for changes to the position of the objective lens during routine microscope operation. We showed that within a ± 1 mm displacement range of the 100X, 1.35 NA objective lens away from its designed position, the PSF size increased by <3% and <11% in the lateral and axial dimensions, respectively, while the error in magnification was <0.5% within volumes extending ± 10 µm about the focal plane. Compared to the more traditional scan-lens/galvo-mirror combination, the two-mirror scanning geometry offers higher light efficiency and a more compact footprint, which could be beneficial to all OPM designs regardless of the use of a commercial base or not.
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Affiliation(s)
- George Sirinakis
- The Gurdon Institute and the Department of Genetics University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom
| | - Edward S Allgeyer
- The Gurdon Institute and the Department of Genetics University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom
| | - Dmitry Nashchekin
- The Gurdon Institute and the Department of Genetics University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom
| | - Daniel St Johnston
- The Gurdon Institute and the Department of Genetics University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom
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6
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Michálková I, Colombel S, Gomes AD, Čižmár T. Generating Airy beams through multimode fibres. OPTICS EXPRESS 2024; 32:6838-6847. [PMID: 38439380 DOI: 10.1364/oe.506926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/17/2023] [Indexed: 03/06/2024]
Abstract
Focussing light through a multimode fibre (MMF) is the basis of holographic endoscopes, which currently enable detailed imaging of deep tissue. Achieving high fidelity and purity diffraction-limited foci has been shown to be possible, when fully controlling the amplitude, phase, and two orthogonal polarisation states of the input field. Yet, generating more complex field distributions with similar performance remains to be assessed. Here, we demonstrate the generation of Airy beams through an MMF containing in excess of 90 % of the optical power delivered by the fibre. We discuss two distinct methods for generating optical landscapes: the direct field and the Fourier domain synthesis. Moreover, we showcase the flexibility of the Fourier domain synthesis to modify the generated beam.
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7
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Li H, Liu G, Zhong Q, Chen SC. Pixel-reassigned line-scanning microscopy for fast volumetric super-resolution imaging. OPTICS EXPRESS 2024; 32:2347-2355. [PMID: 38297767 DOI: 10.1364/oe.507217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/21/2023] [Indexed: 02/02/2024]
Abstract
Super-resolution microscopy has revolutionized the field of biophotonics by revealing detailed 3D biological structures. Nonetheless, the technique is still largely limited by the low throughput and hampered by increased background signals for dense or thick biological specimens. In this paper, we present a pixel-reassigned continuous line-scanning microscope for large-scale high-speed 3D super-resolution imaging, which achieves an imaging resolution of 0.41 µm in the lateral direction, i.e., a 2× resolution enhancement from the raw images. Specifically, the recorded line images are first reassigned to the line-excitation center at each scanning position to enhance the resolution. Next, a modified HiLo algorithm is applied to reduce the background signals. Parametric models have been developed to simulate the imaging results of randomly distributed fluorescent beads. Imaging experiments were designed and performed to verify the predicted performance on various biological samples, which demonstrated an imaging speed of 3400 pixels/ms on millimeter-scale specimens. These results confirm the pixel-reassigned line-scanning microscopy is a facile and powerful method to realize large-area super-resolution imaging on thick or dense biological samples.
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8
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Li C, Rai MR, Cai Y, Ghashghaei HT, Greenbaum A. Enhancing Light-Sheet Fluorescence Microscopy Illumination Beams through Deep Design Optimization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569329. [PMID: 38077074 PMCID: PMC10705487 DOI: 10.1101/2023.11.29.569329] [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: 12/23/2023]
Abstract
Light sheet fluorescence microscopy (LSFM) provides the benefit of optical sectioning coupled with rapid acquisition times for imaging of tissue-cleared specimen. This allows for high-resolution 3D imaging of large tissue volumes. Inherently to LSFM, the quality of the imaging heavily relies on the characteristics of the illumination beam, with the notion that the illumination beam only illuminates a thin section that is being imaged. Therefore, substantial efforts are dedicated to identifying slender, non-diffracting beam profiles that can yield uniform and high-contrast images. An ongoing debate concerns the employment of the most optimal illumination beam; Gaussian, Bessel, Airy patterns and/or others. Comparisons among different beam profiles is challenging as their optimization objective is often different. Given that our large imaging datasets (~0.5TB images per sample) is already analyzed using deep learning models, we envisioned a different approach to this problem by hypothesizing that we can tailor the illumination beam to boost the deep learning models performance. We achieve this by integrating the physical LSFM illumination model after passing through a variable phase mask into the training of a cell detection network. Here we report that the joint optimization continuously updates the phase mask, improving the image quality for better cell detection. Our method's efficacy is demonstrated through both simulations and experiments, revealing substantial enhancements in imaging quality compared to traditional Gaussian light sheet. We offer valuable insights for designing microscopy systems through a computational approach that exhibits significant potential for advancing optics design that relies on deep learning models for analysis of imaging datasets.
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Affiliation(s)
- Chen Li
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
| | - Mani Ratnam Rai
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
| | - Yuheng Cai
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
| | - H. Troy Ghashghaei
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Alon Greenbaum
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
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9
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Fazel M, Grussmayer KS, Ferdman B, Radenovic A, Shechtman Y, Enderlein J, Pressé S. Fluorescence Microscopy: a statistics-optics perspective. ARXIV 2023:arXiv:2304.01456v3. [PMID: 37064525 PMCID: PMC10104198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Fundamental properties of light unavoidably impose features on images collected using fluorescence microscopes. Modeling these features is ever more important in quantitatively interpreting microscopy images collected at scales on par or smaller than light's wavelength. Here we review the optics responsible for generating fluorescent images, fluorophore properties, microscopy modalities leveraging properties of both light and fluorophores, in addition to the necessarily probabilistic modeling tools imposed by the stochastic nature of light and measurement.
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Affiliation(s)
- Mohamadreza Fazel
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
| | - Kristin S Grussmayer
- Department of Bionanoscience, Faculty of Applied Science and Kavli Institute for Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Boris Ferdman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
| | - Yoav Shechtman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University, Göttingen, Germany
| | - Steve Pressé
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
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10
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Liu JTC, Glaser AK, Poudel C, Vaughan JC. Nondestructive 3D Pathology with Light-Sheet Fluorescence Microscopy for Translational Research and Clinical Assays. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:231-252. [PMID: 36854208 DOI: 10.1146/annurev-anchem-091222-092734] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In recent years, there has been a revived appreciation for the importance of spatial context and morphological phenotypes for both understanding disease progression and guiding treatment decisions. Compared with conventional 2D histopathology, which is the current gold standard of medical diagnostics, nondestructive 3D pathology offers researchers and clinicians the ability to visualize orders of magnitude more tissue within their natural volumetric context. This has been enabled by rapid advances in tissue-preparation methods, high-throughput 3D microscopy instrumentation, and computational tools for processing these massive feature-rich data sets. Here, we provide a brief overview of many of these technical advances along with remaining challenges to be overcome. We also speculate on the future of 3D pathology as applied in translational investigations, preclinical drug development, and clinical decision-support assays.
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Affiliation(s)
- Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA;
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA;
- Allen Institute for Neural Dynamics, Seattle, Washington, USA
| | - Chetan Poudel
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA
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11
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Roy S, Wang D, Rudzite AM, Perry B, Scalabrino ML, Thapa M, Gong Y, Sher A, Field GD. Large-scale interrogation of retinal cell functions by 1-photon light-sheet microscopy. CELL REPORTS METHODS 2023; 3:100453. [PMID: 37159670 PMCID: PMC10163030 DOI: 10.1016/j.crmeth.2023.100453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/05/2023] [Accepted: 03/24/2023] [Indexed: 05/11/2023]
Abstract
Visual processing in the retina depends on the collective activity of large ensembles of neurons organized in different layers. Current techniques for measuring activity of layer-specific neural ensembles rely on expensive pulsed infrared lasers to drive 2-photon activation of calcium-dependent fluorescent reporters. We present a 1-photon light-sheet imaging system that can measure the activity in hundreds of neurons in the ex vivo retina over a large field of view while presenting visual stimuli. This allows for a reliable functional classification of different retinal cell types. We also demonstrate that the system has sufficient resolution to image calcium entry at individual synaptic release sites across the axon terminals of dozens of simultaneously imaged bipolar cells. The simple design, large field of view, and fast image acquisition make this a powerful system for high-throughput and high-resolution measurements of retinal processing at a fraction of the cost of alternative approaches.
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Affiliation(s)
- Suva Roy
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Depeng Wang
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Andra M. Rudzite
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Benjamin Perry
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Miranda L. Scalabrino
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
- Stein Eye Institute, Department of Ophthalmology, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Mishek Thapa
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
- Stein Eye Institute, Department of Ophthalmology, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Yiyang Gong
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Alexander Sher
- Santa Cruz Institute for Particle Physics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Greg D. Field
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
- Stein Eye Institute, Department of Ophthalmology, University of California, Los Angeles, Los Angeles, CA 90024, USA
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12
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Liu G, Ruan X, Milkie DE, Görlitz F, Mueller M, Hercule W, Killilea A, Betzig E, Upadhyayula S. Characterization, comparison, and optimization of lattice light sheets. SCIENCE ADVANCES 2023; 9:eade6623. [PMID: 37000868 PMCID: PMC10065451 DOI: 10.1126/sciadv.ade6623] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Lattice light sheet microscopy excels at the noninvasive imaging of three-dimensional (3D) dynamic processes at high spatiotemporal resolution within cells and developing embryos. Recently, several papers have called into question the performance of lattice light sheets relative to the Gaussian sheets most common in light sheet microscopy. Here, we undertake a theoretical and experimental analysis of various forms of light sheet microscopy, which demonstrates and explains why lattice light sheets provide substantial improvements in resolution and photobleaching reduction. The analysis provides a procedure to select the correct light sheet for a desired experiment and specifies the processing that maximizes the use of all fluorescence generated within the light sheet excitation envelope for optimal resolution while minimizing image artifacts and photodamage. We also introduce a new type of "harmonic balanced" lattice light sheet that improves performance at all spatial frequencies within its 3D resolution limits and maintains this performance over lengthened propagation distances allowing for expanded fields of view.
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Affiliation(s)
- Gaoxiang Liu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xiongtao Ruan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniel E. Milkie
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20417, USA
| | - Frederik Görlitz
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Matthew Mueller
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Wilmene Hercule
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alison Killilea
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Eric Betzig
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20417, USA
- Department of Physics, Howard Hughes Medical Institute, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Srigokul Upadhyayula
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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13
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Lu CH, Huang CY, Tian X, Chen P, Chen BC. Large-scale expanded sample imaging with tiling lattice lightsheet microscopy. Int J Biochem Cell Biol 2023; 154:106340. [PMID: 36442734 DOI: 10.1016/j.biocel.2022.106340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
The ability to observe biological nanostructures forms a vital step in understanding their functions. Thanks to the invention of expansion microscopy (ExM) technology, super-resolution features of biological samples can now be easily visualized with conventional light microscopies. However, when the sample is physically expanded, the demand for deep and precise 3D imaging increases. Lattice lightsheet microscopy (LLSM), which utilizes a planar illumination that is confined within the imaging depth of high numerical aperture (NA=1.1) detection objective, fulfils such requirements. In addition, optical tiling could be implemented to increase the field of view (FoV) by moving the lightsheet without mechanically moving the samples or the objective for high-precision 3D imaging. In this review article, we will explain the principle of the tiling lattice lightsheet microscopy (tLLSM), which combines optical tiling and lattice lightsheet, and discuss the applications of tLLSM in ExM.
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Affiliation(s)
- Chieh-Han Lu
- Research Center for Applied Sciences, Academia Sinica, Taipei 115, Taiwan; Institute and Undergraduate Program of Electro-Optical Engineering, National Taiwan Normal University, Taipei 116, Taiwan.
| | - Cheng-Yu Huang
- Research Center for Applied Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Xuejiao Tian
- Research Center for Applied Sciences, Academia Sinica, Taipei 115, Taiwan; Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan; Department of Engineering and System Science, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 115, Taiwan; Institute of Physics, Academia Sinica, Taipei 115, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 115, Taiwan
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14
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Lo Vercio LD, Green RM, Robertson S, Guo S, Dauter A, Marchini M, Vidal-GARCíA M, Zhao X, Mahika A, Marcucio RS, HALLGRíMSSON B, Forkert ND. Segmentation of Tissues and Proliferating Cells in Light-Sheet Microscopy Images of Mouse Embryos Using Convolutional Neural Networks. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2022; 10:105084-105100. [PMID: 36660260 PMCID: PMC9848387 DOI: 10.1109/access.2022.3210542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A variety of genetic mutations affect cell proliferation during organism development, leading to structural birth defects. However, the mechanisms by which these alterations influence the development of the face remain unclear. Cell proliferation and its relation to shape variation can be studied using Light-Sheet Microscopy (LSM) imaging across a range of developmental time points using mouse models. The aim of this work was to develop and evaluate accurate automatic methods based on convolutional neural networks (CNNs) for: (i) tissue segmentation (neural ectoderm and mesenchyme), (ii) cell segmentation in nuclear-stained images, and (iii) segmentation of proliferating cells in phospho-Histone H3 (pHH3)-stained LSM images of mouse embryos. For training and evaluation of the CNN models, 155 to 176 slices from 10 mouse embryo LSM images with corresponding manual segmentations were available depending on the segmentation task. Three U-net CNN models were trained optimizing their loss functions, among other hyper-parameters, depending on the segmentation task. The tissue segmentation achieved a macro-average F-score of 0.84, whereas the inter-observer value was 0.89. The cell segmentation achieved a Dice score of 0.57 and 0.56 for nuclear-stained and pHH3-stained images, respectively, whereas the corresponding inter-observer Dice scores were 0.39 and 0.45, respectively. The proposed pipeline using the U-net CNN architecture can accelerate LSM image analysis and together with the annotated datasets can serve as a reference for comparison of more advanced LSM image segmentation methods in future.
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Affiliation(s)
- Lucas D Lo Vercio
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Rebecca M Green
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Samuel Robertson
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Radiology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Sienna Guo
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Andreas Dauter
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Marta Marchini
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Marta Vidal-GARCíA
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Xiang Zhao
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Anandita Mahika
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Ralph S Marcucio
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA 94115, USA
| | - Benedikt HALLGRíMSSON
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Nils D Forkert
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Radiology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
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15
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Isotropic imaging across spatial scales with axially swept light-sheet microscopy. Nat Protoc 2022; 17:2025-2053. [PMID: 35831614 PMCID: PMC10111370 DOI: 10.1038/s41596-022-00706-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 03/30/2022] [Indexed: 11/09/2022]
Abstract
Light-sheet fluorescence microscopy is a rapidly growing technique that has gained tremendous popularity in the life sciences owing to its high-spatiotemporal resolution and gentle, non-phototoxic illumination. In this protocol, we provide detailed directions for the assembly and operation of a versatile light-sheet fluorescence microscopy variant, referred to as axially swept light-sheet microscopy (ASLM), that delivers an unparalleled combination of field of view, optical resolution and optical sectioning. To democratize ASLM, we provide an overview of its working principle and applications to biological imaging, as well as pragmatic tips for the assembly, alignment and control of its optical systems. Furthermore, we provide detailed part lists and schematics for several variants of ASLM that together can resolve molecular detail in chemically expanded samples, subcellular organization in living cells or the anatomical composition of chemically cleared intact organisms. We also provide software for instrument control and discuss how users can tune imaging parameters to accommodate diverse sample types. Thus, this protocol will serve not only as a guide for both introductory and advanced users adopting ASLM, but as a useful resource for any individual interested in deploying custom imaging technology. We expect that building an ASLM will take ~1-2 months, depending on the experience of the instrument builder and the version of the instrument.
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16
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A quantitative analysis of various patterns applied in lattice light sheet microscopy. Nat Commun 2022; 13:4607. [PMID: 35941165 PMCID: PMC9360440 DOI: 10.1038/s41467-022-32341-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/26/2022] [Indexed: 11/08/2022] Open
Abstract
Light sheet microscopes reduce phototoxicity and background and improve imaging speed compared to widefield and confocal microscopes. However, when equipped with Gaussian beams, the axial resolving power of a light sheet microscope and the observable field of view are inversely related. Light sheets based on dithered optical lattices improve axial resolution and beam uniformity compared Gaussian beams by using axially structured illumination patterns. However, these advantages come at the expense of an increased total illumination to the specimen and a decreased axial confinement of the illumination pattern. Using simulations and experimental measurements in fixed and live cells, we quantify the differences between Gaussian and lattice light sheets on beam uniformity, axial resolution, lateral resolution, and photobleaching. We demonstrate how different optical lattice illumination patterns can be tuned to prioritize either axial resolution or optical sectioning. Finally, we introduce an approach to spectrally fuse sequential acquisitions of different lattice light sheet patterns with complementary optical properties to achieve both high resolution and low background images.
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17
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Ahn B, Chen M, Mazzotti M. Online Monitoring of the Concentrations of Amorphous and Crystalline Mesoscopic Species Present in Solution. CRYSTAL GROWTH & DESIGN 2022; 22:5071-5080. [PMID: 35942122 PMCID: PMC9354028 DOI: 10.1021/acs.cgd.2c00577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/30/2022] [Indexed: 06/01/2023]
Abstract
Despite the growing evidence for the existence of amorphous mesoscopic species in a solution and their crucial roles in crystallization, there has been the lack of a suitable method to measure the time-resolved concentrations of amorphous and crystalline mesospecies in a lab-scale stirred reactor. This has limited experimental investigations to understand the kinetics of amorphous and crystalline mesospecies formation in stirred solutions and made it challenging to measure the crystal nucleation rate directly. Here, we used depolarized light sheet microscopy to achieve time-resolved measurements of amorphous and crystalline mesospecies concentrations in solutions at varying temperatures. After demonstrating that the concentration measurement method is reasonably accurate, precise, and sensitive, we utilized this method to examine mesospecies formation both in a mixture of two miscible liquids and in an undersaturated solution of dl-valine, thus revealing the importance of a temperature change in the formation of metastable and amorphous mesospecies as well as the reproducibility of the measurements. Moreover, we used the presented method to monitor both mesospecies formation and crystal nucleation in dl-valine solutions at four different levels of supersaturation, while achieving the direct measurement of the crystal nucleation rates in stirred solutions. Our results show that, as expected, the inherent variability in nucleation originating from its stochastic nature reduces with increasing supersaturation, and the dependence of the measured nucleation rate on supersaturation is in reasonable agreement with that predicted by the classical nucleation theory.
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18
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biPACT: A method for three-dimensional visualization of mouse spinal cord circuits of long segments with high resolution. J Neurosci Methods 2022; 379:109672. [PMID: 35843371 DOI: 10.1016/j.jneumeth.2022.109672] [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: 01/05/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 11/23/2022]
Abstract
BACKGROUND The spatial complexity of neuronal circuits in the central nervous system is a hurdle in understanding and treating brain and spinal cord injury (SCI). Although several methods have recently been developed to render the spinal cord transparent and label specific neural circuits, three-dimensional visualization of long segments of spinal cord with high resolution remains challenging for SCI researchers. NEW METHOD We present a method that combines tissue staining of neuronal tracts traced with biotinylated dextran amine (BDA) and a modified passive clarity clearing protocol to describe individual fibers in long segments of mouse spinal cord. RESULTS Corticospinal tract was traced with BDA with a mouse model of thoracic spinal cord injury. The spinal cord was stained and cleared in two weeks with four solutions: staining solution, hydrogel solution, clearing solution, and observation solution. The samples were observed with a light-sheet microscope, and three-dimensional reconstruction was performed with ImageJ software. High resolution-images comparable with tissue sections were obtained continuously and circumferentially. By tiling, it was possible to obtain high-resolution images of long segments of the spinal cord. The tissue could be easily re-stained in case of fading. COMPARISON WITH EXISTING METHODS The present method does not require special equipment such as vacuum devices, can label specific circuits without genetic technology, and re-staining rounds can be easily implemented. CONCLUSIONS By using simple neural staining and clearing methods, it was possible to acquire a wide range of high-resolution three-dimensional images of the spinal cord.
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19
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The Effects of Optical Aberrations to Illumination Beam Thickness in Two-Photon Excitation Microscopes. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12147156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
When performing in vivo imaging of live samples, it is a big challenge to penetrate thick tissues while still maintaining high resolution and a large field of view because of the sample-induced aberrations. These requirements can be met by combining the benefits of two-photon excitation, beam modulation and adaptive optics in an illumination path. However, the relationship between aberrations and the performance of such a microscopy system has never been systematically and comprehensively assessed. Here, two-photon Gaussian and Bessel beams are modulated as illumination beams, and how aberrations affect the thickness of the illumination beams is evaluated. It is found that the thickness variation is highly related to the azimuthal order of Zernike modes. The thickness of the two-photon Gaussian beam is more sensitive to Zernike modes with lower azimuthal order, while the thickness of the two-photon Bessel beam is more sensitive to the higher-azimuthal-order Zernike modes. So, it is necessary to design a new strategy to correct aberrations according to the effects of different Zernike modes in order to maximize the correction capability of correctors and reduce the correction errors for those insensitive Zernike modes. These results may provide important guidance for the design and evaluation of adaptive optical systems in a two-photon excitation microscope.
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20
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Taege Y, Borre AL, Veettikazhy M, Schulz SL, Marti D, Andersen PE, Messerschmidt B, Ataman Ç. Design parameters for Airy beams in light-sheet microscopy. APPLIED OPTICS 2022; 61:5315-5319. [PMID: 36256216 DOI: 10.1364/ao.458343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/25/2022] [Indexed: 06/16/2023]
Abstract
We derive analytical expressions for the length, thickness, and curvature of an Airy light sheet in terms of basic parameters of the cubic phase and the paraxially defined focusing optics that form the beam. The length and thickness are defined analogously to the Rayleigh range and beam waist of a Gaussian beam, hence providing a direct and quantitative comparison between the two beam types. The analytical results are confirmed via numerical Fresnel propagation simulations and discussed within the context of light-sheet microscopy, providing a comprehensive guide for the design of the illumination unit.
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21
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Luna-Palacios YY, Licea-Rodriguez J, Camacho-Lopez MD, Teichert I, Riquelme M, Rocha-Mendoza I. Multicolor light-sheet microscopy for a large field of view imaging: A comparative study between Bessel and Gaussian light-sheets configurations. JOURNAL OF BIOPHOTONICS 2022; 15:e202100359. [PMID: 35184408 DOI: 10.1002/jbio.202100359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/17/2022] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Light-sheet fluorescence microscopy (LSFM) is useful for developmental biology studies, which require a simultaneous visualization of dynamic microstructures over large fields of views (FOVs). A comparative study between multicolor Bessel and Gaussian-based LSFM systems is presented. Discussing the chromatic implications to achieve colocalized and large FOVs when both optical arrays are implemented under the same excitation objective is the purpose of this work. The light-sheets FOVs, optical sectioning, and resolution are experimentally characterized and discussed. The advantages of using Bessel beams and the main drawbacks of using Gaussian beams for multicolor imaging are highlighted. Multiple Bessel excitation minimizes the FOV's mismatch's effects due to the beams chromatic defocusing and alleviates the aside object blurring obtained with multiple Gaussian beams. It also offers a fair homogeneous axial resolution and optical sectioning over a larger effective FOV. Imaging over perithecia samples of the fungus Sordaria macrospora demonstrates such advantages. This work complements previous comparative studies that discuss only single wavelengths light-sheets excitations.
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Affiliation(s)
- Yryx Y Luna-Palacios
- Department of Optics, Centro de Investigación Científica y de Educación Superior de Ensenada, CICESE, Carretera Ensenada-Tijuana, Ensenada, Mexico
| | - Jacob Licea-Rodriguez
- Department of Optics, Centro de Investigación Científica y de Educación Superior de Ensenada, CICESE, Carretera Ensenada-Tijuana, Ensenada, Mexico
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada, CICESE, Carretera Ensenada-Tijuana, Ensenada, Mexico
| | - M Dolores Camacho-Lopez
- Cátedras CONACYT-Deparment of Optics, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Mexico
| | - Ines Teichert
- Department of General and Molecular Botany, Ruhr-University Bochum, Bochum, Germany
| | - Meritxell Riquelme
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada, CICESE, Carretera Ensenada-Tijuana, Ensenada, Mexico
| | - Israel Rocha-Mendoza
- Department of Optics, Centro de Investigación Científica y de Educación Superior de Ensenada, CICESE, Carretera Ensenada-Tijuana, Ensenada, Mexico
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22
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Babayekhorasani F, Hosseini M, Spicer PT. Molecular and Colloidal Transport in Bacterial Cellulose Hydrogels. Biomacromolecules 2022; 23:2404-2414. [PMID: 35544686 DOI: 10.1021/acs.biomac.2c00178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial cellulose biofilms are complex networks of strong interwoven nanofibers that control transport and protect bacterial colonies in the film. The design of diverse applications of these bacterial cellulose films also relies on understanding and controlling transport through the fiber mesh, and transport simulations of the films are most accurate when guided by experimental characterization of the structures and the resultant diffusion inside. Diffusion through such films is a function of their key microstructural length scales, determining how molecules, as well as particles and microorganisms, permeate them. We use microscopy to study the unique bacterial cellulose film via its pore structure and quantify the mobility dynamics of various sizes of tracer particles and macromolecules. Mobility is hindered within the films, as confinement and local movement strongly depend on the void size relative to diffusing tracers. The biofilms have a naturally periodic structure of alternating dense and porous layers of nanofiber mesh, and we tune the magnitude of the spacing via fermentation conditions. Micron-sized particles can diffuse through the porous layers but cannot penetrate the dense layers. Tracer mobility in the porous layers is isotropic, indicating a largely random pore structure there. Molecular diffusion through the whole film is only slightly reduced by the structural tortuosity. Knowledge of transport variations within bacterial cellulose networks can be used to guide the design of symbiotic cultures in these structures and enhance their use in applications like biomedical implants, wound dressings, lab-grown meat, clothing textiles, and sensors.
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Affiliation(s)
| | - Maryam Hosseini
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Patrick T Spicer
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
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23
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Tang C, Li J. Quasi-non-diffracting static light sheets generated by holistically optimized pupil masks. OPTICS LETTERS 2022; 47:1737-1740. [PMID: 35363722 DOI: 10.1364/ol.454833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Thin and wide light sheets are crucial for light sheet microscopy with wide field of views and near diffraction-limited resolutions. Non-diffracting light sheets feature wide span ranges but often come with strong sidelobes or increased thicknesses. We develop a computational optimization method for creating light sheets that balance the trade-offs between thickness, non-diffracting range and sidelobes. We show in theory and experiment that our optimized mask extends the static light sheet's non-diffracting range by 50 % while keeping its sidelobes below the 20 % level.
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24
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Teranikar T, Lim J, Ijaseun T, Lee J. Development of Planar Illumination Strategies for Solving Mysteries in the Sub-Cellular Realm. Int J Mol Sci 2022; 23:1643. [PMID: 35163562 PMCID: PMC8835835 DOI: 10.3390/ijms23031643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/22/2021] [Accepted: 01/25/2022] [Indexed: 02/04/2023] Open
Abstract
Optical microscopy has vastly expanded the frontiers of structural and functional biology, due to the non-invasive probing of dynamic volumes in vivo. However, traditional widefield microscopy illuminating the entire field of view (FOV) is adversely affected by out-of-focus light scatter. Consequently, standard upright or inverted microscopes are inept in sampling diffraction-limited volumes smaller than the optical system's point spread function (PSF). Over the last few decades, several planar and structured (sinusoidal) illumination modalities have offered unprecedented access to sub-cellular organelles and 4D (3D + time) image acquisition. Furthermore, these optical sectioning systems remain unaffected by the size of biological samples, providing high signal-to-noise (SNR) ratios for objective lenses (OLs) with long working distances (WDs). This review aims to guide biologists regarding planar illumination strategies, capable of harnessing sub-micron spatial resolution with a millimeter depth of penetration.
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Affiliation(s)
| | | | | | - Juhyun Lee
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX 75022, USA; (T.T.); (J.L.); (T.I.)
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25
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Jannasch A, Szilagyi SA, Burmeister M, Davis QT, Hermsdorf GL, De S, Schäffer E. Fast 3D imaging of giant unilamellar vesicles using reflected light-sheet microscopy with single molecule sensitivity. J Microsc 2021; 285:40-51. [PMID: 34786705 DOI: 10.1111/jmi.13070] [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: 08/13/2021] [Accepted: 10/13/2021] [Indexed: 11/29/2022]
Abstract
Observation of highly dynamic processes inside living cells at the single molecule level is key for a better understanding of biological systems. However, imaging of single molecules in living cells is usually limited by the spatial and temporal resolution, photobleaching and the signal-to-background ratio. To overcome these limitations, light-sheet microscopes with thin selective plane illumination, for example, in a reflected geometry with a high numerical aperture imaging objective, have been developed. Here, we developed a reflected light-sheet microscope with active optics for fast, high contrast, two-colour acquisition of z -stacks. We demonstrate fast volume scanning by imaging a two-colour giant unilamellar vesicle (GUV) hemisphere. In addition, the high contrast enabled the imaging and tracking of single lipids in the GUV cap. The enhanced reflected scanning light-sheet microscope enables fast 3D scanning of artificial membrane systems and potentially live cells with single-molecule sensitivity and thereby could provide quantitative and molecular insight into the operation of cells.
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Affiliation(s)
- Anita Jannasch
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany
| | - Sven A Szilagyi
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany.,Max Planck Institute for Solid State Physics, Heisenbergstrasse 1, Stuttgart, Germany
| | - Moritz Burmeister
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany
| | - Q Tyrell Davis
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany.,School of Life Sciences, University of Dundee, Dow Street, Dundee, Scotland, UK
| | - Gero L Hermsdorf
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany
| | - Suman De
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany.,Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Broomhall, Sheffield, UK
| | - Erik Schäffer
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany
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26
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Lin PY, Hwang SPL, Lee CH, Chen BC. Two-photon scanned light sheet fluorescence microscopy with axicon imaging for fast volumetric imaging. JOURNAL OF BIOMEDICAL OPTICS 2021; 26:JBO-210219RR. [PMID: 34796706 PMCID: PMC8601431 DOI: 10.1117/1.jbo.26.11.116503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/01/2021] [Indexed: 05/31/2023]
Abstract
SIGNIFICANCE Two-photon microscopy has become the standard platform for deep-tissue fluorescence imaging. However, the use of point scanning in conventional two-photon microscopy limits the speed of volumetric image acquisition. AIM To obtain fast and deep volumetric images, we combine two-photon light sheet fluorescence microscopy (2p-LSFM) and axicon imaging that yields an extended depth of field (DOF) in 2p-LSFM. APPROACH Axicon imaging is achieved by imposing an axicon lens in the detection part of LSFM. RESULTS The DOF with axicon imaging is extended more than 20-fold over that of a conventional imaging lens, liberating the synchronized scanning in LSFM. We captured images of dynamic beating hearts and red blood cells in zebrafish larvae at volume acquisition rates up to 30 Hz. CONCLUSIONS We demonstrate the fast three-dimensional imaging capability of 2p-LSFM with axicon imaging by recording the rapid dynamics of physiological processes.
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Affiliation(s)
- Po-Yen Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Sheng-Ping L. Hwang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Chi-Hon Lee
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Bi-Chang Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
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27
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Ebrahimi V, Tang J, Han KY. Incoherent superposition of polychromatic light enables single-shot nondiffracting light-sheet microscopy. OPTICS EXPRESS 2021; 29:32691-32699. [PMID: 34615334 PMCID: PMC8687099 DOI: 10.1364/oe.439338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
We demonstrate single-shot nondiffracting light-sheet microscopy by the incoherent superposition of dispersed polychromatic light sources. We characterized our technique by generating a Bessel light-sheet with a supercontinuum light-source and a C-light-sheet using a diode laser, and demonstrated its applicability to fluorescence microscopy. We emphasize that our method is easily implementable and compatible with the requirements of high-resolution microscopy.
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Affiliation(s)
- Vahid Ebrahimi
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, FL 32816, USA
- These authors contributed equally to this work
| | - Jialei Tang
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, FL 32816, USA
- These authors contributed equally to this work
| | - Kyu Young Han
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, FL 32816, USA
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28
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Aakhte M, Müller HAJ. Multiview tiling light sheet microscopy for 3D high-resolution live imaging. Development 2021; 148:272173. [PMID: 34409448 DOI: 10.1242/dev.199725] [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: 04/18/2021] [Accepted: 08/13/2021] [Indexed: 11/20/2022]
Abstract
Light-sheet or selective plane illumination microscopy (SPIM) is ideally suited for in toto imaging of living specimens at high temporal-spatial resolution. In SPIM, the light scattering that occurs during imaging of opaque specimens brings about limitations in terms of resolution and the imaging field of view. To ameliorate this shortcoming, the illumination beam can be engineered into a highly confined light sheet over a large field of view and multi-view imaging can be performed by applying multiple lenses combined with mechanical rotation of the sample. Here, we present a Multiview tiling SPIM (MT-SPIM) that combines the Multi-view SPIM (M-SPIM) with a confined, multi-tiled light sheet. The MT-SPIM provides high-resolution, robust and rotation-free imaging of living specimens. We applied the MT-SPIM to image nuclei and Myosin II from the cellular to subcellular spatial scale in early Drosophila embryogenesis. We show that the MT-SPIM improves the axial-resolution relative to the conventional M-SPIM by a factor of two. We further demonstrate that this axial resolution enhancement improves the automated segmentation of Myosin II distribution and of nuclear volumes and shapes.
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Affiliation(s)
- Mostafa Aakhte
- Developmental Genetics Group, Institute of Biology, University of Kassel, Heinrich-Plett Strasse 40, 34132 Kassel, Germany
| | - Hans-Arno J Müller
- Developmental Genetics Group, Institute of Biology, University of Kassel, Heinrich-Plett Strasse 40, 34132 Kassel, Germany
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Vargas-Ordaz EJ, Gorelick S, York HM, Liu B, Halls ML, Arumugam S, Neild A, de Marco A, Cadarso VJ. Three-dimensional imaging on a chip using optofluidics light-sheet fluorescence microscopy. LAB ON A CHIP 2021; 21:2945-2954. [PMID: 34124739 DOI: 10.1039/d1lc00098e] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Volumetric, sub-micron to micron level resolution imaging is necessary to assay phenotypes or characteristics at the sub-cellular/organelle scale. However, three-dimensional fluorescence imaging of cells is typically low throughput or compromises on the achievable resolution in space and time. Here, we capitalise on the flow control capabilities of microfluidics and combine it with microoptics to integrate light-sheet based imaging directly into a microfluidic chip. Our optofluidic system flows suspended cells through a sub-micrometer thick light-sheet formed using micro-optical components that are cast directly in polydimethylsiloxane (PDMS). This design ensures accurate alignment, drift-free operation, and easy integration with conventional microfluidics, while providing sufficient spatial resolution, optical sectioning and volumetric data acquisition. We demonstrate imaging rates of 120 ms per cell at sub-μm resolution, that allow extraction of complex cellular phenotypes, exemplified by imaging of cell clusters, receptor distribution, and the analysis of endosomal size changes.
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Affiliation(s)
- Erick J Vargas-Ordaz
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia. and Centre to Impact Antimicrobial Resistance - Sustainable Solutions, Monash University, Clayton, 3800, Victoria, Australia
| | - Sergey Gorelick
- Department of Biochemistry and Molecular Biology, Monash University, 3800 Clayton, Victoria, Australia. and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, 3800 Clayton, Victoria, Australia
| | - Harrison M York
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, 3800 Clayton, Victoria, Australia and European Molecular Biology Laboratory (EMBL) Australia, Monash University, 3800 Clayton, Victoria, Australia and Department of Anatomy and Developmental Biology, Monash University, 3800 Clayton, Victoria, Australia
| | - Bonan Liu
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Michelle L Halls
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Senthil Arumugam
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, 3800 Clayton, Victoria, Australia and European Molecular Biology Laboratory (EMBL) Australia, Monash University, 3800 Clayton, Victoria, Australia and Department of Anatomy and Developmental Biology, Monash University, 3800 Clayton, Victoria, Australia
| | - Adrian Neild
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia.
| | - Alex de Marco
- Department of Biochemistry and Molecular Biology, Monash University, 3800 Clayton, Victoria, Australia. and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, 3800 Clayton, Victoria, Australia
| | - Victor J Cadarso
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia. and Centre to Impact Antimicrobial Resistance - Sustainable Solutions, Monash University, Clayton, 3800, Victoria, Australia and The Melbourne Centre for Nanofabrication, Victorian Node - Australian National Fabrication Facility, Clayton, Victoria 3800, Australia
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Weiss KR, Voigt FF, Shepherd DP, Huisken J. Tutorial: practical considerations for tissue clearing and imaging. Nat Protoc 2021; 16:2732-2748. [PMID: 34021294 PMCID: PMC10542857 DOI: 10.1038/s41596-021-00502-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 01/18/2021] [Indexed: 02/06/2023]
Abstract
Tissue clearing has become a powerful technique for studying anatomy and morphology at scales ranging from entire organisms to subcellular features. With the recent proliferation of tissue-clearing methods and imaging options, it can be challenging to determine the best clearing protocol for a particular tissue and experimental question. The fact that so many clearing protocols exist suggests there is no one-size-fits-all approach to tissue clearing and imaging. Even in cases where a basic level of clearing has been achieved, there are many factors to consider, including signal retention, staining (labeling), uniformity of transparency, image acquisition and analysis. Despite reviews citing features of clearing protocols, it is often unknown a priori whether a protocol will work for a given experiment, and thus some optimization is required by the end user. In addition, the capabilities of available imaging setups often dictate how the sample needs to be prepared. After imaging, careful evaluation of volumetric image data is required for each combination of clearing protocol, tissue type, biological marker, imaging modality and biological question. Rather than providing a direct comparison of the many clearing methods and applications available, in this tutorial we address common pitfalls and provide guidelines for designing, optimizing and imaging in a successful tissue-clearing experiment with a focus on light-sheet fluorescence microscopy (LSFM).
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Affiliation(s)
- Kurt R Weiss
- Morgridge Institute for Research, Madison, WI, USA
| | - Fabian F Voigt
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich & ETH Zurich, Zurich, Switzerland
| | - Douglas P Shepherd
- Department of Physics, Arizona State University, Tempe, AZ, USA
- Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Jan Huisken
- Morgridge Institute for Research, Madison, WI, USA.
- Department of Integrative Biology, University of Wisconsin, Madison, WI, USA.
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31
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Liu JTC, Glaser AK, Bera K, True LD, Reder NP, Eliceiri KW, Madabhushi A. Harnessing non-destructive 3D pathology. Nat Biomed Eng 2021; 5:203-218. [PMID: 33589781 PMCID: PMC8118147 DOI: 10.1038/s41551-020-00681-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 12/17/2020] [Indexed: 02/08/2023]
Abstract
High-throughput methods for slide-free three-dimensional (3D) pathological analyses of whole biopsies and surgical specimens offer the promise of modernizing traditional histology workflows and delivering improvements in diagnostic performance. Advanced optical methods now enable the interrogation of orders of magnitude more tissue than previously possible, where volumetric imaging allows for enhanced quantitative analyses of cell distributions and tissue structures that are prognostic and predictive. Non-destructive imaging processes can simplify laboratory workflows, potentially reducing costs, and can ensure that samples are available for subsequent molecular assays. However, the large size of the feature-rich datasets that they generate poses challenges for data management and computer-aided analysis. In this Perspective, we provide an overview of the imaging technologies that enable 3D pathology, and the computational tools-machine learning, in particular-for image processing and interpretation. We also discuss the integration of various other diagnostic modalities with 3D pathology, along with the challenges and opportunities for clinical adoption and regulatory approval.
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Affiliation(s)
- Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
| | - Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Kaustav Bera
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Lawrence D True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Nicholas P Reder
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Kevin W Eliceiri
- Department of Medical Physics, University of Wisconsin, Madison, WI, USA.
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA.
- Morgridge Institute for Research, Madison, WI, USA.
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA.
- Louis Stokes Cleveland Veterans Administration Medical Center, Cleveland, OH, USA.
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Deng S, Ding Z, Yuan D, Liu M, Zhou H. Investigation of the extended focusing capability of the spherical aberration to enlarge the field of view in light-sheet fluorescence microscopy. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2021; 38:19-24. [PMID: 33362148 DOI: 10.1364/josaa.410209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/11/2020] [Indexed: 06/12/2023]
Abstract
In light-sheet fluorescence microscopy (LSFM), using Gaussian beams for light-sheet generation results in a trade-off between the thickness and the field of view (FOV). Here we present a theoretical analysis of using spherical aberration to enlarge the FOV while keeping the light-sheet thickness small. Such spherical aberration can arise when focusing beams through an interface between materials of mismatched refractive indices. The depth-of-focus extension of the Gaussian beam is achieved when using air objectives to focus light into the samples dipped in the immersion medium with a higher refractive index. By scanning this elongated beam, a thin light sheet with a wide FOV can be used for LSFM imaging. Meanwhile, the accompanied sidelobes with the spherical aberrated light sheet, which are mainly distributed in the rear part of the light sheet, are also discussed. Simulation results show that an extended FOV of 64.4µm is possible for an objective lens of NA=0.3, which is about 5 times that of the unaberrated case. For such an extended FOV, a comparatively thin thickness of 1.38µm as well as the first sidelobe about 11.1% of the peak intensity in the center are also demonstrated.
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Xu T, Lim YJ, Zheng Y, Jung M, Gaus K, Gardiner EE, Lee WM. Modified inverted selective plane illumination microscopy for sub-micrometer imaging resolution in polydimethylsiloxane soft lithography devices. LAB ON A CHIP 2020; 20:3960-3969. [PMID: 32940306 DOI: 10.1039/d0lc00598c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Moldable, transparent polydimethylsiloxane (PDMS) elastomer microdevices enable a broad range of complex studies of three-dimensional cellular networks in their microenvironment in vitro. However, the uneven distribution of refractive index change, external to PDMS devices and internally in the sample chamber, creates a significant optical path difference (OPD) that distorts the light sheet beam and so restricts diffraction limited performance. We experimentally showed that an OPD of 120 μm results in the broadening of the lateral point spread function by over 4-fold. In this paper, we demonstrate steps to adapt a commercial inverted selective plane illumination microscope (iSPIM) and remove the OPD so as to achieve sub-micrometer imaging ranging from 0.6 ± 0.04 μm to 0.91 ± 0.03 μm of a fluorescence biological sample suspended in regular saline (RI ≈1.34) enclosed in 1.2 to 2 mm thick micromolded PDMS microdevices. We have proven that the removal of the OPD from the external PDMS layer by refractive index (RI) matching with a readily accessible, inexpensive sucrose solution is critical to achieve a >3-fold imaging resolution improvement. To monitor the RI matching process, a single-mode fiber (SMF) illuminator was integrated into the iSPIM. To remove the OPD inside the PDMS channel, we used an electrically tunable lens (ETL) that par-focuses the light sheet beam with the detection objective lens and so minimised axial distortions to attain sub-micrometer imaging resolution. We termed this new light sheet imaging protocol as modified inverted selective plane illumination microscopy (m-iSPIM). Using the high spatial-temporal 3D imaging of m-iSPIM, we experimentally captured single platelet (≈2 μm) recruitment to a platelet aggregate (22.5 μm × 22.5 μm × 6 μm) under flow at a 150 μm depth within a microfluidic channel. m-iSPIM paves the way for the application of light sheet imaging to a wide range of 3D biological models in microfluidic devices which recapitulate features of the physiological microenvironment and elucidate subcellular responses.
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Affiliation(s)
- Tienan Xu
- Research School of Electrical, Energy and Materials Engineering, College of Engineering and Computer Science, The Australian National University, Canberra, ACT 2601, Australia.
| | - Yean Jin Lim
- Research School of Electrical, Energy and Materials Engineering, College of Engineering and Computer Science, The Australian National University, Canberra, ACT 2601, Australia. and ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Yujie Zheng
- Research School of Electrical, Energy and Materials Engineering, College of Engineering and Computer Science, The Australian National University, Canberra, ACT 2601, Australia.
| | - MoonSun Jung
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Elizabeth E Gardiner
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Woei Ming Lee
- Research School of Electrical, Energy and Materials Engineering, College of Engineering and Computer Science, The Australian National University, Canberra, ACT 2601, Australia. and ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia and ARC Centre of Excellence in Advanced Molecular Imaging, The Australian National University, Canberra, ACT 2601, Australia
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Chang BJ, Dean KM, Fiolka R. Systematic and quantitative comparison of lattice and Gaussian light-sheets. OPTICS EXPRESS 2020; 28:27052-27077. [PMID: 32906967 PMCID: PMC7679196 DOI: 10.1364/oe.400164] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
The axial resolving power of a light-sheet microscope is determined by the thickness of the illumination beam and the numerical aperture of its detection optics. Bessel-beam based optical lattices have generated significant interest owing to their reportedly narrow beam waist and propagation-invariant characteristics. Yet, despite their significant use in lattice light-sheet microscopy and recent incorporation into commercialized systems, there are very few quantitative reports on their physical properties and how they compare to standard Gaussian illumination beams. Here, we measure the beam properties in the transmission of dithered square lattices, which is the most commonly used variant of lattice light-sheet microscopy, and Gaussian-based light-sheets. After a systematic analysis, we find that square lattices are very similar to Gaussian-based light-sheets in terms of thickness, confocal parameter, propagation length and overall imaging performance.
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Affiliation(s)
- Bo-Jui Chang
- Department of Cell Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Kevin M. Dean
- Department of Cell Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Reto Fiolka
- Department of Cell Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
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Bishop KW, Glaser AK, Liu JTC. Performance tradeoffs for single- and dual-objective open-top light-sheet microscope designs: a simulation-based analysis. BIOMEDICAL OPTICS EXPRESS 2020; 11:4627-4650. [PMID: 32923068 PMCID: PMC7449713 DOI: 10.1364/boe.397052] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 05/16/2023]
Abstract
Light-sheet microscopy (LSM) has emerged as a powerful tool for high-speed volumetric imaging of live model organisms and large optically cleared specimens. When designing cleared-tissue LSM systems with certain desired imaging specifications (e.g. resolution, contrast, and working distance), various design parameters must be taken into consideration. In order to elucidate some of the key design tradeoffs for LSM systems, we present a diffraction-based analysis of single- and dual-objective LSM configurations using simulations of LSM point spread functions. We assume Gaussian illumination is utilized. Specifically, we analyze the effects of the illumination and collection numerical aperture (NA), as well as their crossing angle, on spatial resolution and contrast. Assuming an open-top light-sheet (OTLS) architecture, we constrain these parameters based on fundamental geometric considerations as well as those imposed by currently available microscope objectives. In addition to revealing the performance tradeoffs of various single- and dual-objective LSM configurations, our analysis showcases the potential advantages of a novel, non-orthogonal dual-objective (NODO) architecture, especially for moderate-resolution imaging applications (collection NA of 0.5 to 0.8).
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Affiliation(s)
- Kevin W Bishop
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
- Department of Mechanical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Jonathan T C Liu
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
- Department of Mechanical Engineering, University of Washington, Seattle, Washington 98195, USA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington 98195, USA
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Light-Sheet Fluorescence Microscopy with Scanning Non-diffracting Beams. Sci Rep 2020; 10:8501. [PMID: 32444603 PMCID: PMC7244762 DOI: 10.1038/s41598-020-63847-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 04/05/2020] [Indexed: 12/02/2022] Open
Abstract
Light-sheet fluorescence microscopy (LSFM) has now become a unique tool in different fields ranging from three-dimensional (3D) tissue imaging to real-time functional imaging of neuronal activities. Nevertheless, obtaining high-quality artifact-free images from large, dense and inhomogeneous samples is the main challenge of the method that still needs to be adequately addressed. Here, we demonstrate significant enhancement of LSFM image qualities by using scanning non-diffracting illuminating beams, both through experimental and numerical investigations. The effect of static and scanning illumination with several beams are analyzed and compared, and it is shown that scanning 2D Airy light-sheet is minimally affected by the inhomogeneities in the samples, and provides higher contrasts and uniform resolution over a wide field-of-view, due to its reduced spatial coherence, self-healing feature and longer penetration depth. Further, the capabilities of the illumination scheme is utilized for both single-and double-wavelength 3D imaging of large and dense mammospheres of cancer tumor cells as complex inhomogeneous biological samples.
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