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Hu K, Hu X, He T, Liu J, Liu S, Zhang J, Tan Y, Yang X, Wang H, Liang Y, Ye J. Structured Illumination Microscopy of Mitochondrial in Mouse Hepatocytes with an Improved Image Reconstruction Algorithm. MICROMACHINES 2023; 14:642. [PMID: 36985049 PMCID: PMC10055965 DOI: 10.3390/mi14030642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/04/2023] [Accepted: 03/10/2023] [Indexed: 06/18/2023]
Abstract
In this paper, a structured illumination microscopy (SIM) image reconstruction algorithm combined with notch function (N-SIM) is proposed. This method suppresses the defocus signal in the imaging process by processing the low-frequency signal of the image. The existing super-resolution image reconstruction algorithm produces streak artifacts caused by defocus signal. The experimental results show that the algorithm proposed in our study can well suppress the streak artifacts caused by defocused signals during the imaging process without losing the effective information of the image. The image reconstruction algorithm is used to analyze the mouse hepatocytes, and the image processing tool developed by MATLAB is applied to identify, detect and count the reconstructed images of mitochondria and lipid droplets, respectively. It is found that the mitochondrial activity in oxidative stress induced growth inhibitor 1 (OSGIN1) overexpressed mouse hepatocytes is higher than that in normal cells, and the interaction with lipid droplets is more obvious. This paper provides a reliable subcellular observation platform, which is very meaningful for biomedical work.
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Affiliation(s)
- Kai Hu
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
| | - Xuejuan Hu
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
- College of Physics and Photoelectric Engineering, Shenzhen University, Shenzhen 518060, China
| | - Ting He
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
- College of Physics and Photoelectric Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jingxin Liu
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
| | - Shiqian Liu
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
| | - Jiaming Zhang
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
| | - Yadan Tan
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
- College of Physics Science and Technology, Guangxi Normal University, Guilin 541001, China
| | - Xiaokun Yang
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
| | - Hengliang Wang
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
| | - Yifei Liang
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
- College of Physics Science and Technology, Guangxi Normal University, Guilin 541001, China
| | - Jianze Ye
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen 518118, China
- Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Provincial Higher Education Institute, Shenzhen Technology University, Shenzhen 518118, China
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Zhai J, Shi R, Fan K, Kong L. Background inhibited and speed-loss-free volumetric imaging in vivo based on structured-illumination Fourier light field microscopy. Front Neurosci 2022; 16:1004228. [PMID: 36248666 PMCID: PMC9558295 DOI: 10.3389/fnins.2022.1004228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Benefiting from its advantages in fast volumetric imaging for recording biodynamics, Fourier light field microscopy (FLFM) has a wide range of applications in biomedical research, especially in neuroscience. However, the imaging quality of the FLFM is always deteriorated by both the out-of-focus background and the strong scattering in biological samples. Here we propose a structured-illumination and interleaved-reconstruction based Fourier light field microscopy (SI-FLFM), in which we can filter out the background fluorescence in FLFM without sacrificing imaging speed. We demonstrate the superiority of our SI-FLFM in high-speed, background-inhibited volumetric imaging of various biodynamics in larval zebrafish and mice in vivo. The signal-to-background ratio (SBR) is improved by tens of times. And the volumetric imaging speed can be up to 40 Hz, avoiding artifacts caused by temporal under-sampling in conventional structured illumination microscopy. These suggest that our SI-FLFM is suitable for applications of weak fluorescence signals but high imaging speed requirements.
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Affiliation(s)
- Jiazhen Zhai
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
| | - Ruheng Shi
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
| | - Kuikui Fan
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
| | - Lingjie Kong
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- *Correspondence: Lingjie Kong,
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Image improvement of temporal focusing multiphoton microscopy via superior spatial modulation excitation and Hilbert-Huang transform decomposition. Sci Rep 2022; 12:10079. [PMID: 35710746 PMCID: PMC9203560 DOI: 10.1038/s41598-022-14367-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/06/2022] [Indexed: 11/08/2022] Open
Abstract
Temporal focusing-based multiphoton excitation microscopy (TFMPEM) just provides the advantage of widefield optical sectioning ability with axial resolution of several micrometers. However, under the plane excitation, the photons emitted from the molecules in turbid tissues undergo scattering, resulting in complicated background noise and an impaired widefield image quality. Accordingly, this study constructs a general and comprehensive numerical model of TFMPEM utilizing Fourier optics and performs simulations to determine the superior spatial frequency and orientation of the structured pattern which maximize the axial excitation confinement. It is shown experimentally that the optimized pattern minimizes the intensity of the out-of-focus signal, and hence improves the quality of the image reconstructed using the Hilbert transform (HT). However, the square-like reflection components on digital micromirror device leads to pattern residuals in the demodulated image when applying high spatial frequency of structured pattern. Accordingly, the HT is replaced with Hilbert-Huang transform (HHT) in order to sift out the low-frequency background noise and pattern residuals in the demodulation process. The experimental results obtained using a kidney tissue sample show that the HHT yields a significant improvement in the TFMPEM image quality.
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Alonso JR, Silva A, Fernández A, Arocena M. Computational multifocus fluorescence microscopy for three-dimensional visualization of multicellular tumor spheroids. JOURNAL OF BIOMEDICAL OPTICS 2022; 27:JBO-210320SSR. [PMID: 35655357 PMCID: PMC9162503 DOI: 10.1117/1.jbo.27.6.066501] [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: 10/18/2021] [Accepted: 05/23/2022] [Indexed: 05/27/2023]
Abstract
SIGNIFICANCE Three-dimensional (3D) visualization of multicellular tumor spheroids (MCTS) in fluorescence microscopy can rapidly provide qualitative morphological information about the architecture of these cellular aggregates, which can recapitulate key aspects of their in vivo counterpart. AIM The present work is aimed at overcoming the shallow depth-of-field (DoF) limitation in fluorescence microscopy while achieving 3D visualization of thick biological samples under study. APPROACH A custom-built fluorescence microscope with an electrically focus-tunable lens was developed to optically sweep in-depth the structure of MCTS. Acquired multifocus stacks were combined by means of postprocessing algorithms performed in the Fourier domain. RESULTS Images with relevant characteristics as extended DoF, stereoscopic pairs as well as reconstructed viewpoints of MCTS were obtained without segmentation of the focused regions or estimation of the depth map. The reconstructed images allowed us to observe the 3D morphology of cell aggregates. CONCLUSIONS Computational multifocus fluorescence microscopy can provide 3D visualization in MCTS. This tool is a promising development in assessing the morphological structure of different cellular aggregates while preserving a robust yet simple optical setup.
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Affiliation(s)
- Julia R. Alonso
- Universidad de la República, Instituto de Física, Facultad de Ingeniería, Montevideo, Uruguay
| | - Alejandro Silva
- Universidad de la República, Instituto de Física, Facultad de Ingeniería, Montevideo, Uruguay
| | - Ariel Fernández
- Universidad de la República, Instituto de Física, Facultad de Ingeniería, Montevideo, Uruguay
| | - Miguel Arocena
- Instituto de Investigaciones Biológicas Clemente Estable, Departamento de Genómica, Montevideo, Uruguay
- Universidad de la República, Cátedra de Bioquímica y Biofísica, Facultad de Odontología, Montevideo, Uruguay
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Shi R, Li Y, Kong L. High-speed volumetric imaging in vivo based on structured illumination microscopy with interleaved reconstruction. JOURNAL OF BIOPHOTONICS 2021; 14:e202000513. [PMID: 33502121 DOI: 10.1002/jbio.202000513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 06/12/2023]
Abstract
Wide-field fluorescence microscopy (WFFM) is widely adopted in biomedical studies, due to its high imaging speed over large field-of-views. However, WFFM is susceptible to out-of-focus background. To overcome this problem, structured illumination microscopy (SIM) was proposed as a wide-field, optical-sectioning technique, which needs multiple raw images for image reconstruction and thus has a lower imaging speed. Here we propose SIM with interleaved reconstruction, to make SIM of lossless speed. We apply this method in volumetric imaging of neural network dynamics in brains of zebrafish larva in vivo.
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Affiliation(s)
- Ruheng Shi
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
| | - Yuting Li
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
| | - Lingjie Kong
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
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Zhang Y, Lang S, Wang H, Liao J, Gong Y. Super-resolution algorithm based on Richardson-Lucy deconvolution for three-dimensional structured illumination microscopy. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2019; 36:173-178. [PMID: 30874094 DOI: 10.1364/josaa.36.000173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/11/2018] [Indexed: 05/21/2023]
Abstract
Three-dimensional structured illumination microscopy (3D-SIM) is a wide-field super-resolution technique in fluorescent imaging that can double the resolution beyond its classical limit. We introduce, to the best of our knowledge, a new 3D reconstruction algorithm based on the Richardson-Lucy deconvolution. The 3D-SIM imaging principle and the reconstruction steps are demonstrated in detail. Microspheres and biological specimen are used to present the performance of this method. The background of the out-of-focus portion is effectively suppressed, and true optical sectioning and super-resolution can be achieved simultaneously. For the custom-built 3D-SIM and this reconstruction algorithm, the measured resolution was 99.5±5 nm laterally and 294±9 nm axially.
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Jia H, Yu X, Yang Y, Zhou X, Yan S, Liu C, Lei M, Yao B. Axial resolution enhancement of light-sheet microscopy by double scanning of Bessel beam and its complementary beam. JOURNAL OF BIOPHOTONICS 2019; 12:e201800094. [PMID: 30043551 DOI: 10.1002/jbio.201800094] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/23/2018] [Indexed: 05/25/2023]
Abstract
The side lobes of Bessel beam will create significant out-of-focus background when scanned in light-sheet fluorescence microscopy (LSFM), limiting the axial resolution of the imaging system. Here, we propose to overcome this issue by scanning the sample twice with zeroth-order Bessel beam and another type of propagation-invariant beam, complementary to the zeroth-order Bessel beam, which greatly reduces the out-of-focus background created in the first scan. The axial resolution can be improved from 1.68 μm of the Bessel light-sheet to 1.07 μm by subtraction of the two scanned images across a whole field-of-view of up to 300 μm × 200 μm × 200 μm. The optimization procedure to create the complementary beam is described in detail and it is experimentally generated with a spatial light modulator. The imaging performance is validated experimentally with fluorescent beads as well as eGFP-labeled mouse brain neurons.
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Affiliation(s)
- Hao Jia
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an, 710119, China
- School of Materials, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianghua Yu
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an, 710119, China
| | - Yanlong Yang
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an, 710119, China
| | - Xing Zhou
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an, 710119, China
- School of Materials, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shaohui Yan
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an, 710119, China
| | - Chao Liu
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an, 710119, China
- School of Materials, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming Lei
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an, 710119, China
| | - Baoli Yao
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an, 710119, China
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Wang Z, Cai Y, Liang Y, Zhou X, Yan S, Dan D, Bianco PR, Lei M, Yao B. Single shot, three-dimensional fluorescence microscopy with a spatially rotating point spread function. BIOMEDICAL OPTICS EXPRESS 2017; 8:5493-5506. [PMID: 29296483 PMCID: PMC5745098 DOI: 10.1364/boe.8.005493] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/03/2017] [Accepted: 11/06/2017] [Indexed: 05/25/2023]
Abstract
A wide-field fluorescence microscope with a double-helix point spread function (PSF) is constructed to obtain the specimen's three-dimensional distribution with a single snapshot. Spiral-phase-based computer-generated holograms (CGHs) are adopted to make the depth-of-field of the microscope adjustable. The impact of system aberrations on the double-helix PSF at high numerical aperture is analyzed to reveal the necessity of the aberration correction. A modified cepstrum-based reconstruction scheme is promoted in accordance with properties of the new double-helix PSF. The extended depth-of-field images and the corresponding depth maps for both a simulated sample and a tilted section slice of bovine pulmonary artery endothelial (BPAE) cells are recovered, respectively, verifying that the depth-of-field is properly extended and the depth of the specimen can be estimated at a precision of 23.4nm. This three-dimensional fluorescence microscope with a framerate-rank time resolution is suitable for studying the fast developing process of thin and sparsely distributed micron-scale cells in extended depth-of-field.
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Affiliation(s)
- Zhaojun Wang
- State Key Laboratory of Transient Optics and Photonics, Xi' an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi' an 710119, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanan Cai
- State Key Laboratory of Transient Optics and Photonics, Xi' an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi' an 710119, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yansheng Liang
- State Key Laboratory of Transient Optics and Photonics, Xi' an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi' an 710119, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing Zhou
- State Key Laboratory of Transient Optics and Photonics, Xi' an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi' an 710119, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shaohui Yan
- State Key Laboratory of Transient Optics and Photonics, Xi' an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi' an 710119, China
| | - Dan Dan
- State Key Laboratory of Transient Optics and Photonics, Xi' an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi' an 710119, China
| | - Piero R Bianco
- University at Buffalo, Department of Microbiology and Immunology, No. 12 Capen Hall, Buffalo, New York 14214, USA
| | - Ming Lei
- State Key Laboratory of Transient Optics and Photonics, Xi' an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi' an 710119, China
| | - Baoli Yao
- State Key Laboratory of Transient Optics and Photonics, Xi' an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi' an 710119, China
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Lu Y, Li R, Lu R. Gram-Schmidt orthonormalization for retrieval of amplitude images under sinusoidal patterns of illumination. APPLIED OPTICS 2016; 55:6866-6873. [PMID: 27607260 DOI: 10.1364/ao.55.006866] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Structured illumination using sinusoidal patterns has been used for optical imaging of biological tissues in biomedical research, and of horticultural products in food quality evaluation. Implementation of structured-illumination imaging relies on retrieval of amplitude images, which is conventionally achieved by a phase-shifting technique that requires collecting a minimum of three phase-shifted images. In this study, we have proposed Gram-Schmidt orthonormalization (GSO) to retrieve amplitude component (AC) images using only two phase-shifted images. We have proposed two forms of GSO implementation, and prior to GSO processing, we eliminated the direct component (DC) background by subtracting a DC image we recovered using a spiral phase function (SPF) in the Fourier space. We demonstrated the GSO methods through numerical simulations and application examples of detection of bruise defects in apples by structured-illumination reflectance imaging (SIRI). GSO performed comparably to conventional three-phase-based demodulation. It is simple, fast and effective for amplitude retrieval and requires no prior phase information, which could facilitate fast implementation of structured-illumination imaging.
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