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GILLES M, NASHED Y, DU M, JACOBSEN C, WILD S. 3D X-Ray Imaging of Continuous Objects beyond the Depth of Focus Limit. Optica 2018; 5:1078-1086. [PMID: 30406160 PMCID: PMC6217975 DOI: 10.1364/optica.5.001078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/02/2018] [Indexed: 05/08/2023]
Abstract
X-ray ptychography is becoming the standard method for sub-30 nm imaging of thick extended samples. Available algorithms and computing power have traditionally restricted sample reconstruction to 2D slices. We build on recent progress in optimization algorithms and high performance computing to solve the ptychographic phase retrieval problem directly in 3D. Our approach addresses samples that do not fit entirely within the depth of focus of the imaging system. Such samples pose additional challenges because of internal diffraction effects within the sample. We demonstrate our approach on a computational sample modeled with 17 million complex variables.
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Affiliation(s)
- M.A. GILLES
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
- Center for Applied Mathematics, Cornell University, Ithaca, New York 14853, USA
| | - Y.S.G. NASHED
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - M. DU
- Department of Materials Science & Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - C. JACOBSEN
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
- Department of Physics & Astronomy, Northwestern University, Evanston, Illinois 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, USA
| | - S.M. WILD
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
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2
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Man T, Wan Y, Yan W, Wang XH, Peterman EJG, Wang D. Adaptive optics via self-interference digital holography for non-scanning three-dimensional imaging in biological samples. Biomed Opt Express 2018; 9:2614-2626. [PMID: 30258677 PMCID: PMC6154187 DOI: 10.1364/boe.9.002614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/26/2018] [Accepted: 04/27/2018] [Indexed: 05/18/2023]
Abstract
Three-dimensional imaging in biological samples usually suffers from performance degradation caused by optical inhomogeneities. Here we proposed an approach to adaptive optics in fluorescence microscopy where the aberrations are measured by self-interference holographic recording and then corrected by a post-processing optimization procedure. In our approach, only one complex-value hologram is sufficient to measure and then correct the aberrations, which results in fast acquisition speed, lower exposure time, and the ability to image in three-dimensions without the need to scan the sample or any other element in the system. We show proof-of-principle experiments on a tissue phantom containing fluorescence particles. Furthermore, we present three-dimensional reconstructions of actin-labeled MCF7 breast cancer cells, showing improved resolution after the correction of aberrations. Both experiments demonstrate the validity of our method and show the great potential of non-scanning adaptive three-dimensional microscopy in imaging biological samples with improved resolution and signal-to-noise ratio.
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Affiliation(s)
- Tianlong Man
- Institute of Information Photonics Technology, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing 100124, China
- College of Applied Sciences, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing 100124, China
| | - Yuhong Wan
- Institute of Information Photonics Technology, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing 100124, China
- College of Applied Sciences, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing 100124, China
| | - Wujuan Yan
- Laboratory for Biomedical Photonics, Institute of Laser Engineering, Beijing University of Technology, Beijing 100124, China
| | - Xiu-Hong Wang
- Laboratory for Biomedical Photonics, Institute of Laser Engineering, Beijing University of Technology, Beijing 100124, China
| | - Erwin J. G. Peterman
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands
- LaserLaB Amsterdam, Vrije Universiteit, Amsterdam, The Netherlands
| | - Dayong Wang
- Institute of Information Photonics Technology, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing 100124, China
- College of Applied Sciences, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing 100124, China
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3
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Zickus V, Taylor JM. 3D + time blood flow mapping using SPIM-microPIV in the developing zebrafish heart. Biomed Opt Express 2018; 9:2418-2435. [PMID: 29760998 PMCID: PMC5946799 DOI: 10.1364/boe.9.002418] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/17/2018] [Indexed: 05/08/2023]
Abstract
We present SPIM-μPIV as a flow imaging system, capable of measuring in vivo flow information with 3D micron-scale resolution. Our system was validated using a phantom experiment consisting of a flow of beads in a 50 μm diameter FEP tube. Then, with the help of optical gating techniques, we obtained 3D + time flow fields throughout the full heartbeat in a ∼3 day old zebrafish larva using fluorescent red blood cells as tracer particles. From this we were able to recover 3D flow fields at 31 separate phases in the heartbeat. From our measurements of this specimen, we found the net pumped blood volume through the atrium to be 0.239 nL per beat. SPIM-μPIV enables high quality in vivo measurements of flow fields that will be valuable for studies of heart function and fluid-structure interaction in a range of small-animal models.
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4
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Toda K, Isobe K, Namiki K, Kawano H, Miyawaki A, Midorikawa K. Interferometric temporal focusing microscopy using three-photon excitation fluorescence. Biomed Opt Express 2018; 9:1510-1519. [PMID: 29675298 PMCID: PMC5905902 DOI: 10.1364/boe.9.001510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/06/2018] [Accepted: 02/14/2018] [Indexed: 06/08/2023]
Abstract
Super-resolution microscopy has become a powerful tool for biological research. However, its spatial resolution and imaging depth are limited, largely due to background light. Interferometric temporal focusing (ITF) microscopy, which combines structured illumination microscopy and three-photon excitation fluorescence microscopy, can overcome these limitations. Here, we demonstrate ITF microscopy using three-photon excitation fluorescence, which has a spatial resolution of 106 nm at an imaging depth of 100 µm with an excitation wavelength of 1060 nm.
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Affiliation(s)
- Keisuke Toda
- RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
| | - Keisuke Isobe
- RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Kana Namiki
- Laboratory for Cell Function Dynamics, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Kawano
- Laboratory for Cell Function Dynamics, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Atsushi Miyawaki
- RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Laboratory for Cell Function Dynamics, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Katsumi Midorikawa
- RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
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5
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Patwary N, Doblas A, Preza C. Image restoration approach to address reduced modulation contrast in structured illumination microscopy. Biomed Opt Express 2018; 9:1630-1647. [PMID: 29675307 PMCID: PMC5905911 DOI: 10.1364/boe.9.001630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 02/05/2018] [Accepted: 02/28/2018] [Indexed: 06/08/2023]
Abstract
The performance of structured illumination microscopy (SIM) is hampered in many biological applications due to the inability to modulate the light when imaging deep into the sample. This is in part because sample-induced aberration reduces the modulation contrast of the structured pattern. In this paper, we present an image restoration approach suitable for processing raw incoherent-grid-projection SIM data with a low fringe contrast. Restoration results from simulated and experimental ApoTome SIM data show results with improved signal-to-noise ratio (SNR) and optical sectioning compared to the results obtained from existing methods, such as 2D demodulation and 3D SIM deconvolution. Our proposed method provides satisfactory results (quantified by the achieved SNR and normalized mean square error) even when the modulation contrast of the illumination pattern is as low as 7%.
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Scrofani G, Sola-Pikabea J, Llavador A, Sanchez-Ortiga E, Barreiro JC, Saavedra G, Garcia-Sucerquia J, Martínez-Corral M. FIMic: design for ultimate 3D-integral microscopy of in-vivo biological samples. Biomed Opt Express 2018; 9:335-346. [PMID: 29359107 PMCID: PMC5772586 DOI: 10.1364/boe.9.000335] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/09/2017] [Accepted: 12/10/2017] [Indexed: 05/12/2023]
Abstract
In this work, Fourier integral microscope (FIMic), an ultimate design of 3D-integral microscopy, is presented. By placing a multiplexing microlens array at the aperture stop of the microscope objective of the host microscope, FIMic shows extended depth of field and enhanced lateral resolution in comparison with regular integral microscopy. As FIMic directly produces a set of orthographic views of the 3D-micrometer-sized sample, it is suitable for real-time imaging. Following regular integral-imaging reconstruction algorithms, a 2.75-fold enhanced depth of field and [Formula: see text]-time better spatial resolution in comparison with conventional integral microscopy is reported. Our claims are supported by theoretical analysis and experimental images of a resolution test target, cotton fibers, and in-vivo 3D-imaging of biological specimens.
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Affiliation(s)
- G. Scrofani
- Department of Optics, University of Valencia, E-46100 Burjassot, Spain
| | - J. Sola-Pikabea
- Department of Optics, University of Valencia, E-46100 Burjassot, Spain
| | - A. Llavador
- Department of Optics, University of Valencia, E-46100 Burjassot, Spain
| | - E. Sanchez-Ortiga
- Department of Optics, University of Valencia, E-46100 Burjassot, Spain
| | - J. C. Barreiro
- Department of Optics, University of Valencia, E-46100 Burjassot, Spain
| | - G. Saavedra
- Department of Optics, University of Valencia, E-46100 Burjassot, Spain
| | - J. Garcia-Sucerquia
- Universidad Nacional de Colombia, Sede Medellin, School of Physics, A.A. 3840 Medellín 050034, Colombia
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7
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Zhang Q, Yang X, Hu Q, Bai K, Yin F, Li N, Gang Y, Wang X, Zeng S. High axial resolution imaging system for large volume tissues using combination of inclined selective plane illumination and mechanical sectioning. Biomed Opt Express 2017; 8:5767-5775. [PMID: 29296503 PMCID: PMC5745118 DOI: 10.1364/boe.8.005767] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/06/2017] [Accepted: 09/22/2017] [Indexed: 05/31/2023]
Abstract
To resolve fine structures of biological systems like neurons, it is required to realize microscopic imaging with sufficient spatial resolution in three dimensional systems. With regular optical imaging systems, high lateral resolution is accessible while high axial resolution is hard to achieve in a large volume. We introduce an imaging system for high 3D resolution fluorescence imaging of large volume tissues. Selective plane illumination was adopted to provide high axial resolution. A scientific CMOS working in sub-array mode kept the imaging area in the sample surface, which restrained the adverse effect of aberrations caused by inclined illumination. Plastic embedding and precise mechanical sectioning extended the axial range and eliminated distortion during the whole imaging process. The combination of these techniques enabled 3D high resolution imaging of large tissues. Fluorescent bead imaging showed resolutions of 0.59 μm, 0.47μm, and 0.59 μm in the x, y, and z directions, respectively. Data acquired from the volume sample of brain tissue demonstrated the applicability of this imaging system. Imaging of different depths showed uniform performance where details could be recognized in either the near-soma area or terminal area, and fine structures of neurons could be seen in both the xy and xz sections.
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Affiliation(s)
- Qi Zhang
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiong Yang
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Qinglei Hu
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ke Bai
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Fangfang Yin
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ning Li
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yadong Gang
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaojun Wang
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shaoqun Zeng
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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8
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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. Biomed Opt 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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Chowdhury S, Eldridge WJ, Wax A, Izatt JA. Structured illumination microscopy for dual-modality 3D sub-diffraction resolution fluorescence and refractive-index reconstruction. Biomed Opt Express 2017; 8:5776-5793. [PMID: 29296504 PMCID: PMC5745119 DOI: 10.1364/boe.8.005776] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/12/2017] [Accepted: 11/13/2017] [Indexed: 05/20/2023]
Abstract
Though structured illumination (SI) microscopy is a popular imaging technique conventionally associated with fluorescent super-resolution, recent works have suggested its applicability towards sub-diffraction resolution coherent imaging with quantitative endogenous biological contrast. Here, we demonstrate that SI can efficiently integrate together the principles of fluorescent super-resolution and coherent synthetic aperture to achieve 3D dual-modality sub-diffraction resolution, fluorescence and refractive-index (RI) visualizations of biological samples. We experimentally demonstrate this framework by introducing a SI microscope capable of 3D sub-diffraction resolution fluorescence and RI imaging, and verify its biological visualization capabilities by experimentally reconstructing 3D RI/fluorescence visualizations of fluorescent calibration microspheres as well as alveolar basal epithelial adenocarcinoma (A549) and human colorectal adenocarcinmoa (HT-29) cells, fluorescently stained for F-actin. This demonstration may suggest SI as an especially promising imaging technique to enable future biological studies that explore synergistically operating biophysical/biochemical and molecular mechanisms at sub-diffraction resolutions.
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Affiliation(s)
- Shwetadwip Chowdhury
- Department of Biomedical Engineering, Fitzpatrick Institute for Photonics, 1427 FCIEMAS, 101 Science Drive Box 90281, Durham, North Carolina 27708, USA
| | - Will J. Eldridge
- Department of Biomedical Engineering, Fitzpatrick Institute for Photonics, 1427 FCIEMAS, 101 Science Drive Box 90281, Durham, North Carolina 27708, USA
| | - Adam Wax
- Department of Biomedical Engineering, Fitzpatrick Institute for Photonics, 1427 FCIEMAS, 101 Science Drive Box 90281, Durham, North Carolina 27708, USA
| | - Joseph A. Izatt
- Department of Biomedical Engineering, Fitzpatrick Institute for Photonics, 1427 FCIEMAS, 101 Science Drive Box 90281, Durham, North Carolina 27708, USA
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10
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Kim K, Park WS, Na S, Kim S, Kim T, Heo WD, Park Y. Correlative three-dimensional fluorescence and refractive index tomography: bridging the gap between molecular specificity and quantitative bioimaging. Biomed Opt Express 2017; 8:5688-5697. [PMID: 29296497 PMCID: PMC5745112 DOI: 10.1364/boe.8.005688] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/12/2017] [Accepted: 11/13/2017] [Indexed: 05/20/2023]
Abstract
Optical diffraction tomography (ODT) provides label-free three-dimensional (3D) refractive index (RI) measurement of biological samples. However, due to the nature of the RI values of biological specimens, ODT has limited access to molecular specific information. Here, we present an optical setup combining ODT with three-channel 3D fluorescence microscopy, to enhance the molecular specificity of the 3D RI measurement. The 3D RI distribution and 3D deconvoluted fluorescence images of HeLa cells and NIH-3T3 cells are measured, and the cross-correlative analysis between RI and fluorescence of live cells are presented.
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Affiliation(s)
- Kyoohyun Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
- KI for Health Science and Technology (KIHST), KAIST, Daejeon 34141, South Korea
- Current address: Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Wei Sun Park
- Department of Biological Sciences, KAIST, Daejeon 34141, South Korea
| | | | | | | | - Won Do Heo
- Department of Biological Sciences, KAIST, Daejeon 34141, South Korea
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon 34141, South Korea
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
- KI for Health Science and Technology (KIHST), KAIST, Daejeon 34141, South Korea
- TomoCube Inc., Daejeon 34051, South Korea
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11
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Nguyen D, Marchand PJ, Planchette AL, Nilsson J, Sison M, Extermann J, Lopez A, Sylwestrzak M, Sordet-Dessimoz J, Schmidt-Christensen A, Holmberg D, Van De Ville D, Lasser T. Optical projection tomography for rapid whole mouse brain imaging. Biomed Opt Express 2017; 8:5637-5650. [PMID: 29296493 PMCID: PMC5745108 DOI: 10.1364/boe.8.005637] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/31/2017] [Accepted: 10/31/2017] [Indexed: 05/21/2023]
Abstract
In recent years, three-dimensional mesoscopic imaging has gained significant importance in life sciences for fundamental studies at the whole-organ level. In this manuscript, we present an optical projection tomography (OPT) method designed for imaging of the intact mouse brain. The system features an isotropic resolution of ~50 µm and an acquisition time of four to eight minutes, using a 3-day optimized clearing protocol. Imaging of the brain autofluorescence in 3D reveals details of the neuroanatomy, while the use of fluorescent labels displays the vascular network and amyloid deposition in 5xFAD mice, an important model of Alzheimer's disease (AD). Finally, the OPT images are compared with histological slices.
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Affiliation(s)
- David Nguyen
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
| | - Paul J. Marchand
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
| | - Arielle L. Planchette
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
| | - Julia Nilsson
- Autoimmunity, Department of Experimental Medical Sciences, Lund University Diabetes Centre, 20502 Malmö,
Sweden
| | - Miguel Sison
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
| | - Jérôme Extermann
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
| | - Antonio Lopez
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
| | - Marcin Sylwestrzak
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
| | - Jessica Sordet-Dessimoz
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
| | - Anja Schmidt-Christensen
- Autoimmunity, Department of Experimental Medical Sciences, Lund University Diabetes Centre, 20502 Malmö,
Sweden
| | - Dan Holmberg
- Autoimmunity, Department of Experimental Medical Sciences, Lund University Diabetes Centre, 20502 Malmö,
Sweden
| | - Dimitri Van De Ville
- Medical Image Processing Lab, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1202 Genève,
Switzerland
| | - Theo Lasser
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
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12
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Jumelle C, Hamri A, Egaud G, Mauclair C, Reynaud S, Dumas V, Pereira S, Garcin T, Gain P, Thuret G. Comparison of four methods of surface roughness assessment of corneal stromal bed after lamellar cutting. Biomed Opt Express 2017; 8:4974-4986. [PMID: 29188095 PMCID: PMC5695945 DOI: 10.1364/boe.8.004974] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/30/2017] [Accepted: 09/02/2017] [Indexed: 06/07/2023]
Abstract
Corneal lamellar cutting with a blade or femtosecond laser (FSL) is commonly used during refractive surgery and corneal grafts. Surface roughness of the cutting plane influences postoperative visual acuity but is difficult to assess reliably. For the first time, we compared chromatic confocal microscopy (CCM) with scanning electron microscopy, atomic force microscopy (AFM) and focus-variation microscopy (FVM) to characterize surfaces of variable roughness after FSL cutting. The small area allowed by AFM hinders conclusive roughness analysis, especially with irregular cuts. FVM does not always differentiate between smooth and rough surfaces. Finally, CCM allows analysis of large surfaces and differentiates between surface states.
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Affiliation(s)
- Clotilde Jumelle
- Corneal Graft Biology, Engineering and Imaging Laboratory, BiiGC, EA2521, Federative Institute of Research in Sciences and Health Engineering, Faculty of Medicine, Jean Monnet University, 10 rue de la Marandière, 42055 Saint-Etienne Cédex 02, France
| | - Alina Hamri
- GIE-Manutech-Ultrafast Surface Design, 20 rue Benoit Lauras, 42000 Saint-Etienne, France
| | - Gregory Egaud
- GIE-Manutech-Ultrafast Surface Design, 20 rue Benoit Lauras, 42000 Saint-Etienne, France
| | - Cyril Mauclair
- GIE-Manutech-Ultrafast Surface Design, 20 rue Benoit Lauras, 42000 Saint-Etienne, France
- Hubert Curien Laboratory, UMR-CNRS 5516, Jean Monnet University, 18 rue Benoit Lauras, 42000 Saint-Etienne, France
| | - Stephanie Reynaud
- Hubert Curien Laboratory, UMR-CNRS 5516, Jean Monnet University, 18 rue Benoit Lauras, 42000 Saint-Etienne, France
| | - Virginie Dumas
- Ecole Nationale d’Ingénieurs de Saint-Etienne (ENISE), Laboratoire de Tribologie et Dynamique des Systèmes, UMR 5513 CNRS, 58 rue Jean Parot, 42023 Saint-Etienne, France
| | - Sandrine Pereira
- Eye Bank, French Blood Center, 25 boulevard Pasteur, 42023 Saint-Etienne, France
| | - Thibaud Garcin
- Corneal Graft Biology, Engineering and Imaging Laboratory, BiiGC, EA2521, Federative Institute of Research in Sciences and Health Engineering, Faculty of Medicine, Jean Monnet University, 10 rue de la Marandière, 42055 Saint-Etienne Cédex 02, France
- Ophthalmology Department, University Hospital, avenue Albert Raimond, 42055 Saint-Etienne Cédex 02, France
| | - Philippe Gain
- Corneal Graft Biology, Engineering and Imaging Laboratory, BiiGC, EA2521, Federative Institute of Research in Sciences and Health Engineering, Faculty of Medicine, Jean Monnet University, 10 rue de la Marandière, 42055 Saint-Etienne Cédex 02, France
- Ophthalmology Department, University Hospital, avenue Albert Raimond, 42055 Saint-Etienne Cédex 02, France
| | - Gilles Thuret
- Corneal Graft Biology, Engineering and Imaging Laboratory, BiiGC, EA2521, Federative Institute of Research in Sciences and Health Engineering, Faculty of Medicine, Jean Monnet University, 10 rue de la Marandière, 42055 Saint-Etienne Cédex 02, France
- Ophthalmology Department, University Hospital, avenue Albert Raimond, 42055 Saint-Etienne Cédex 02, France
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris, France
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13
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Hall G, Liang W, Li X. Fitting-free algorithm for efficient quantification of collagen fiber alignment in SHG imaging applications. Biomed Opt Express 2017; 8:4609-4620. [PMID: 29082088 PMCID: PMC5654803 DOI: 10.1364/boe.8.004609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 09/13/2017] [Accepted: 09/13/2017] [Indexed: 05/29/2023]
Abstract
Collagen fiber alignment derived from second harmonic generation (SHG) microscopy images can be important for disease diagnostics. Image processing algorithms are needed to robustly quantify the alignment in images with high sensitivity and reliability. Fourier transform (FT) magnitude, 2D power spectrum, and image autocorrelation have previously been used to extract fiber information from images by assuming a certain mathematical model (e.g. Gaussian distribution of the fiber-related parameters) and fitting. The fitting process is slow and fails to converge when the data is not Gaussian. Herein we present an efficient constant-time deterministic algorithm which characterizes the symmetricity of the FT magnitude image in terms of a single parameter, named the fiber alignment anisotropy R ranging from 0 (randomized fibers) to 1 (perfect alignment). This represents an important improvement of the technology and may bring us one step closer to utilizing the technology for various applications in real time. In addition, we present a digital image phantom-based framework for characterizing and validating the algorithm, as well as assessing the robustness of the algorithm against different perturbations.
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Affiliation(s)
- Gunnsteinn Hall
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205 USA
- These authors contributed equally
| | - Wenxuan Liang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205 USA
- These authors contributed equally
| | - Xingde Li
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205 USA
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14
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Hedde PN, Malacrida L, Ahrar S, Siryaporn A, Gratton E. sideSPIM - selective plane illumination based on a conventional inverted microscope. Biomed Opt Express 2017; 8:3918-3937. [PMID: 29026679 PMCID: PMC5611913 DOI: 10.1364/boe.8.003918] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/18/2017] [Accepted: 07/18/2017] [Indexed: 05/22/2023]
Abstract
Previously described selective plane illumination microscopy techniques typically offset ease of use and sample handling for maximum imaging performance or vice versa. Also, to reduce cost and complexity while maximizing flexibility, it is highly desirable to implement light sheet microscopy such that it can be added to a standard research microscope instead of setting up a dedicated system. We devised a new approach termed sideSPIM that provides uncompromised imaging performance and easy sample handling while, at the same time, offering new applications of plane illumination towards fluidics and high throughput 3D imaging of multiple specimen. Based on an inverted epifluorescence microscope, all of the previous functionality is maintained and modifications to the existing system are kept to a minimum. At the same time, our implementation is able to take full advantage of the speed of the employed sCMOS camera and piezo stage to record data at rates of up to 5 stacks/s. Additionally, sample handling is compatible with established methods and switching magnification to change the field of view from single cells to whole organisms does not require labor intensive adjustments of the system.
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Affiliation(s)
- Per Niklas Hedde
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA
| | - Leonel Malacrida
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA
- Área de Investigación Respiratoria, Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Uruguay
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur of Montevideo, Montevideo, Uruguay
| | - Siavash Ahrar
- Department of Physics and Astronomy, University of California Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Albert Siryaporn
- Department of Physics and Astronomy, University of California Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA
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15
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Abrahamsson S, Blom H, Agostinho A, Jans DC, Jost A, Müller M, Nilsson L, Bernhem K, Lambert TJ, Heintzmann R, Brismar H. Multifocus structured illumination microscopy for fast volumetric super-resolution imaging. Biomed Opt Express 2017; 8:4135-4140. [PMID: 28966852 PMCID: PMC5611928 DOI: 10.1364/boe.8.004135] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 05/04/2023]
Abstract
We here report for the first time the synergistic implementation of structured illumination microscopy (SIM) and multifocus microscopy (MFM). This imaging modality is designed to alleviate the problem of insufficient volumetric acquisition speed in super-resolution biological imaging. SIM is a wide-field super-resolution technique that allows imaging with visible light beyond the classical diffraction limit. Employing multifocus diffractive optics we obtain simultaneous wide-field 3D imaging capability in the SIM acquisition sequence, improving volumetric acquisition speed by an order of magnitude. Imaging performance is demonstrated on biological specimens.
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Affiliation(s)
- Sara Abrahamsson
- Lulu and Anthony Wang Laboratory for Neural Circuits and Behavior, The Rockefeller University New York, NY 10021, USA
| | - Hans Blom
- Department of Applied Physics, KTH (Royal Institute of Technology), Science for Life Laboratory, Stockholm, Sweden
| | - Ana Agostinho
- Department of Cell- and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel C. Jans
- Department of Applied Physics, KTH (Royal Institute of Technology), Science for Life Laboratory, Stockholm, Sweden
| | - Aurelie Jost
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University Jena, Germany
- Leibniz-Institute of Photonic Technology, Jena, Germany
| | - Marcel Müller
- Biomolecular Photonics, Department of Physics, Bielefeld University, Bielefeld, Germany
| | - Linnea Nilsson
- Department of Applied Physics, KTH (Royal Institute of Technology), Science for Life Laboratory, Stockholm, Sweden
| | - Kristoffer Bernhem
- Department of Applied Physics, KTH (Royal Institute of Technology), Science for Life Laboratory, Stockholm, Sweden
| | - Talley J. Lambert
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Rainer Heintzmann
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University Jena, Germany
- Leibniz-Institute of Photonic Technology, Jena, Germany
| | - Hjalmar Brismar
- Department of Applied Physics, KTH (Royal Institute of Technology), Science for Life Laboratory, Stockholm, Sweden
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16
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Sato M, Motegi Y, Yagi S, Gengyo-Ando K, Ohkura M, Nakai J. Fast varifocal two-photon microendoscope for imaging neuronal activity in the deep brain. Biomed Opt Express 2017; 8:4049-4060. [PMID: 28966846 PMCID: PMC5611922 DOI: 10.1364/boe.8.004049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/31/2017] [Accepted: 08/01/2017] [Indexed: 05/04/2023]
Abstract
Fluorescence microendoscopy is becoming a promising approach for deep brain imaging, but the current technology for visualizing neurons on a single focal plane limits the experimental efficiency and the pursuit of three-dimensional functional neural circuit architectures. Here we present a novel fast varifocal two-photon microendoscope system equipped with a gradient refractive index (GRIN) lens and an electrically tunable lens (ETL). This microendoscope enables quasi-simultaneous imaging of the neuronal network activity of deep brain areas at multiple focal planes separated by 85-120 µm at a fast scan rate of 7.5-15 frames per second per plane, as demonstrated in calcium imaging of the mouse dorsal CA1 hippocampus and amygdala in vivo.
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Affiliation(s)
- Masaaki Sato
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
- Brain and Body System Science Institute, Saitama University, Saitama 338-8570, Japan
- RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Yuki Motegi
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
- Brain and Body System Science Institute, Saitama University, Saitama 338-8570, Japan
| | - Shogo Yagi
- NTT Advanced Technology Corporation, Atsugi, Kanagawa, 243-0198, Japan
| | - Keiko Gengyo-Ando
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
- Brain and Body System Science Institute, Saitama University, Saitama 338-8570, Japan
- RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Masamichi Ohkura
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
- Brain and Body System Science Institute, Saitama University, Saitama 338-8570, Japan
| | - Junichi Nakai
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
- Brain and Body System Science Institute, Saitama University, Saitama 338-8570, Japan
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17
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Shu X, Li H, Dong B, Sun C, Zhang HF. Quantifying melanin concentration in retinal pigment epithelium using broadband photoacoustic microscopy. Biomed Opt Express 2017; 8:2851-2865. [PMID: 28663911 PMCID: PMC5480434 DOI: 10.1364/boe.8.002851] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/20/2017] [Accepted: 04/20/2017] [Indexed: 05/20/2023]
Abstract
Melanin is the dominant light absorber in retinal pigment epithelium (RPE). The loss of RPE melanin is a sign of ocular senescence and is both a risk factor and a symptom of age-related macular degeneration (AMD). Quantifying the RPE melanin concentration provides insight into the pathological role of RPE in ocular aging and the onset and progression of AMD. The main challenge in accurate quantification of RPE melanin concentration is to distinguish this ten-micrometer-thick cell monolayer from the underlying choroid, which also contains melanin but carries different pathognomonic information. In this work, we investigated a three-dimensional photoacoustic microscopic (PAM) method with high axial resolution, empowered by broad acoustic detection bandwidth, to distinguish RPE from choroid and quantify melanin concentrations in the RPE ex vivo. We first conducted numerical simulation on photoacoustic generation in the RPE, which suggested that a PAM system with at least 100-MHz detection bandwidth provided sufficient axial resolution to distinguish the melanin in RPE from that in choroid. Based on simulation results, we integrated a transparent broadband micro-ring resonator (MRR) based detector in a homebuilt PAM system. We imaged ex vivo RPE-choroid complexes (RCCs) from both porcine and human eyes and quantified the absolute melanin concentrations in the RPE and choroid, respectively. In our study, the measured melanin concentrations were 14.7 mg/mL and 17.0 mg/mL in human and porcine RPE, and 12 mg/mL and 61 mg/mL in human and porcine choroid, respectively. This study suggests that broadband PAM is capable of quantifying the RPE melanin concentration from RCCs ex vivo.
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Affiliation(s)
- Xiao Shu
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60201, USA
- Both authors contributed equally to this work
| | - Hao Li
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60201, USA
- Both authors contributed equally to this work
| | - Biqin Dong
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60201, USA
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60201, USA
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60201, USA
| | - Hao F. Zhang
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60201, USA
- Department of Ophthalmology, Northwestern University, 645 North Michigan Ave., Chicago, IL 60611, USA
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18
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Chowdhury S, Eldridge WJ, Wax A, Izatt JA. Structured illumination multimodal 3D-resolved quantitative phase and fluorescence sub-diffraction microscopy. Biomed Opt Express 2017; 8:2496-2518. [PMID: 28663887 PMCID: PMC5480494 DOI: 10.1364/boe.8.002496] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/28/2017] [Accepted: 03/30/2017] [Indexed: 05/07/2023]
Abstract
Sub-diffraction resolution imaging has played a pivotal role in biological research by visualizing key, but previously unresolvable, sub-cellular structures. Unfortunately, applications of far-field sub-diffraction resolution are currently divided between fluorescent and coherent-diffraction regimes, and a multimodal sub-diffraction technique that bridges this gap has not yet been demonstrated. Here we report that structured illumination (SI) allows multimodal sub-diffraction imaging of both coherent quantitative-phase (QP) and fluorescence. Due to SI's conventionally fluorescent applications, we first demonstrate the principle of SI-enabled three-dimensional (3D) QP sub-diffraction imaging with calibration microspheres. Image analysis confirmed enhanced lateral and axial resolutions over diffraction-limited QP imaging, and established striking parallels between coherent SI and conventional optical diffraction tomography. We next introduce an optical system utilizing SI to achieve 3D sub-diffraction, multimodal QP/fluorescent visualization of A549 biological cells fluorescently tagged for F-actin. Our results suggest that SI has a unique utility in studying biological phenomena with significant molecular, biophysical, and biochemical components.
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19
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Cernat R, Bradu A, Israelsen NM, Bang O, Rivet S, Keane PA, Heath DG, Rajendram R, Podoleanu A. Gabor fusion master slave optical coherence tomography. Biomed Opt Express 2017; 8:813-827. [PMID: 28270987 PMCID: PMC5330593 DOI: 10.1364/boe.8.000813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/06/2017] [Accepted: 01/06/2017] [Indexed: 06/01/2023]
Abstract
This paper describes the application of the Gabor filtering protocol to a Master/Slave (MS) swept source optical coherence tomography (SS)-OCT system at 1300 nm. The MS-OCT system delivers information from selected depths, a property that allows operation similar to that of a time domain OCT system, where dynamic focusing is possible. The Gabor filtering processing following collection of multiple data from different focus positions is different from that utilized by a conventional swept source OCT system using a Fast Fourier transform (FFT) to produce an A-scan. Instead of selecting the bright parts of A-scans for each focus position, to be placed in a final B-scan image (or in a final volume), and discarding the rest, the MS principle can be employed to advantageously deliver signal from the depths within each focus range only. The MS procedure is illustrated on creating volumes of data of constant transversal resolution from a cucumber and from an insect by repeating data acquisition for 4 different focus positions. In addition, advantage is taken from the tolerance to dispersion of the MS principle that allows automatic compensation for dispersion created by layers above the object of interest. By combining the two techniques, Gabor filtering and Master/Slave, a powerful imaging instrument is demonstrated. The master/slave technique allows simultaneous display of three categories of images in one frame: multiple depth en-face OCT images, two cross-sectional OCT images and a confocal like image obtained by averaging the en-face ones. We also demonstrate the superiority of MS-OCT over its FFT based counterpart when used with a Gabor filtering OCT instrument in terms of the speed of assembling the fused volume. For our case, we show that when more than 4 focus positions are required to produce the final volume, MS is faster than the conventional FFT based procedure.
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Affiliation(s)
- Ramona Cernat
- Applied Optics Group, School of Physical Sciences, University of Kent, Canterbury CT2 7NH, Kent, UK
| | - Adrian Bradu
- Applied Optics Group, School of Physical Sciences, University of Kent, Canterbury CT2 7NH, Kent, UK
| | - Niels Møller Israelsen
- DTU Fotonik, Department of Photonics Engineering, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Ole Bang
- DTU Fotonik, Department of Photonics Engineering, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Sylvain Rivet
- Université de Bretagne Occidentale, EA 938 Laboratoire de Spectrométrie et Optique Laser, 6 Avenue Le Gorgeu, C.S. 93837, 29238 Brest Cedex 3, France
| | - Pearse A. Keane
- NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, EC1V 9EL UK
| | - David-Garway Heath
- NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, EC1V 9EL UK
| | - Ranjan Rajendram
- NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, EC1V 9EL UK
| | - Adrian Podoleanu
- Applied Optics Group, School of Physical Sciences, University of Kent, Canterbury CT2 7NH, Kent, UK
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20
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Xu D, Zhou W, Peng L. Cellular resolution multiplexed FLIM tomography with dual-color Bessel beam. Biomed Opt Express 2017; 8:570-578. [PMID: 28270968 PMCID: PMC5330577 DOI: 10.1364/boe.8.000570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 05/23/2023]
Abstract
Fourier multiplexed FLIM (FmFLIM) tomography enables multiplexed 3D lifetime imaging of whole embryos. In our previous FmFLIM system, the spatial resolution was limited to 25 μm because of the trade-off between the spatial resolution and the imaging depth. In order to achieve cellular resolution imaging of thick specimens, we built a tomography system with dual-color Bessel beam. In combination with FmFLIM, the Bessel FmFLIM tomography system can perform parallel 3D lifetime imaging on multiple excitation-emission channels at a cellular resolution of 2.8 μm. The image capability of the Bessel FmFLIM tomography system was demonstrated by 3D lifetime imaging of dual-labeled transgenic zebrafish embryos.
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Affiliation(s)
- Dongli Xu
- College of Optical Sciences, the University of Arizona, 1630 East University Blvd., Tucson, AZ 85721, USA
| | - Weibin Zhou
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, MI 48109, USA
| | - Leilei Peng
- College of Optical Sciences, the University of Arizona, 1630 East University Blvd., Tucson, AZ 85721, USA
- Department of Molecular and Cell Biology, University of Arizona, 1007 E. Lowell Street, Tucson. AZ 85721, USA
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21
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Ashley TT, Gan EL, Pan J, Andersson SB. Tracking single fluorescent particles in three dimensions via extremum seeking. Biomed Opt Express 2016; 7:3355-3376. [PMID: 27699104 PMCID: PMC5030016 DOI: 10.1364/boe.7.003355] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 05/27/2023]
Abstract
The ability to track single fluorescent particles in three-dimensions with sub-diffraction limit precision as well as sub-millisecond temporal resolution has enabled the understanding of many biophysical phenomena at the nanometer scale. While there are several techniques for achieving this, most require complicated experimental setups that are expensive to implement. These methods can offer superb performance but their complexity may be overwhelming to the end-user whose aim is only to understand the feature being imaged. In this work, we describe a method for tracking a single fluorescent particle using a standard confocal or multi-photon microscope configuration. It relies only on the assumption that the relative position of the measurement point and the particle can be actuated and that the point spread function has a global maximum that coincides with the particle's position. The method uses intensity feedback to calculate real-time position commands that "seek" the extremum of the point spread function as the particle moves through its environment. We demonstrate the method by tracking a diffusing quantum dot in a hydrogel on a standard epifluorescent confocal microscope.
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Affiliation(s)
- Trevor T. Ashley
- Department of Mechanical Engineering, Boston University, Boston, MA 02215,
USA
| | - Eric L. Gan
- Dougherty Valley High School, San Ramon, California, 94582,
USA
| | - Jane Pan
- Medfield High School, Medfield, MA, 02052,
USA
| | - Sean B. Andersson
- Department of Mechanical Engineering, Boston University, Boston, MA 02215,
USA
- Division of Systems Engineering, Boston University, Boston, MA, 02215,
USA
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22
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Olson E, Levene MJ, Torres R. Multiphoton microscopy with clearing for three dimensional histology of kidney biopsies. Biomed Opt Express 2016; 7:3089-96. [PMID: 27570700 PMCID: PMC4986816 DOI: 10.1364/boe.7.003089] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/17/2016] [Accepted: 07/19/2016] [Indexed: 05/03/2023]
Abstract
We present a multiphoton microscopy approach with clearing optimized for pathology evaluation producing image quality comparable to traditional histology. Use of benzyl alcohol/benzyl benzoate with 4',6-diamidino-2-phenylindole and eosin in an optimized imaging setup results in optical sections nearly indistinguishable from traditionally-cut sections. Application to human renal tissue demonstrates diagnostic-level image quality can be maintained through 1 millimeter of tissue. Three dimensional perspectives reveal changes of glomerular capsule cells not evident on single sections. Collagen-derived second harmonic generation can be visualized through entire biopsies. Multiphoton microscopy with clearing has potential for increasing the yield of histologic evaluation of biopsy specimens.
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Affiliation(s)
- Eben Olson
- Dept of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Richard Torres
- Dept of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06510, USA
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23
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Abstract
This paper presents a technique to image the complex index of refraction of a sample across three dimensions. The only required hardware is a standard microscope and an array of LEDs. The method, termed Fourier ptychographic tomography (FPT), first captures a sequence of intensity-only images of a sample under angularly varying illumination. Then, using principles from ptychography and diffraction tomography, it computationally solves for the sample structure in three dimensions. The experimental microscope demonstrates a lateral spatial resolution of 0.39 μm and an axial resolution of 3.7 μm at the Nyquist-Shannon sampling limit (0.54 and 5.0 μm at the Sparrow limit, respectively) across a total imaging depth of 110 μm. Unlike competing methods, this technique quantitatively measures the volumetric refractive index of primarily transparent and contiguous sample features without the need for interferometry or any moving parts. Wide field-of-view reconstructions of thick biological specimens suggest potential applications in pathology and developmental biology.
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Affiliation(s)
- Roarke Horstmeyer
- Department of Electrical Engineering, California Institute of Technology, Pasadena, California 91125, USA
- Bioimaging and Neurophotonics Lab, NeuroCure Cluster of Excellence, Charité Berlin, Humboldt University, Berlin 10117, Germany
- Corresponding author:
| | - Jaebum Chung
- Department of Electrical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Xiaoze Ou
- Department of Electrical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Guoan Zheng
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Changhuei Yang
- Department of Electrical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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24
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Meddens MBM, Liu S, Finnegan PS, Edwards TL, James CD, Lidke KA. Single objective light-sheet microscopy for high-speed whole-cell 3D super-resolution. Biomed Opt Express 2016; 7:2219-36. [PMID: 27375939 PMCID: PMC4918577 DOI: 10.1364/boe.7.002219] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/12/2016] [Accepted: 05/09/2016] [Indexed: 05/07/2023]
Abstract
We have developed a method for performing light-sheet microscopy with a single high numerical aperture lens by integrating reflective side walls into a microfluidic chip. These 45° side walls generate light-sheet illumination by reflecting a vertical light-sheet into the focal plane of the objective. Light-sheet illumination of cells loaded in the channels increases image quality in diffraction limited imaging via reduction of out-of-focus background light. Single molecule super-resolution is also improved by the decreased background resulting in better localization precision and decreased photo-bleaching, leading to more accepted localizations overall and higher quality images. Moreover, 2D and 3D single molecule super-resolution data can be acquired faster by taking advantage of the increased illumination intensities as compared to wide field, in the focused light-sheet.
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Affiliation(s)
- Marjolein B. M. Meddens
- Department of Physics and Astronomy, University of New Mexico, 1919 Lomas Blvd NE, Albuquerque, NM 87131,
USA
- Department of Pathology, University of New Mexico, 2325 Camino de Salud, Albuquerque, NM 87131,
USA
| | - Sheng Liu
- Department of Physics and Astronomy, University of New Mexico, 1919 Lomas Blvd NE, Albuquerque, NM 87131,
USA
- Current address: Weldon School of Biomedical Engineering, College of Engineering, Purdue University, West Lafayette, IN 47907,
USA
| | | | - Thayne L. Edwards
- Sandia National Laboratories, 1515 Eubank SE, Albuquerque, NM 87123,
USA
| | - Conrad D. James
- Sandia National Laboratories, 1515 Eubank SE, Albuquerque, NM 87123,
USA
| | - Keith A. Lidke
- Department of Physics and Astronomy, University of New Mexico, 1919 Lomas Blvd NE, Albuquerque, NM 87131,
USA
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25
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Oudjedi L, Fiche JB, Abrahamsson S, Mazenq L, Lecestre A, Calmon PF, Cerf A, Nöllmann M. Astigmatic multifocus microscopy enables deep 3D super-resolved imaging. Biomed Opt Express 2016; 7:2163-73. [PMID: 27375935 PMCID: PMC4918573 DOI: 10.1364/boe.7.002163] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/22/2016] [Accepted: 03/17/2016] [Indexed: 05/15/2023]
Abstract
We have developed a 3D super-resolution microscopy method that enables deep imaging in cells. This technique relies on the effective combination of multifocus microscopy and astigmatic 3D single-molecule localization microscopy. We describe the optical system and the fabrication process of its key element, the multifocus grating. Then, two strategies for localizing emitters with our imaging method are presented and compared with a previously described deep 3D localization algorithm. Finally, we demonstrate the performance of the method by imaging the nuclear envelope of eukaryotic cells reaching a depth of field of ~4µm.
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Affiliation(s)
- Laura Oudjedi
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Sara Abrahamsson
- Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Laurent Mazenq
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400 Toulouse, France
- Université de Toulouse, LAAS, F-31031 Toulouse, France
| | - Aurélie Lecestre
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400 Toulouse, France
- Université de Toulouse, LAAS, F-31031 Toulouse, France
| | - Pierre-François Calmon
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400 Toulouse, France
- Université de Toulouse, LAAS, F-31031 Toulouse, France
| | - Aline Cerf
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400 Toulouse, France
- Université de Toulouse, LAAS, F-31031 Toulouse, France
| | - Marcelo Nöllmann
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
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26
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Chang CY, Hu YY, Lin CY, Lin CH, Chang HY, Tsai SF, Lin TW, Chen SJ. Fast volumetric imaging with patterned illumination via digital micro-mirror device-based temporal focusing multiphoton microscopy. Biomed Opt Express 2016; 7:1727-36. [PMID: 27231617 PMCID: PMC4871077 DOI: 10.1364/boe.7.001727] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 03/30/2016] [Accepted: 04/03/2016] [Indexed: 05/27/2023]
Abstract
Temporal focusing multiphoton microscopy (TFMPM) has the advantage of area excitation in an axial confinement of only a few microns; hence, it can offer fast three-dimensional (3D) multiphoton imaging. Herein, fast volumetric imaging via a developed digital micromirror device (DMD)-based TFMPM has been realized through the synchronization of an electron multiplying charge-coupled device (EMCCD) with a dynamic piezoelectric stage for axial scanning. The volumetric imaging rate can achieve 30 volumes per second according to the EMCCD frame rate of more than 400 frames per second, which allows for the 3D Brownian motion of one-micron fluorescent beads to be spatially observed. Furthermore, it is demonstrated that the dynamic HiLo structural multiphoton microscope can reject background noise by way of the fast volumetric imaging with high-speed DMD patterned illumination.
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Affiliation(s)
- Chia-Yuan Chang
- Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan
- Center for Micro/Nano Science and Technology, National Cheng Kung University, Tainan 701, Taiwan
| | - Yvonne Yuling Hu
- Department of Photonics, National Cheng Kung University, Tainan 701, Taiwan
| | - Chun-Yu Lin
- Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan
- Center for Micro/Nano Science and Technology, National Cheng Kung University, Tainan 701, Taiwan
| | - Cheng-Han Lin
- Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan
| | - Hsin-Yu Chang
- Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan
- Center for Micro/Nano Science and Technology, National Cheng Kung University, Tainan 701, Taiwan
| | - Sheng-Feng Tsai
- Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Tzu-Wei Lin
- Faculty of Health and Sport Sciences, University of Tsukuba, Tsukuba 305-8574, Japan
| | - Shean-Jen Chen
- Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan
- Center for Micro/Nano Science and Technology, National Cheng Kung University, Tainan 701, Taiwan
- Advanced Optoelectronic Technology Center, National Cheng Kung University, Tainan 701, Taiwan
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27
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Rupprecht P, Prendergast A, Wyart C, Friedrich RW. Remote z-scanning with a macroscopic voice coil motor for fast 3D multiphoton laser scanning microscopy. Biomed Opt Express 2016; 7:1656-71. [PMID: 27231612 PMCID: PMC4871072 DOI: 10.1364/boe.7.001656] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/29/2016] [Accepted: 03/29/2016] [Indexed: 05/21/2023]
Abstract
There is a high demand for 3D multiphoton imaging in neuroscience and other fields but scanning in axial direction presents technical challenges. We developed a focusing technique based on a remote movable mirror that is conjugate to the specimen plane and translated by a voice coil motor. We constructed cost-effective z-scanning modules from off-the-shelf components that can be mounted onto standard multiphoton laser scanning microscopes to extend scan patterns from 2D to 3D. Systems were designed for large objectives and provide high resolution, high speed and a large z-scan range (>300 μm). We used these systems for 3D multiphoton calcium imaging in the adult zebrafish brain and measured odor-evoked activity patterns across >1500 neurons with single-neuron resolution and high signal-to-noise ratio.
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Affiliation(s)
- Peter Rupprecht
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
- University of Basel, 4003 Basel, Switzerland
| | - Andrew Prendergast
- Institut du Cerveau et de la Moelle Épinière (ICM), 75013 Paris, France
- Inserm UMRS 1127, France
- CNRS UMR 7225, France
- UPMC Univ Paris 06, F75005, Paris, France
| | - Claire Wyart
- Institut du Cerveau et de la Moelle Épinière (ICM), 75013 Paris, France
- Inserm UMRS 1127, France
- CNRS UMR 7225, France
- UPMC Univ Paris 06, F75005, Paris, France
| | - Rainer W Friedrich
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
- University of Basel, 4003 Basel, Switzerland
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28
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Apelian C, Harms F, Thouvenin O, Boccara AC. Dynamic full field optical coherence tomography: subcellular metabolic contrast revealed in tissues by interferometric signals temporal analysis. Biomed Opt Express 2016; 7:1511-24. [PMID: 27446672 PMCID: PMC4929658 DOI: 10.1364/boe.7.001511] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 05/14/2023]
Abstract
We developed a new endogenous approach to reveal subcellular metabolic contrast in fresh ex vivo tissues taking advantage of the time dependence of the full field optical coherence tomography interferometric signals. This method reveals signals linked with local activity of the endogenous scattering elements which can reveal cells where other OCT-based techniques fail or need exogenous contrast agents. We benefit from the micrometric transverse resolution of full field OCT to image intracellular features. We used this time dependence to identify different dynamics at the millisecond scale on a wide range of organs in normal or pathological conditions.
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Affiliation(s)
- Clement Apelian
- Institut Langevin–ESPCI ParisTech, PSL Research University 1 Rue Jussieu, 75005, Paris, France
- LLTech SAS, Pépinière Paris Santé Cochin 29 Rue du Faubourg Saint Jacques, 75014, Paris, France
| | - Fabrice Harms
- LLTech SAS, Pépinière Paris Santé Cochin 29 Rue du Faubourg Saint Jacques, 75014, Paris, France
| | - Olivier Thouvenin
- Institut Langevin–ESPCI ParisTech, PSL Research University 1 Rue Jussieu, 75005, Paris, France
| | - A. Claude Boccara
- Institut Langevin–ESPCI ParisTech, PSL Research University 1 Rue Jussieu, 75005, Paris, France
- LLTech SAS, Pépinière Paris Santé Cochin 29 Rue du Faubourg Saint Jacques, 75014, Paris, France
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29
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Momey F, Berdeu A, Bordy T, Dinten JM, Marcel FK, Picollet-D’hahan N, Gidrol X, Allier C. Lensfree diffractive tomography for the imaging of 3D cell cultures. Biomed Opt Express 2016; 7:949-62. [PMID: 27231600 PMCID: PMC4866467 DOI: 10.1364/boe.7.000949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/18/2015] [Accepted: 01/15/2016] [Indexed: 05/05/2023]
Abstract
New microscopes are needed to help realize the full potential of 3D organoid culture studies. In order to image large volumes of 3D organoid cultures while preserving the ability to catch every single cell, we propose a new imaging platform based on lensfree microscopy. We have built a lensfree diffractive tomography setup performing multi-angle acquisitions of 3D organoid culture embedded in Matrigel and developed a dedicated 3D holographic reconstruction algorithm based on the Fourier diffraction theorem. With this new imaging platform, we have been able to reconstruct a 3D volume as large as 21.5 mm (3) of a 3D organoid culture of prostatic RWPE1 cells showing the ability of these cells to assemble in 3D intricate cellular network at the mesoscopic scale. Importantly, comparisons with 2D images show that it is possible to resolve single cells isolated from the main cellular structure with our lensfree diffractive tomography setup.
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Affiliation(s)
- F. Momey
- Univ. Grenoble Alpes, F-38000 Grenoble,
France
- CEA, LETI, MINATEC Campus, F-38054 Grenoble,
France
- The authors have equally contributed to this work
| | - A. Berdeu
- Univ. Grenoble Alpes, F-38000 Grenoble,
France
- CEA, LETI, MINATEC Campus, F-38054 Grenoble,
France
- The authors have equally contributed to this work
| | - T. Bordy
- Univ. Grenoble Alpes, F-38000 Grenoble,
France
- CEA, LETI, MINATEC Campus, F-38054 Grenoble,
France
| | - J.-M. Dinten
- Univ. Grenoble Alpes, F-38000 Grenoble,
France
- CEA, LETI, MINATEC Campus, F-38054 Grenoble,
France
| | - F. Kermarrec Marcel
- Univ. Grenoble Alpes, F-38000 Grenoble,
France
- CEA, iRTSV-Biologie Grande Echelle, F-38054 Grenoble,
France
- INSERM, U1038, F-38054 Grenoble,
France
| | - N. Picollet-D’hahan
- Univ. Grenoble Alpes, F-38000 Grenoble,
France
- CEA, iRTSV-Biologie Grande Echelle, F-38054 Grenoble,
France
- INSERM, U1038, F-38054 Grenoble,
France
| | - X. Gidrol
- Univ. Grenoble Alpes, F-38000 Grenoble,
France
- CEA, iRTSV-Biologie Grande Echelle, F-38054 Grenoble,
France
- INSERM, U1038, F-38054 Grenoble,
France
| | - C. Allier
- Univ. Grenoble Alpes, F-38000 Grenoble,
France
- CEA, LETI, MINATEC Campus, F-38054 Grenoble,
France
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30
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Abrahamsson S, Ilic R, Wisniewski J, Mehl B, Yu L, Chen L, Davanco M, Oudjedi L, Fiche JB, Hajj B, Jin X, Pulupa J, Cho C, Mir M, El Beheiry M, Darzacq X, Nollmann M, Dahan M, Wu C, Lionnet T, Liddle JA, Bargmann CI. Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging. Biomed Opt Express 2016; 7:855-69. [PMID: 27231594 PMCID: PMC4866461 DOI: 10.1364/boe.7.000855] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/10/2016] [Accepted: 02/03/2016] [Indexed: 05/05/2023]
Abstract
Multifocus microscopy (MFM) allows high-resolution instantaneous three-dimensional (3D) imaging and has been applied to study biological specimens ranging from single molecules inside cells nuclei to entire embryos. We here describe pattern designs and nanofabrication methods for diffractive optics that optimize the light-efficiency of the central optical component of MFM: the diffractive multifocus grating (MFG). We also implement a "precise color" MFM layout with MFGs tailored to individual fluorophores in separate optical arms. The reported advancements enable faster and brighter volumetric time-lapse imaging of biological samples. In live microscopy applications, photon budget is a critical parameter and light-efficiency must be optimized to obtain the fastest possible frame rate while minimizing photodamage. We provide comprehensive descriptions and code for designing diffractive optical devices, and a detailed methods description for nanofabrication of devices. Theoretical efficiencies of reported designs is ≈90% and we have obtained efficiencies of > 80% in MFGs of our own manufacture. We demonstrate the performance of a multi-phase MFG in 3D functional neuronal imaging in living C. elegans.
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Affiliation(s)
- Sara Abrahamsson
- HHMI and Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, NY 10065, USA
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Rob Ilic
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Jan Wisniewski
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - Brian Mehl
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - Liya Yu
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Lei Chen
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Marcelo Davanco
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Laura Oudjedi
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Bassam Hajj
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
- Laboratoire Physico Chimie, Institut Curie, CNRS UMR 168, Université Pierre et Marie Curie-Paris 6, 11 rue Pierre et Marie Curie, 75005 Paris France
| | - Xin Jin
- HHMI and Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Joan Pulupa
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Christine Cho
- HHMI and Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Mustafa Mir
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
- University of California, Berkeley, CA 94720, USA
| | - Mohamed El Beheiry
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
- Laboratoire Physico Chimie, Institut Curie, CNRS UMR 168, Université Pierre et Marie Curie-Paris 6, 11 rue Pierre et Marie Curie, 75005 Paris France
| | - Xavier Darzacq
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
- University of California, Berkeley, CA 94720, USA
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Maxime Dahan
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
- Laboratoire Physico Chimie, Institut Curie, CNRS UMR 168, Université Pierre et Marie Curie-Paris 6, 11 rue Pierre et Marie Curie, 75005 Paris France
| | - Carl Wu
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - Timothée Lionnet
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - J. Alexander Liddle
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Cornelia I. Bargmann
- HHMI and Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, NY 10065, USA
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31
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Kummer M, Kirmse K, Witte OW, Haueisen J, Holthoff K. Method to quantify accuracy of position feedback signals of a three-dimensional two-photon laser-scanning microscope. Biomed Opt Express 2015; 6:3678-93. [PMID: 26504620 PMCID: PMC4605029 DOI: 10.1364/boe.6.003678] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/24/2015] [Accepted: 07/24/2015] [Indexed: 05/10/2023]
Abstract
Two-photon laser-scanning microscopy enables to record neuronal network activity in three-dimensional space while maintaining single-cellular resolution. One of the proposed approaches combines galvanometric x-y scanning with piezo-driven objective movements and employs hardware feedback signals for position monitoring. However, readily applicable methods to quantify the accuracy of those feedback signals are currently lacking. Here we provide techniques based on contact-free laser reflection and laser triangulation for the quantification of positioning accuracy of each spatial axis. We found that the lateral feedback signals are sufficiently accurate (defined as <2.5 µm) for a wide range of scan trajectories and frequencies. We further show that axial positioning accuracy does not only depend on objective acceleration and mass but also its geometry. We conclude that the introduced methods allow a reliable quantification of position feedback signals in a cost-efficient, easy-to-install manner and should be applicable for a wide range of two-photon laser scanning microscopes.
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Affiliation(s)
- Michael Kummer
- Experimentelle Neurologie, Hans-Berger-Klinik für Neurologie, Universitätsklinikum Jena, Erlanger Allee 101, D-07747 Jena, Germany
| | - Knut Kirmse
- Experimentelle Neurologie, Hans-Berger-Klinik für Neurologie, Universitätsklinikum Jena, Erlanger Allee 101, D-07747 Jena, Germany
| | - Otto W. Witte
- Experimentelle Neurologie, Hans-Berger-Klinik für Neurologie, Universitätsklinikum Jena, Erlanger Allee 101, D-07747 Jena, Germany
| | - Jens Haueisen
- Institut für Biomedizinische Technik und Informatik, Technische Universität Ilmenau Gustav-Kirchhoff Str. 2, D-98693 Ilmenau, Germany
| | - Knut Holthoff
- Experimentelle Neurologie, Hans-Berger-Klinik für Neurologie, Universitätsklinikum Jena, Erlanger Allee 101, D-07747 Jena, Germany
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32
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Chiu MH, Tan CT, Tsai MH, Yang YH. Full-field transmission-type angle-deviation optical microscope with reflectivity-height transformation. Biomed Opt Express 2015; 6:3952-62. [PMID: 26504645 PMCID: PMC4605054 DOI: 10.1364/boe.6.003952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 06/05/2023]
Abstract
This full-field transmission-type three-dimensional (3D) optical microscope is constructed based on the angle deviation method (ADM) and the algorithm of reflectivity-height transformation (RHT). The surface height is proportional to the deviation angle of light passing through the object. The angle deviation and surface height can be measured based on the reflectivity closed to the critical angle using a parallelogram prism and two CCDs.
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Affiliation(s)
- Ming-Hung Chiu
- Department of Electro-Optical Engineering, National Formosa University,No. 64, Wunhua Road, Huwei, Yunlin 632, Taiwan
| | - Chen-Tai Tan
- Department of Electro-Optical Engineering, National Formosa University,No. 64, Wunhua Road, Huwei, Yunlin 632, Taiwan
| | - Ming-Hung Tsai
- Department of Electro-Optical Engineering, National Formosa University,No. 64, Wunhua Road, Huwei, Yunlin 632, Taiwan
| | - Ya-Hsin Yang
- Department of Electro-Optical Engineering, National Formosa University,No. 64, Wunhua Road, Huwei, Yunlin 632, Taiwan
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33
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Yoon J, Kim K, Park H, Choi C, Jang S, Park Y. Label-free characterization of white blood cells by measuring 3D refractive index maps. Biomed Opt Express 2015; 6:3865-75. [PMID: 26504637 PMCID: PMC4605046 DOI: 10.1364/boe.6.003865] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/07/2015] [Accepted: 09/01/2015] [Indexed: 05/02/2023]
Abstract
The characterization of white blood cells (WBCs) is crucial for blood analyses and disease diagnoses. However, current standard techniques rely on cell labeling, a process which imposes significant limitations. Here we present three-dimensional (3D) optical measurements and the label-free characterization of mouse WBCs using optical diffraction tomography. 3D refractive index (RI) tomograms of individual WBCs are constructed from multiple two-dimensional quantitative phase images of samples illuminated at various angles of incidence. Measurements of the 3D RI tomogram of WBCs enable the separation of heterogeneous populations of WBCs using quantitative morphological and biochemical information. Time-lapse tomographic measurements also provide the 3D trajectory of micrometer-sized beads ingested by WBCs. These results demonstrate that optical diffraction tomography can be a useful and versatile tool for the study of WBCs.
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Affiliation(s)
- Jonghee Yoon
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, South Korea
| | - Kyoohyun Kim
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, South Korea
| | - HyunJoo Park
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, South Korea
| | - Chulhee Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701, South Korea
| | - Seongsoo Jang
- Department of Laboratory Medicine, University of Ulsan, College of Medicine and Asan Medical Center, Seoul 138-736, South Korea
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, South Korea
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34
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Lin X, Wu J, Zheng G, Dai Q. Camera array based light field microscopy. Biomed Opt Express 2015; 6:3179-89. [PMID: 26417490 PMCID: PMC4574646 DOI: 10.1364/boe.6.003179] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/27/2015] [Accepted: 07/29/2015] [Indexed: 05/20/2023]
Abstract
This paper proposes a novel approach for high-resolution light field microscopy imaging by using a camera array. In this approach, we apply a two-stage relay system for expanding the aperture plane of the microscope into the size of an imaging lens array, and utilize a sensor array for acquiring different sub-apertures images formed by corresponding imaging lenses. By combining the rectified and synchronized images from 5 × 5 viewpoints with our prototype system, we successfully recovered color light field videos for various fast-moving microscopic specimens with a spatial resolution of 0.79 megapixels at 30 frames per second, corresponding to an unprecedented data throughput of 562.5 MB/s for light field microscopy. We also demonstrated the use of the reported platform for different applications, including post-capture refocusing, phase reconstruction, 3D imaging, and optical metrology.
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Affiliation(s)
- Xing Lin
- Department of Automation, Tsinghua University, Beijing, 100084,
China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, 100084,
China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing, 100084,
China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, 100084,
China
| | - Guoan Zheng
- Biomedical Engineering & Electrical Engineering, University of Connecticut, Storrs, Connecticut, 06269,
USA
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, 100084,
China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, 100084,
China
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35
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Yang Z, Piksarv P, Ferrier DE, Gunn-Moore FJ, Dholakia K. Macro-optical trapping for sample confinement in light sheet microscopy. Biomed Opt Express 2015; 6:2778-85. [PMID: 26309743 PMCID: PMC4541507 DOI: 10.1364/boe.6.002778] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/18/2015] [Accepted: 06/29/2015] [Indexed: 05/18/2023]
Abstract
Light sheet microscopy is a powerful approach to construct three-dimensional images of large specimens with minimal photo-damage and photo-bleaching. To date, the specimens are usually mounted in agents such as agarose, potentially restricting the development of live samples, and also highly mobile specimens need to be anaesthetized before imaging. To overcome these problems, here we demonstrate an integrated light sheet microscope which solely uses optical forces to trap and hold the sample using a counter-propagating laser beam geometry. Specifically, tobacco plant cells and living Spirobranchus lamarcki larvae were successfully trapped and sectional images acquired. This novel approach has the potential to significantly expand the range of applications for light sheet imaging.
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Affiliation(s)
- Zhengyi Yang
- SUPA, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, KY16 9SS,
UK
| | - Peeter Piksarv
- SUPA, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, KY16 9SS,
UK
- Institute of Physics, University of Tartu, Ravila 14c, Tartu, 50411,
Estonia
| | - David E.K. Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St. Andrews, East Sands, St. Andrews, KY16 8LB,
UK
| | - Frank J. Gunn-Moore
- School of Biology, Medical and Biological Sciences Building, University of St. Andrews, North Haugh, St. Andrews, KY16 9TF,
UK
| | - Kishan Dholakia
- SUPA, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, KY16 9SS,
UK
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36
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Singh A, McMullen JD, Doris EA, Zipfel WR. Comparison of objective lenses for multiphoton microscopy in turbid samples. Biomed Opt Express 2015; 6:3113-27. [PMID: 26309771 PMCID: PMC4541535 DOI: 10.1364/boe.6.003113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 07/20/2015] [Accepted: 07/20/2015] [Indexed: 05/20/2023]
Abstract
Optimization of illumination and detection optics is pivotal for multiphoton imaging in highly scattering tissue and the objective lens is the central component in both of these pathways. To better understand how basic lens parameters (NA, magnification, field number) affect fluorescence collection and image quality, a two-detector setup was used with a specialized sample cell to separate measurement of total excitation from epifluorescence collection. Our data corroborate earlier findings that low-mag lenses can be superior at collecting scattered photons, and we compare a set of commonly used multiphoton objective lenses in terms of their ability to collect scattered fluorescence, providing guidance for the design of multiphoton imaging systems. For example, our measurements of epi-fluorescence beam divergence in the presence of scattering reveal minimal beam broadening, indicating that often-advocated over-sized collection optics are not as advantageous as previously thought. These experiments also provide a framework for choosing objective lenses for multiphoton imaging by relating the results of our measurements to various design parameters of the objectives lenses used.
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Affiliation(s)
- Avtar Singh
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Jesse D. McMullen
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Eli A. Doris
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Warren R. Zipfel
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
- Department of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
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37
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Llavador A, Sánchez-Ortiga E, Barreiro JC, Saavedra G, Martínez-Corral M. Resolution enhancement in integral microscopy by physical interpolation. Biomed Opt Express 2015; 6:2854-63. [PMID: 26309749 PMCID: PMC4541513 DOI: 10.1364/boe.6.002854] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/20/2015] [Accepted: 06/20/2015] [Indexed: 05/09/2023]
Abstract
Integral-imaging technology has demonstrated its capability for computing depth images from the microimages recorded after a single shot. This capability has been shown in macroscopic imaging and also in microscopy. Despite the possibility of refocusing different planes from one snap-shot is crucial for the study of some biological processes, the main drawback in integral imaging is the substantial reduction of the spatial resolution. In this contribution we report a technique, which permits to increase the two-dimensional spatial resolution of the computed depth images in integral microscopy by a factor of √2. This is made by a double-shot approach, carried out by means of a rotating glass plate, which shifts the microimages in the sensor plane. We experimentally validate the resolution enhancement as well as we show the benefit of applying the technique to biological specimens.
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38
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Yang T, Zheng T, Shang Z, Wang X, Lv X, Yuan J, Zeng S. Rapid imaging of large tissues using high-resolution stage-scanning microscopy. Biomed Opt Express 2015; 6:1867-75. [PMID: 26137386 PMCID: PMC4467712 DOI: 10.1364/boe.6.001867] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/17/2015] [Accepted: 04/17/2015] [Indexed: 05/22/2023]
Abstract
Rapid and high-resolution imaging of large tissues is essential in biological research, like brain neuron connectivity research and cancer margins imaging. Here a novel stage-scanning confocal microscopy was developed for rapid imaging of large tissues. Line scanning methods and strip imaging strategy were used to increase the imaging speed. The scientific CMOS was used as line detector in sub-array mode and the optical sectioning ability can be easily adjusted by changing the number of line detectors according to different samples. Fluorescent beads imaging showed resolutions of 0.47 μm, 0.56 μm, and 1.56 μm in the X, Y, and Z directions, respectively, with a 40 × objective lens. A 10 × 10 mm(2) coronal plane with enough signal intensity could be imaged in about 88 sec at a sampling resolution of 0.16 μm/pixel. Rapid imaging of mouse brain slices demonstrated the applicability of this system in visualizing neuronal details at high frame rate.
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Affiliation(s)
- Tao Yang
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan 430074,
China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074,
China
| | - Ting Zheng
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan 430074,
China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074,
China
| | - Zhenhua Shang
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan 430074,
China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074,
China
| | - Xiaojun Wang
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan 430074,
China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074,
China
| | - Xiaohua Lv
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan 430074,
China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074,
China
| | - Jing Yuan
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan 430074,
China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074,
China
| | - Shaoqun Zeng
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan 430074,
China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074,
China
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39
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Chen Y, Liu JT. Characterizing the beam steering and distortion of Gaussian and Bessel beams focused in tissues with microscopic heterogeneities. Biomed Opt Express 2015; 6:1318-30. [PMID: 25909015 PMCID: PMC4399670 DOI: 10.1364/boe.6.001318] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 05/07/2023]
Abstract
Bessel beams have recently been investigated as a means of improving deep-tissue microscopy in highly scattering and heterogeneous media. It has been suggested that the long depth-of-field and self-reconstructing property of a Bessel beam enables an increased penetration depth of the focused beam in tissues compared to a conventional Gaussian beam. However, a study is needed to better quantify the magnitude of the beam steering as well as the distortion of focused Gaussian and Bessel beams in tissues with microscopic heterogeneities. Here, we have developed an imaging method and quantitative metrics to evaluate the motion and distortion of low-numerical-aperture (NA) Gaussian and Bessel beams focused in water, heterogeneous phantoms, and fresh mouse esophagus tissues. Our results indicate that low-NA Bessel beams exhibit reduced beam-steering artifacts and distortions compared to Gaussian beams, and are therefore potentially useful for microscopy applications in which pointing accuracy and beam quality are critical, such as dual-axis confocal (DAC) microscopy.
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Affiliation(s)
- Ye Chen
- Department of Biomedical Engineering, Stony Brook University (SUNY), Stony Brook, NY 11794
USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98195
USA
| | - Jonathan T.C. Liu
- Department of Biomedical Engineering, Stony Brook University (SUNY), Stony Brook, NY 11794
USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98195
USA
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40
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Gao L. Optimization of the excitation light sheet in selective plane illumination microscopy. Biomed Opt Express 2015; 6:881-90. [PMID: 25798312 PMCID: PMC4361442 DOI: 10.1364/boe.6.000881] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 02/15/2015] [Accepted: 02/16/2015] [Indexed: 05/12/2023]
Abstract
Selective plane illumination microscopy (SPIM) allows rapid 3D live fluorescence imaging on biological specimens with high 3D spatial resolution, good optical sectioning capability and minimal photobleaching and phototoxic effect. SPIM gains its advantage by confining the excitation light near the detection focal plane, and its performance is determined by the ability to create a thin, large and uniform excitation light sheet. Several methods have been developed to create such an excitation light sheet for SPIM. However, each method has its own strengths and weaknesses, and tradeoffs must be made among different aspects in SPIM imaging. In this work, we present a strategy to select the excitation light sheet among the latest SPIM techniques, and to optimize its geometry based on spatial resolution, field of view, optical sectioning capability, and the sample to be imaged. Besides the light sheets discussed in this work, the proposed strategy is also applicable to estimate the SPIM performance using other excitation light sheets.
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Affiliation(s)
- Liang Gao
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794,
USA
- Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, NY, 11794,
USA
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41
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Kwon KC, Jeong JS, Erdenebat MU, Piao YL, Yoo KH, Kim N. Resolution-enhancement for an orthographic-view image display in an integral imaging microscope system. Biomed Opt Express 2015; 6:736-46. [PMID: 25798299 PMCID: PMC4361429 DOI: 10.1364/boe.6.000736] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/12/2015] [Accepted: 02/03/2015] [Indexed: 05/09/2023]
Abstract
Due to the limitations of micro lens arrays and camera sensors, images on display devices through the integral imaging microscope systems have been suffering for a low-resolution. In this paper, a resolution-enhanced orthographic-view image display method for integral imaging microscopy is proposed and demonstrated. Iterative intermediate-view reconstructions are performed based on bilinear interpolation using neighborhood elemental image information, and a graphics processing unit parallel processing algorithm is applied for fast image processing. The proposed method is verified experimentally and the effective results are presented in this paper.
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Affiliation(s)
- Ki-Chul Kwon
- School of Information and Communication Engineering, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, Chungbuk 362-763,
South Korea
| | - Ji-Seong Jeong
- Department of Digital Informatics and Convergence, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, Chungbuk 362-763,
South Korea
| | - Munkh-Uchral Erdenebat
- School of Information and Communication Engineering, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, Chungbuk 362-763,
South Korea
| | - Yan-Ling Piao
- School of Information and Communication Engineering, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, Chungbuk 362-763,
South Korea
| | - Kwan-Hee Yoo
- Department of Digital Informatics and Convergence, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, Chungbuk 362-763,
South Korea
| | - Nam Kim
- School of Information and Communication Engineering, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, Chungbuk 362-763,
South Korea
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42
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Huang J, Sun M, Gumpper K, Chi Y, Ma J. 3D multifocus astigmatism and compressed sensing (3D MACS) based superresolution reconstruction. Biomed Opt Express 2015; 6:902-17. [PMID: 25798314 PMCID: PMC4361444 DOI: 10.1364/boe.6.000902] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/02/2015] [Accepted: 01/15/2015] [Indexed: 05/15/2023]
Abstract
Single molecule based superresolution techniques (STORM/PALM) achieve nanometer spatial resolution by integrating the temporal information of the switching dynamics of fluorophores (emitters). When emitter density is low for each frame, they are located to the nanometer resolution. However, when the emitter density rises, causing significant overlapping, it becomes increasingly difficult to accurately locate individual emitters. This is particularly apparent in three dimensional (3D) localization because of the large effective volume of the 3D point spread function (PSF). The inability to precisely locate the emitters at a high density causes poor temporal resolution of localization-based superresolution technique and significantly limits its application in 3D live cell imaging. To address this problem, we developed a 3D high-density superresolution imaging platform that allows us to precisely locate the positions of emitters, even when they are significantly overlapped in three dimensional space. Our platform involves a multi-focus system in combination with astigmatic optics and an ℓ 1-Homotopy optimization procedure. To reduce the intrinsic bias introduced by the discrete formulation of compressed sensing, we introduced a debiasing step followed by a 3D weighted centroid procedure, which not only increases the localization accuracy, but also increases the computation speed of image reconstruction. We implemented our algorithms on a graphic processing unit (GPU), which speeds up processing 10 times compared with central processing unit (CPU) implementation. We tested our method with both simulated data and experimental data of fluorescently labeled microtubules and were able to reconstruct a 3D microtubule image with 1000 frames (512×512) acquired within 20 seconds.
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Affiliation(s)
- Jiaqing Huang
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210,
USA
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH, 43210,
USA
- These authors contribute equally to this work
| | - Mingzhai Sun
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210,
USA
- These authors contribute equally to this work
| | - Kristyn Gumpper
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210,
USA
| | - Yuejie Chi
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH, 43210,
USA
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210,
USA
| | - Jianjie Ma
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210,
USA
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43
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Rupprecht P, Prevedel R, Groessl F, Haubensak WE, Vaziri A. Optimizing and extending light-sculpting microscopy for fast functional imaging in neuroscience. Biomed Opt Express 2015; 6:353-68. [PMID: 25780729 PMCID: PMC4354592 DOI: 10.1364/boe.6.000353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/01/2014] [Accepted: 12/01/2014] [Indexed: 05/08/2023]
Abstract
A number of questions in system biology such as understanding how dynamics of neuronal networks are related to brain function require the ability to capture the functional dynamics of large cellular populations at high speed. Recently, this has driven the development of a number of parallel and high speed imaging techniques such as light-sculpting microscopy, which has been used to capture neuronal dynamics at the whole brain and single cell level in small model organisms. However, the broader applicability of light-sculpting microcopy is limited by the size of volumes for which high speed imaging can be obtained and scattering in brain tissue. Here, we present strategies for optimizing the present tradeoffs in light-sculpting microscopy. Various scanning modalities in light-sculpting microscopy are theoretically and experimentally evaluated, and strategies to maximize the obtainable volume speeds, and depth penetration in brain tissue using different laser systems are provided. Design-choices, important parameters and their trade-offs are experimentally demonstrated by performing calcium-imaging in acute mouse-brain slices. We further show that synchronization of line-scanning techniques with rolling-shutter read-out of the camera can reduce scattering effects and enhance image contrast at depth.
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Affiliation(s)
- Peter Rupprecht
- Research Institute of Molecular Pathology, Vienna,
Austria
- Max F. Perutz Laboratories, University of Vienna, Vienna,
Austria
- Research Platform Quantum Phenomena & Nanoscale Biological Systems (QuNaBioS), University of Vienna, Vienna,
Austria
- Current address: Friedrich Miescher Institute, Basel,
Switzerland
| | - Robert Prevedel
- Research Institute of Molecular Pathology, Vienna,
Austria
- Max F. Perutz Laboratories, University of Vienna, Vienna,
Austria
- Research Platform Quantum Phenomena & Nanoscale Biological Systems (QuNaBioS), University of Vienna, Vienna,
Austria
| | | | | | - Alipasha Vaziri
- Research Institute of Molecular Pathology, Vienna,
Austria
- Max F. Perutz Laboratories, University of Vienna, Vienna,
Austria
- Research Platform Quantum Phenomena & Nanoscale Biological Systems (QuNaBioS), University of Vienna, Vienna,
Austria
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44
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Bégin S, Dupont-Therrien O, Bélanger E, Daradich A, Laffray S, De Koninck Y, Côté DC. Automated method for the segmentation and morphometry of nerve fibers in large-scale CARS images of spinal cord tissue. Biomed Opt Express 2014; 5:4145-4161. [PMID: 25574428 PMCID: PMC4285595 DOI: 10.1364/boe.5.004145] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 09/26/2014] [Accepted: 10/02/2014] [Indexed: 06/04/2023]
Abstract
A fully automated method for large-scale segmentation of nerve fibers from coherent anti-Stokes Raman scattering (CARS) microscopy images is presented. The method is specifically designed for CARS images of transverse cross sections of nervous tissue but is also suitable for use with standard light microscopy images. After a detailed description of the two-part segmentation algorithm, its accuracy is quantified by comparing the resulting binary images to manually segmented images. We then demonstrate the ability of our method to retrieve morphological data from CARS images of nerve tissue. Finally, we present the segmentation of a large mosaic of CARS images covering more than half the area of a mouse spinal cord cross section and show evidence of clusters of neurons with similar g-ratios throughout the spinal cord.
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Affiliation(s)
- Steve Bégin
- Centre de recherche de l’Institut universitaire en santé mentale de Québec (CRIUSMQ), Université Laval, Québec,
Canada
- Département de physique, génie physique et optique, Université Laval, Québec,
Canada
- Centre d’optique, photonique et laser (COPL), Université Laval, Québec,
Canada
| | - Olivier Dupont-Therrien
- Centre de recherche de l’Institut universitaire en santé mentale de Québec (CRIUSMQ), Université Laval, Québec,
Canada
- Centre d’optique, photonique et laser (COPL), Université Laval, Québec,
Canada
| | - Erik Bélanger
- Centre de recherche de l’Institut universitaire en santé mentale de Québec (CRIUSMQ), Université Laval, Québec,
Canada
- Département de physique, génie physique et optique, Université Laval, Québec,
Canada
- Centre d’optique, photonique et laser (COPL), Université Laval, Québec,
Canada
| | - Amy Daradich
- Centre de recherche de l’Institut universitaire en santé mentale de Québec (CRIUSMQ), Université Laval, Québec,
Canada
- Département de physique, génie physique et optique, Université Laval, Québec,
Canada
- Centre d’optique, photonique et laser (COPL), Université Laval, Québec,
Canada
| | - Sophie Laffray
- Centre de recherche de l’Institut universitaire en santé mentale de Québec (CRIUSMQ), Université Laval, Québec,
Canada
- Centre d’optique, photonique et laser (COPL), Université Laval, Québec,
Canada
| | - Yves De Koninck
- Centre de recherche de l’Institut universitaire en santé mentale de Québec (CRIUSMQ), Université Laval, Québec,
Canada
- Département de psychiatrie et de neurosciences, Université Laval, Québec,
Canada
| | - Daniel C. Côté
- Centre de recherche de l’Institut universitaire en santé mentale de Québec (CRIUSMQ), Université Laval, Québec,
Canada
- Département de physique, génie physique et optique, Université Laval, Québec,
Canada
- Centre d’optique, photonique et laser (COPL), Université Laval, Québec,
Canada
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45
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Thomas G, van Voskuilen J, Truong H, Song JY, Gerritsen HC, Sterenborg HJCM. In vivo nonlinear spectral imaging as a tool to monitor early spectroscopic and metabolic changes in a murine cutaneous squamous cell carcinoma model. Biomed Opt Express 2014; 5:4281-99. [PMID: 25574438 PMCID: PMC4285605 DOI: 10.1364/boe.5.004281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/06/2014] [Accepted: 11/07/2014] [Indexed: 05/11/2023]
Abstract
Timely detection of cutaneous squamous cell carcinoma with non-invasive modalities like nonlinear spectral imaging (NLSI) can ensure efficient preventive or therapeutic measures for patients. In this study, in vivo NLSI was used to study spectral characteristics in murine skin treated with 7, 12-dimethylbenz(a)anthracene. The results show that NLSI could detect emission spectral changes during the early preclinical stages of skin carcinogenesis. Analyzing these emission spectra using simulated band-pass filters at 450-460 nm and 525-535 nm, gave parameters that were expressed as a ratio. This ratio was increased and thus suggestive of elevated metabolic activity in early stages of skin carcinogenesis.
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Affiliation(s)
- Giju Thomas
- Department of Biomedical Engineering and Physics, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam, The
Netherlands
- Centre for Optical Diagnostics and Therapy, Erasmus Medical Centre, Post Box 2040, 3000 CA, Rotterdam, The
Netherlands
| | - Johan van Voskuilen
- Department of Molecular Biophysics, Utrecht University, 3508 TA, Utrecht, The
Netherlands
| | - Hoa Truong
- Department of Molecular Biophysics, Utrecht University, 3508 TA, Utrecht, The
Netherlands
| | - Ji-Ying Song
- Department of Experimental Animal Pathology, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Amsterdam, The
Netherlands
| | - Hans C. Gerritsen
- Department of Molecular Biophysics, Utrecht University, 3508 TA, Utrecht, The
Netherlands
| | - H. J. C. M. Sterenborg
- Department of Biomedical Engineering and Physics, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam, The
Netherlands
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46
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Min J, Holden SJ, Carlini L, Unser M, Manley S, Ye JC. 3D high-density localization microscopy using hybrid astigmatic/ biplane imaging and sparse image reconstruction. Biomed Opt Express 2014; 5:3935-48. [PMID: 26526603 PMCID: PMC4242028 DOI: 10.1364/boe.5.003935] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Localization microscopy achieves nanoscale spatial resolution by iterative localization of sparsely activated molecules, which generally leads to a long acquisition time. By implementing advanced algorithms to treat overlapping point spread functions (PSFs), imaging of densely activated molecules can improve the limited temporal resolution, as has been well demonstrated in two-dimensional imaging. However, three-dimensional (3D) localization of high-density data remains challenging since PSFs are far more similar along the axial dimension than the lateral dimensions. Here, we present a new, high-density 3D imaging system and algorithm. The hybrid system is implemented by combining astigmatic and biplane imaging. The proposed 3D reconstruction algorithm is extended from our state-of-the art 2D high-density localization algorithm. Using mutual coherence analysis of model PSFs, we validated that the hybrid system is more suitable than astigmatic or biplane imaging alone for 3D localization of high-density data. The efficacy of the proposed method was confirmed via simulation and real data of microtubules. Furthermore, we also successfully demonstrated fluorescent-protein-based live cell 3D localization microscopy with a temporal resolution of just 3 seconds, capturing fast dynamics of the endoplasmic recticulum.
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Affiliation(s)
- Junhong Min
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon,
Republic of Korea
| | - Seamus J. Holden
- Institute of the Physics of Biological Systems, École polytechnique Fédérale de Lausanne,
Switzerland
| | - Lina Carlini
- Institute of the Physics of Biological Systems, École polytechnique Fédérale de Lausanne,
Switzerland
| | - Michael Unser
- Biomedical Imaging Group, École polytechnique fédérale de Lausanne,
Switzerland
| | - Suliana Manley
- Institute of the Physics of Biological Systems, École polytechnique Fédérale de Lausanne,
Switzerland
| | - Jong Chul Ye
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon,
Republic of Korea
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47
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Hamel V, Guichard P, Fournier M, Guiet R, Flückiger I, Seitz A, Gönczy P. Correlative multicolor 3D SIM and STORM microscopy. Biomed Opt Express 2014; 5:3326-36. [PMID: 25360353 PMCID: PMC4206305 DOI: 10.1364/boe.5.003326] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 08/22/2014] [Accepted: 08/22/2014] [Indexed: 05/25/2023]
Abstract
Within the last decade, super-resolution methods that surpass the diffraction limit of light microscopy have provided invaluable insight into a variety of biological questions. Each of these approaches has inherent advantages and limitations, such that their combination is a powerful means to transform them into versatile tools for the life sciences. Here, we report the development of a combined SIM and STORM setup that maintains the optimal resolution of both methods and which is coupled to image registration to localize biological structures in 3D using multicolor labeling. We utilized this workflow to determine the localization of Bld12p/CrSAS-6 in purified basal bodies of Chlamydomonas reinhardtii with utmost precision, demonstrating its usefulness for accurate molecular mapping in 3D.
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Affiliation(s)
- Virginie Hamel
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- These authors contributed equally to this work
| | - Paul Guichard
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- These authors contributed equally to this work
| | - Mathias Fournier
- Bioimaging and Optics platform (BIOP), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- These authors contributed equally to this work
| | - Romain Guiet
- Bioimaging and Optics platform (BIOP), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Isabelle Flückiger
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Arne Seitz
- Bioimaging and Optics platform (BIOP), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
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48
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Yang Z, Prokopas M, Nylk J, Coll-Lladó C, Gunn-Moore FJ, Ferrier DEK, Vettenburg T, Dholakia K. A compact Airy beam light sheet microscope with a tilted cylindrical lens. Biomed Opt Express 2014; 5:3434-42. [PMID: 25360362 PMCID: PMC4206314 DOI: 10.1364/boe.5.003434] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/18/2014] [Accepted: 08/22/2014] [Indexed: 05/18/2023]
Abstract
Light-sheet imaging is rapidly gaining importance for imaging intact biological specimens. Many of the latest innovations rely on the propagation-invariant Bessel or Airy beams to form an extended light sheet to provide high resolution across a large field of view. Shaping light to realize propagation-invariant beams often relies on complex programming of spatial light modulators or specialized, custom made, optical elements. Here we present a straightforward and low-cost modification to the traditional light-sheet setup, based on the open-access light-sheet microscope OpenSPIM, to achieve Airy light-sheet illumination. This brings wide field single-photon light-sheet imaging to a broader range of endusers. Fluorescent microspheres embedded in agarose and a zebrafish larva were imaged to demonstrate how such a microscope can have a minimal footprint and cost without compromising on imaging quality.
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Affiliation(s)
- Zhengyi Yang
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS,
UK
| | - Martynas Prokopas
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS,
UK
| | - Jonathan Nylk
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS,
UK
- School of Biology, Medical and Biological Sciences Building, University of St Andrews, North Haugh, St Andrews, KY16 9TF,
UK
| | - Clara Coll-Lladó
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, East Sands, St Andrews, KY16 8LB,
UK
| | - Frank J. Gunn-Moore
- School of Biology, Medical and Biological Sciences Building, University of St Andrews, North Haugh, St Andrews, KY16 9TF,
UK
| | - David E. K. Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, East Sands, St Andrews, KY16 8LB,
UK
| | - Tom Vettenburg
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS,
UK
| | - Kishan Dholakia
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS,
UK
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49
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O’Holleran K, Shaw M. Optimized approaches for optical sectioning and resolution enhancement in 2D structured illumination microscopy. Biomed Opt Express 2014; 5:2580-90. [PMID: 25136487 PMCID: PMC4132990 DOI: 10.1364/boe.5.002580] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/08/2014] [Accepted: 04/28/2014] [Indexed: 05/10/2023]
Abstract
The use of structured illumination in fluorescence microscopy allows the suppression of out of focus light and an increase in effective spatial resolution. In this paper we consider different approaches for reconstructing 2D structured illumination images in order to combine these two attributes, to allow fast, optically sectioned, superresolution imaging. We present a linear reconstruction method that maximizes the axial frequency extent of the combined 2D structured illumination passband along with an empirically optimized approximation to this scheme. These reconstruction methods are compared to other schemes using structured illumination images of fluorescent samples. For sinusoidal excitation at half the incoherent cutoff frequency we find that removing information in the zero order passband except for a small region close to the excitation frequency, where it replaces the complementary information from the displaced first order passband, enables optimal reconstruction of optically sectioned images with enhanced spatial resolution.
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Affiliation(s)
- Kevin O’Holleran
- Cambridge Advanced Imaging Centre, University of Cambridge, Anatomy Building, Cambridge, CB2 3DY, UK
| | - Michael Shaw
- Analytical Science Division, National Physical Laboratory, Hampton Road, Teddington, Middlesex, TW11 0LW, UK
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50
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Faridian A, Pedrini G, Osten W. Opposed-view dark-field digital holographic microscopy. Biomed Opt Express 2014; 5:728-36. [PMID: 24688809 PMCID: PMC3959838 DOI: 10.1364/boe.5.000728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 01/22/2014] [Accepted: 02/05/2014] [Indexed: 05/05/2023]
Abstract
Scattering and absorption belong to the major problems in imaging the internal layers of a biological specimen. Due to the structural inhomogeneity of the specimen, the distribution of the structures in the upper layers of a given internal structure of interest is different from the lower layers that may result in different interception of scattered light, falling into the angular aperture of the microscope objective, from the object in each imaging view. Therefore, different spatial frequencies of the scattered light can be acquired from different (top and bottom) views. We have arranged an opposed-view dark-field digital holographic microscope (DHM) to collect the scattered light concurrently from both views with the aim to increase the contrast of internal structures and improve the signal-to-noise ratio. Implementing a DHM system gives the possibility to implement digital refocusing process and obtain multilayer images from each side without a depth scan of the object. The method is explained and the results are presented exemplary for a Drosophila embryo.
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