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Jiao Z, Pan M, Yousaf K, Doveiko D, Maclean M, Griffin D, Chen Y, Li DDU. Smartphone-based optical sectioning (SOS) microscopy with a telecentric design for fluorescence imaging. J Microsc 2024. [PMID: 38808665 DOI: 10.1111/jmi.13334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 04/15/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024]
Abstract
We propose a smartphone-based optical sectioning (SOS) microscope based on the HiLo technique, with a single smartphone replacing a high-cost illumination source and a camera sensor. We built our SOS with off-the-shelf optical, mechanical cage systems with 3D-printed adapters to seamlessly integrate the smartphone with the SOS main body. The liquid light guide can be integrated with the adapter, guiding the smartphone's LED light to the digital mirror device (DMD) with neglectable loss. We used an electrically tuneable lens (ETL) instead of a mechanical translation stage to realise low-cost axial scanning. The ETL was conjugated to the objective lens's back pupil plane (BPP) to construct a telecentric design by a 4f configuration to maintain the lateral magnification for different axial positions. SOS has a 571.5 µm telecentric scanning range and an 11.7 µm axial resolution. The broadband smartphone LED torch can effectively excite fluorescent polystyrene (PS) beads. We successfully used SOS for high-contrast fluorescent PS beads imaging with different wavelengths and optical sectioning imaging of multilayer fluorescent PS beads. To our knowledge, the proposed SOS is the first smartphone-based HiLo optical sectioning microscopy (£1965), which can save around £7035 compared with a traditional HiLo system (£9000). It is a powerful tool for biomedical research in resource-limited areas.
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Affiliation(s)
- Ziao Jiao
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, Scotland, UK
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | - Mingliang Pan
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, Scotland, UK
| | - Khadija Yousaf
- Department of Physics, University of Strathclyde, Glasgow, Scotland, UK
| | - Daniel Doveiko
- Department of Physics, University of Strathclyde, Glasgow, Scotland, UK
| | - Michelle Maclean
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, Scotland, UK
- Department of Electronic & Electrical Engineering, The Robertson Trust Laboratory for Electronic Sterilisation Technologies (ROLEST), University of Strathclyde, Glasgow, UK
| | - David Griffin
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, Scotland, UK
| | - Yu Chen
- Department of Physics, University of Strathclyde, Glasgow, Scotland, UK
| | - David Day Uei Li
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, Scotland, UK
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
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2
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Eddy CZ, Naylor A, Cunningham CT, Sun B. Facilitating cell segmentation with the projection-enhancement network. Phys Biol 2023; 20:10.1088/1478-3975/acfe53. [PMID: 37769666 PMCID: PMC10586931 DOI: 10.1088/1478-3975/acfe53] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
Contemporary approaches to instance segmentation in cell science use 2D or 3D convolutional networks depending on the experiment and data structures. However, limitations in microscopy systems or efforts to prevent phototoxicity commonly require recording sub-optimally sampled data that greatly reduces the utility of such 3D data, especially in crowded sample space with significant axial overlap between objects. In such regimes, 2D segmentations are both more reliable for cell morphology and easier to annotate. In this work, we propose the projection enhancement network (PEN), a novel convolutional module which processes the sub-sampled 3D data and produces a 2D RGB semantic compression, and is trained in conjunction with an instance segmentation network of choice to produce 2D segmentations. Our approach combines augmentation to increase cell density using a low-density cell image dataset to train PEN, and curated datasets to evaluate PEN. We show that with PEN, the learned semantic representation in CellPose encodes depth and greatly improves segmentation performance in comparison to maximum intensity projection images as input, but does not similarly aid segmentation in region-based networks like Mask-RCNN. Finally, we dissect the segmentation strength against cell density of PEN with CellPose on disseminated cells from side-by-side spheroids. We present PEN as a data-driven solution to form compressed representations of 3D data that improve 2D segmentations from instance segmentation networks.
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Affiliation(s)
| | - Austin Naylor
- Oregon State University, Department of Physics, Corvallis, 97331, USA
| | | | - Bo Sun
- Oregon State University, Department of Physics, Corvallis, 97331, USA
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3
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Deng L, Chen J, Li Y, Han Y, Fan G, Yang J, Cao D, Lu B, Ning K, Nie S, Zhang Z, Shen D, Zhang Y, Fu W, Wang WE, Wan Y, Li S, Feng YQ, Luo Q, Yuan J. Cryo-Fluorescence Micro-Optical Sectioning Tomography for Volumetric Imaging of Various Whole Organs with Subcellular Resolution. iScience 2022; 25:104805. [PMID: 35992061 PMCID: PMC9389242 DOI: 10.1016/j.isci.2022.104805] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 06/17/2022] [Accepted: 07/15/2022] [Indexed: 11/20/2022] Open
Abstract
Optical visualization of complex microstructures in the entire organ is essential for biomedical research. However, the existing methods fail to accurately acquire the detailed microstructures of whole organs with good morphological and biochemical preservation. This study proposes a cryo-fluorescence micro-optical sectioning tomography (cryo-fMOST) to image whole organs in three dimensions (3D) with submicron resolution. The system comprises a line-illumination microscope module, cryo-microtome, three-stage refrigeration module, and heat insulation device. To demonstrate the imaging capacity and wide applicability of the system, we imaged and reconstructed various organs of mice in 3D, including the healthy tongue, kidney, and brain, as well as the infarcted heart. More importantly, imaged brain slices were performed sugar phosphates determination and fluorescence in situ hybridization imaging to verify the compatibility of multi-omics measurements. The results demonstrated that cryo-fMOST is capable of acquiring high-resolution morphological details of various whole organs and may be potentially useful for spatial multi-omics. Cryo-fluorescence micro-optical sectioning tomography (Cryo-fMOST) was achieved 3D imaging of whole mouse tongue, kidney, heart, and brain at submicron resolution Frozen state well preserves tissues’ original morphology and biochemical information Cryo-fMOST is compatible with sugar phosphates determination and FISH measurement
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Affiliation(s)
- Lei Deng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jianwei Chen
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yafeng Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yutong Han
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Guoqing Fan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jie Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Dongjian Cao
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Bolin Lu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Kefu Ning
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shuo Nie
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zoutao Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Dan Shen
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yunfei Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Wenbin Fu
- Department of Cardiology, Daping Hospital, Army Medical University, Chongqing 400038, China
| | - Wei Eric Wang
- Department of Cardiology, Daping Hospital, Army Medical University, Chongqing 400038, China
| | - Ying Wan
- Biomedical Analysis Center, Army Medical University, Chongqing 400038, China
- Chongqing Key Laboratory of Cytomics, Chongqing 400038, China
| | - Sha Li
- Department of Chemistry, Wuhan University, Wuhan 430072, China
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Yu-Qi Feng
- Department of Chemistry, Wuhan University, Wuhan 430072, China
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- School of Biomedical Engineering, Hainan University, Haikou, 570228, China
- Corresponding author
| | - Jing Yuan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, 215123, China
- Corresponding author
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4
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Bando K, Yabuuchi S, Li M, Kubo T, Oketani R, Smith NI, Fujita K. Bessel-beam illumination Raman microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:3161-3170. [PMID: 35781960 PMCID: PMC9208613 DOI: 10.1364/boe.456138] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
We demonstrate the use of Bessel beams for side illumination slit-scanning Raman imaging for label-free and hyperspectral analysis of cell spheroids. The background elimination by the side illumination and the aberration-resistant Bessel beam drastically improves the image contrast in Raman observation, allowing label-free investigation of intracellular molecules in thick biological samples. Live cell spheroids were observed to confirm the improvement in image contrast and background reduction with Bessel illumination compared to conventional epi-line illumination.
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Affiliation(s)
- Kazuki Bando
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shumpei Yabuuchi
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Menglu Li
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- AIST-Osaka University Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshiki Kubo
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ryosuke Oketani
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Nicholas I. Smith
- Immunology Frontier Research Center, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Katsumasa Fujita
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- AIST-Osaka University Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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5
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Kubo T, Temma K, Smith NI, Lu K, Matsuda T, Nagai T, Fujita K. Hyperspectral two-photon excitation microscopy using visible wavelength. OPTICS LETTERS 2021; 46:37-40. [PMID: 33362007 DOI: 10.1364/ol.413526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 11/08/2020] [Indexed: 05/28/2023]
Abstract
We demonstrate hyperspectral imaging by visible-wavelength two-photon excitation microscopy using line illumination and slit-confocal detection. A femtosecond pulsed laser light at 530 nm was used for the simultaneous excitation of fluorescent proteins with different emission wavelengths. The use of line illumination enabled efficient detection of hyperspectral images and achieved simultaneous detection of three fluorescence spectra in the observation of living HeLa cells with an exposure time of 1 ms per line, which is equivalent to about 2 µs per pixel in point scanning, with 160 data points per spectrum. On combining linear spectral unmixing techniques, localization of fluorescent probes in the cells was achieved. A theoretical investigation of the imaging property revealed high-depth discrimination property attained through the combination of nonlinear excitation and slit detection.
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6
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Weng CH, Tang J, Han KY. Optimizing the performance of multiline-scanning confocal microscopy. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2020; 54:105401. [PMID: 34483365 PMCID: PMC8412417 DOI: 10.1088/1361-6463/abc84b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Line-scanning confocal microscopy provides high imaging speed and moderate optical sectioning strength, which makes it a useful tool for imaging various biospecimens ranging from living cells to fixed tissues. Conventional line-scanning systems have only used a single excitation line and slit, and thus have not fully exploited benefits of parallelization. Here we investigate the optical performance of multi-line scanning confocal microscopy (mLS) by employing a digital micro-mirror that provides programmable patterns of the illumination beam and the detection slit. Through experimental results and optical simulations, we assess the depth discrimination of mLS under different optical parameters and compare it with multi-point systems such as scanning disk confocal microscopy (SDCM). Under the same illumination duty cycle, we find that mLS has better optical sectioning than SDCM at a high degree of parallelization. The optimized mLS provides a low photobleaching rate and video-rate imaging while its optical sectioning is similar to single line-scanning confocal microscopy.
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Affiliation(s)
- Chun Hung Weng
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
| | - Jialei Tang
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
| | - Kyu Young Han
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
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7
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Tang J, Han KY. Low-photobleaching line-scanning confocal microscopy using dual inclined beams. JOURNAL OF BIOPHOTONICS 2019; 12:e201900075. [PMID: 31111688 DOI: 10.1002/jbio.201900075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/22/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
Confocal microscopy is an indispensable tool for biological imaging due to its high resolution and optical sectioning capability. However, its slow imaging speed and severe photobleaching have largely prevented further applications. Here, we present dual inclined beam line-scanning (LS) confocal microscopy. The reduced excitation intensity of our imaging method enabled a 2-fold longer observation time of fluorescence compared to traditional LS microscopy while maintaining a good sectioning capability and single-molecule sensitivity. We characterized the performance of our method and applied it to subcellular imaging and three-dimensional single-molecule RNA imaging in mammalian cells.
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Affiliation(s)
- Jialei Tang
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida
| | - Kyu Young Han
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida
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8
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Khadir S, Chaumet PC, Baffou G, Sentenac A. Quantitative model of the image of a radiating dipole through a microscope. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2019; 36:478-484. [PMID: 31044960 DOI: 10.1364/josaa.36.000478] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/01/2019] [Indexed: 05/22/2023]
Abstract
In this paper, we introduce a formalism to determine the relationship between the full vectorial electric field existing at the object plane of a microscope and that existing at the image plane. The model is then used to quantitatively simulate, in both phase and intensity, the image of a radiating electric dipole placed either in a homogeneous medium or in the vicinity of a substrate. These simulations are compared with experimental measurements on single gold nanoparticles carried out by quadriwave lateral shearing interferometry.
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9
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Chang SJ, Li S, Andreasen A, Sha XZ, Zhai XY. A reference-free method for brightness compensation and contrast enhancement of micrographs of serial sections. PLoS One 2015; 10:e0127855. [PMID: 26020531 PMCID: PMC4447386 DOI: 10.1371/journal.pone.0127855] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 04/20/2015] [Indexed: 11/18/2022] Open
Abstract
Three-dimensional (3D) reconstruction of an organ or tissue from a stack of histologic serial sections provides valuable morphological information. The procedure includes section preparation of the organ or tissue, micrographs acquisition, image registration, 3D reconstruction, and visualization. However, the brightness and contrast through the image stack may not be consistent due to imperfections in the staining procedure, which may cause difficulties in micro-structure identification using virtual sections, region segmentation, automatic target tracing, etc. In the present study, a reference-free method, Sequential Histogram Fitting Algorithm (SHFA), is therefore developed for adjusting the severe and irregular variance of brightness and contrast within the image stack. To apply the SHFA, the gray value histograms of individual images are first calculated over the entire image stack and a set of landmark gray values are chosen. Then the histograms are transformed so that there are no abrupt changes in progressing through the stack. Finally, the pixel gray values of the original images are transformed into the desired ones based on the relationship between the original and the transformed histograms. The SHFA is tested on an image stacks from mouse kidney sections stained with toluidine blue, and captured by a slide scanner. As results, the images through the entire stack reveal homogenous brightness and consistent contrast. In addition, subtle color differences in the tissue are well preserved so that the morphological details can be recognized, even in virtual sections. In conclusion, compared with the existing histogram-based methods, the present study provides a practical method suitable for compensating brightness, and improving contrast of images derived from a large number of serial sections of biological organ.
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Affiliation(s)
- Shi-Jie Chang
- Department of Biomedical Engineering, China Medical University, Shenyang, Liaoning, China
| | - Shuo Li
- Department of Biochemistry, China Medical University, Shenyang, Liaoning, China
| | - Arne Andreasen
- Department of Biomedicine—Anatomy, Aarhus University, Aarhus, Denmark
| | - Xian-Zheng Sha
- Department of Biomedical Engineering, China Medical University, Shenyang, Liaoning, China
| | - Xiao-Yue Zhai
- Department of Histology and Embryology, China Medical University, Shenyang, Liaoning, China
- * E-mail:
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10
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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. BIOMEDICAL OPTICS 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] [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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11
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Cole RW, Thibault M, Bayles CJ, Eason B, Girard AM, Jinadasa T, Opansky C, Schulz K, Brown CM. International test results for objective lens quality, resolution, spectral accuracy and spectral separation for confocal laser scanning microscopes. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2013; 19:1653-1668. [PMID: 24103552 DOI: 10.1017/s1431927613013470] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
As part of an ongoing effort to increase image reproducibility and fidelity in addition to improving cross-instrument consistency, we have proposed using four separate instrument quality tests to augment the ones we have previously reported. These four tests assessed the following areas: (1) objective lens quality, (2) resolution, (3) accuracy of the wavelength information from spectral detectors, and (4) the accuracy and quality of spectral separation algorithms. Data were received from 55 laboratories located in 18 countries. The largest source of errors across all tests was user error which could be subdivided between failure to follow provided protocols and improper use of the microscope. This truly emphasizes the importance of proper rigorous training and diligence in performing confocal microscopy experiments and equipment evaluations. It should be noted that there was no discernible difference in quality between confocal microscope manufactures. These tests, as well as others previously reported, will help assess the quality of confocal microscopy equipment and will provide a means to track equipment performance over time. From 62 to 97% of the data sets sent in passed the various tests demonstrating the usefulness and appropriateness of these tests as part of a larger performance testing regiment.
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Affiliation(s)
- Richard W Cole
- New York State Department of Health, Wadsworth Center, P.O. Box 509, Albany, NY 12201, USA
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12
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Kumar AN, Short KW, Piston DW. A motion correction framework for time series sequences in microscopy images. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2013; 19:433-50. [PMID: 23410911 PMCID: PMC4135398 DOI: 10.1017/s1431927612014250] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
With the advent of in vivo laser scanning fluorescence microscopy techniques, time-series and three-dimensional volumes of living tissue and vessels at micron scales can be acquired to firmly analyze vessel architecture and blood flow. Analysis of a large number of image stacks to extract architecture and track blood flow manually is cumbersome and prone to observer bias. Thus, an automated framework to accomplish these analytical tasks is imperative. The first initiative toward such a framework is to compensate for motion artifacts manifest in these microscopy images. Motion artifacts in in vivo microscopy images are caused by respiratory motion, heart beats, and other motions from the specimen. Consequently, the amount of motion present in these images can be large and hinders further analysis of these images. In this article, an algorithmic framework for the correction of time-series images is presented. The automated algorithm is comprised of a rigid and a nonrigid registration step based on shape contexts. The framework performs considerably well on time-series image sequences of the islets of Langerhans and provides for the pivotal step of motion correction in the further automatic analysis of microscopy images.
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Affiliation(s)
- Ankur N. Kumar
- Department of Electrical Engineering, 367 Jacobs Hall, Vanderbilt University, Nashville, TN 37212, USA
| | - Kurt W. Short
- Department of Molecular Physiology & Biophysics, 747 Light Hall, Vanderbilt University, Nashville, TN 37232, USA
| | - David W. Piston
- Department of Molecular Physiology & Biophysics, 747 Light Hall, Vanderbilt University, Nashville, TN 37232, USA
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13
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Mei E, Fomitchov PA, Graves R, Campion M. A line scanning confocal fluorescent microscope using a CMOS rolling shutter as an adjustable aperture. J Microsc 2013; 247:269-76. [PMID: 22906014 DOI: 10.1111/j.1365-2818.2012.03642.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Traditional confocal microscopy uses a physical aperture barrier to prevent out-of-focus light from reaching the detector. The physical nature of a conventional aperture limits control over the system confocality. We describe a new line scanning confocal microscope that eliminates a need for a physical aperture by employing a software-controllable rolling shutter on a CMOS camera. A confocal image is obtained by synchronizing motion of the rolling shutter and the laser line scanning over a sample. Confocal resolution of this microscope is adjustable in real time and independently established for each fluorescence channel by changing the rolling shutter width. This technology has been implemented in the IN Cell Analyzer 6000 system by GE Healthcare.
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Affiliation(s)
- E Mei
- GE Healthcare, Life Sciences Division, Piscataway, NJ 08854, USA.
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14
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Dudás L, Sinkó J, Erdélyi M, Szabó G. Confocal line-scanning microscope with modified illumination. OPTICS LETTERS 2012; 37:4293-4295. [PMID: 23073441 DOI: 10.1364/ol.37.004293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A modified illumination-based method has been proposed to improve resolution of a confocal line-scanning system by 20%. Phase-only apodization is applied to the illumination and combined with confocal detection. The method was studied both theoretically and experimentally. Measurements were performed on silver nanospheres as subresolution test samples, and the captured data were analyzed to determine the modulation transfer function and ultimately the spatial resolution of the system.
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Affiliation(s)
- László Dudás
- Department of Optics and Quantum Electronics, University of Szeged, Dom ter 9, Szeged 6720, Hungary
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15
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A deconvolution method to improve automated 3D-analysis of dendritic spines: application to a mouse model of Huntington’s disease. Brain Struct Funct 2011; 217:421-34. [DOI: 10.1007/s00429-011-0340-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 07/23/2011] [Indexed: 12/27/2022]
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16
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Analysis of protein mobilities and interactions in living cells by multifocal fluorescence fluctuation microscopy. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 38:813-28. [DOI: 10.1007/s00249-009-0499-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 05/24/2009] [Accepted: 05/25/2009] [Indexed: 11/25/2022]
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17
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Oberlaender M, Broser PJ, Sakmann B, Hippler S. Shack-Hartmann wave front measurements in cortical tissue for deconvolution of large three-dimensional mosaic transmitted light brightfield micrographs. J Microsc 2009; 233:275-89. [PMID: 19220694 DOI: 10.1111/j.1365-2818.2009.03118.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel approach for deconvolution of 3D image stacks of cortical tissue taken by mosaic/optical-sectioning technology, using a transmitted light brightfield microscope. Mosaic/optical-sectioning offers the possibility of imaging large volumes (e.g. from cortical sections) on a millimetre scale at sub-micrometre resolution. However, a blurred contribution from out-of-focus light results in an image quality that usually prohibits 3D quantitative analysis. Such quantitative analysis is only possible after deblurring by deconvolution. The resulting image quality is strongly dependent on how accurate the point spread function used for deconvolution resembles the properties of the imaging system. Since direct measurement of the true point spread function is laborious and modelled point spread functions usually deviate from measured ones, we present a method of optimizing the microscope until it meets almost ideal imaging conditions. These conditions are validated by measuring the aberration function of the microscope and tissue using a Shack-Hartmann sensor. The analysis shows that cortical tissue from rat brains embedded in Mowiol and imaged by an oil-immersion objective can be regarded as having a homogeneous index of refraction. In addition, the amount of spherical aberration that is caused by the optics or the specimen is relatively low. Consequently the image formation is simplified to refraction between the embedding and immersion medium and to 3D diffraction at the finite entrance pupil of the objective. The resulting model point spread function is applied to the image stacks by linear or iterative deconvolution algorithms. For the presented dataset of large 3D images the linear approach proves to be superior. The linear deconvolution yields a significant improvement in signal-to-noise ratio and resolution. This novel approach allows a quantitative analysis of the cortical image stacks such as the reconstruction of biocytin-stained neuronal dendrites and axons.
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Affiliation(s)
- M Oberlaender
- Max Planck Institute of Neurobiology Research Group 'Cortical Column In Silico', Am Klopferspitz 18, Martinsried 82152, Germany.
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18
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Dossin FDM, Dufour A, Dusch E, Siqueira-Neto JL, Moraes CB, Yang GS, Cano MI, Genovesio A, Freitas-Junior LH. Automated nuclear analysis of Leishmania major telomeric clusters reveals changes in their organization during the parasite's life cycle. PLoS One 2008; 3:e2313. [PMID: 18545650 PMCID: PMC2396463 DOI: 10.1371/journal.pone.0002313] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2008] [Accepted: 04/20/2008] [Indexed: 12/16/2022] Open
Abstract
Parasite virulence genes are usually associated with telomeres. The clustering of the telomeres, together with their particular spatial distribution in the nucleus of human parasites such as Plasmodium falciparum and Trypanosoma brucei, has been suggested to play a role in facilitating ectopic recombination and in the emergence of new antigenic variants. Leishmania parasites, as well as other trypanosomes, have unusual gene expression characteristics, such as polycistronic and constitutive transcription of protein-coding genes. Leishmania subtelomeric regions are even more unique because unlike these regions in other trypanosomes they are devoid of virulence genes. Given these peculiarities of Leishmania, we sought to investigate how telomeres are organized in the nucleus of Leishmania major parasites at both the human and insect stages of their life cycle. We developed a new automated and precise method for identifying telomere position in the three-dimensional space of the nucleus, and we found that the telomeres are organized in clusters present in similar numbers in both the human and insect stages. While the number of clusters remained the same, their distribution differed between the two stages. The telomeric clusters were found more concentrated near the center of the nucleus in the human stage than in the insect stage suggesting reorganization during the parasite's differentiation process between the two hosts. These data provide the first 3D analysis of Leishmania telomere organization. The possible biological implications of these findings are discussed.
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Affiliation(s)
| | | | - Elodie Dusch
- Image Mining Group, Institut Pasteur Korea, Seoul, South Korea
| | | | - Carolina B. Moraes
- Systems Biology of Pathogens Group, Institut Pasteur Korea, Seoul, South Korea
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gyong Seon Yang
- Systems Biology of Pathogens Group, Institut Pasteur Korea, Seoul, South Korea
| | - Maria Isabel Cano
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
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Cylindrical illumination confocal spectroscopy: rectifying the limitations of confocal single molecule spectroscopy through one-dimensional beam shaping. Biophys J 2008; 95:2964-75. [PMID: 18515376 DOI: 10.1529/biophysj.108.132472] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cylindrical illumination confocal spectroscopy (CICS) is a new implementation of single molecule detection that can be generically incorporated into any microfluidic system and allows highly quantitative and accurate analysis of single fluorescent molecules. Through theoretical modeling of confocal optics and Monte Carlo simulations, one-dimensional beam shaping is used to create a highly uniform sheet-like observation volume that enables the detection of digital fluorescence bursts while retaining single fluorophore sensitivity. First, we theoretically show that when used to detect single molecules in a microchannel, CICS can be optimized to obtain near 100% mass detection efficiency, <10% relative SD in burst heights, and a high signal/noise ratio. As a result, CICS is far less sensitive to thresholding artifacts than traditional single molecule detection and significantly more accurate at determining both burst rate and burst parameters. CICS is then experimentally implemented, optically characterized, and integrated into separate two microfluidic devices for the analysis of fluorescently stained plasmid DNA and single Cy5 labeled oligonucleotides. CICS rectifies the limitations of traditional confocal spectroscopy-based single molecule detection without the significant operational complications of competing technologies.
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