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Zhang Y, Wang M, Zhu Q, Guo Y, Liu B, Li J, Yao X, Kong C, Zhang Y, Huang Y, Qi H, Wu J, Guo ZV, Dai Q. Long-term mesoscale imaging of 3D intercellular dynamics across a mammalian organ. Cell 2024; 187:6104-6122.e25. [PMID: 39276776 DOI: 10.1016/j.cell.2024.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 06/06/2024] [Accepted: 08/13/2024] [Indexed: 09/17/2024]
Abstract
A comprehensive understanding of physio-pathological processes necessitates non-invasive intravital three-dimensional (3D) imaging over varying spatial and temporal scales. However, huge data throughput, optical heterogeneity, surface irregularity, and phototoxicity pose great challenges, leading to an inevitable trade-off between volume size, resolution, speed, sample health, and system complexity. Here, we introduce a compact real-time, ultra-large-scale, high-resolution 3D mesoscope (RUSH3D), achieving uniform resolutions of 2.6 × 2.6 × 6 μm3 across a volume of 8,000 × 6,000 × 400 μm3 at 20 Hz with low phototoxicity. Through the integration of multiple computational imaging techniques, RUSH3D facilitates a 13-fold improvement in data throughput and an orders-of-magnitude reduction in system size and cost. With these advantages, we observed premovement neural activity and cross-day visual representational drift across the mouse cortex, the formation and progression of multiple germinal centers in mouse inguinal lymph nodes, and heterogeneous immune responses following traumatic brain injury-all at single-cell resolution, opening up a horizon for intravital mesoscale study of large-scale intercellular interactions at the organ level.
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Affiliation(s)
- Yuanlong Zhang
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Mingrui Wang
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518071, China
| | - Qiyu Zhu
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yuduo Guo
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518071, China
| | - Bo Liu
- School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Laboratory of Dynamic Immunobiology, Institute for Immunology, Tsinghua University, Beijing 100084, China
| | - Jiamin Li
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiao Yao
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Chui Kong
- School of Information Science and Technology, Fudan University, Shanghai 200433, China
| | - Yi Zhang
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Yuchao Huang
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Hai Qi
- School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Laboratory of Dynamic Immunobiology, Institute for Immunology, Tsinghua University, Beijing 100084, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China.
| | - Zengcai V Guo
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China.
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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; 296:10-23. [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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Munshi R. How Transcription Factor Clusters Shape the Transcriptional Landscape. Biomolecules 2024; 14:875. [PMID: 39062589 PMCID: PMC11274464 DOI: 10.3390/biom14070875] [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: 06/01/2024] [Revised: 07/14/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
In eukaryotic cells, gene transcription typically occurs in discrete periods of promoter activity, interspersed with intervals of inactivity. This pattern deviates from simple stochastic events and warrants a closer examination of the molecular interactions that activate the promoter. Recent studies have identified transcription factor (TF) clusters as key precursors to transcriptional bursting. Often, these TF clusters form at chromatin segments that are physically distant from the promoter, making changes in chromatin conformation crucial for promoter-TF cluster interactions. In this review, I explore the formation and constituents of TF clusters, examining how the dynamic interplay between chromatin architecture and TF clustering influences transcriptional bursting. Additionally, I discuss techniques for visualizing TF clusters and provide an outlook on understanding the remaining gaps in this field.
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Affiliation(s)
- Rahul Munshi
- Joseph Henry Laboratories of Physics and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
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4
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Jiang T, Gong H, Yuan J. Whole-brain Optical Imaging: A Powerful Tool for Precise Brain Mapping at the Mesoscopic Level. Neurosci Bull 2023; 39:1840-1858. [PMID: 37715920 PMCID: PMC10661546 DOI: 10.1007/s12264-023-01112-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/08/2023] [Indexed: 09/18/2023] Open
Abstract
The mammalian brain is a highly complex network that consists of millions to billions of densely-interconnected neurons. Precise dissection of neural circuits at the mesoscopic level can provide important structural information for understanding the brain. Optical approaches can achieve submicron lateral resolution and achieve "optical sectioning" by a variety of means, which has the natural advantage of allowing the observation of neural circuits at the mesoscopic level. Automated whole-brain optical imaging methods based on tissue clearing or histological sectioning surpass the limitation of optical imaging depth in biological tissues and can provide delicate structural information in a large volume of tissues. Combined with various fluorescent labeling techniques, whole-brain optical imaging methods have shown great potential in the brain-wide quantitative profiling of cells, circuits, and blood vessels. In this review, we summarize the principles and implementations of various whole-brain optical imaging methods and provide some concepts regarding their future development.
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Affiliation(s)
- Tao Jiang
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China
| | - Hui Gong
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jing Yuan
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China.
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
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Greene J, Xue Y, Alido J, Matlock A, Hu G, Kiliç K, Davison I, Tian L. Pupil engineering for extended depth-of-field imaging in a fluorescence miniscope. NEUROPHOTONICS 2023; 10:044302. [PMID: 37215637 PMCID: PMC10197144 DOI: 10.1117/1.nph.10.4.044302] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023]
Abstract
Significance Fluorescence head-mounted microscopes, i.e., miniscopes, have emerged as powerful tools to analyze in-vivo neural populations but exhibit a limited depth-of-field (DoF) due to the use of high numerical aperture (NA) gradient refractive index (GRIN) objective lenses. Aim We present extended depth-of-field (EDoF) miniscope, which integrates an optimized thin and lightweight binary diffractive optical element (DOE) onto the GRIN lens of a miniscope to extend the DoF by 2.8× between twin foci in fixed scattering samples. Approach We use a genetic algorithm that considers the GRIN lens' aberration and intensity loss from scattering in a Fourier optics-forward model to optimize a DOE and manufacture the DOE through single-step photolithography. We integrate the DOE into EDoF-Miniscope with a lateral accuracy of 70 μm to produce high-contrast signals without compromising the speed, spatial resolution, size, or weight. Results We characterize the performance of EDoF-Miniscope across 5- and 10-μm fluorescent beads embedded in scattering phantoms and demonstrate that EDoF-Miniscope facilitates deeper interrogations of neuronal populations in a 100-μm-thick mouse brain sample and vessels in a whole mouse brain sample. Conclusions Built from off-the-shelf components and augmented by a customizable DOE, we expect that this low-cost EDoF-Miniscope may find utility in a wide range of neural recording applications.
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Affiliation(s)
- Joseph Greene
- Boston University, Department of Electrical and Computer Engineering, Boston, Massachusetts, United States
| | - Yujia Xue
- Boston University, Department of Electrical and Computer Engineering, Boston, Massachusetts, United States
| | - Jeffrey Alido
- Boston University, Department of Electrical and Computer Engineering, Boston, Massachusetts, United States
| | - Alex Matlock
- Boston University, Department of Electrical and Computer Engineering, Boston, Massachusetts, United States
| | - Guorong Hu
- Boston University, Department of Electrical and Computer Engineering, Boston, Massachusetts, United States
| | - Kivilcim Kiliç
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Boston University, Neurophotonics Center, Boston, Massachusetts, United States
| | - Ian Davison
- Boston University, Neurophotonics Center, Boston, Massachusetts, United States
- Boston University, Department of Biology, Boston, Massachusetts, United States
| | - Lei Tian
- Boston University, Department of Electrical and Computer Engineering, Boston, Massachusetts, United States
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Boston University, Neurophotonics Center, Boston, Massachusetts, United States
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6
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Scarbrough D, Thomas A, Field J, Bartels R, Squier J. Cascaded domain multiphoton spatial frequency modulation imaging. JOURNAL OF BIOMEDICAL OPTICS 2023; 28:106502. [PMID: 37799937 PMCID: PMC10548116 DOI: 10.1117/1.jbo.28.10.106502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/07/2023]
Abstract
Significance Multiphoton microscopy is a powerful imaging tool for biomedical applications. A variety of techniques and respective benefits exist for multiphoton microscopy, but an enhanced resolution is especially desired. Additionally multiphoton microscopy requires ultrafast pulses for excitation, so optimization of the pulse duration at the sample is critical for strong signals. Aim We aim to perform enhanced resolution imaging that is robust to scattering using a structured illumination technique while also providing a rapid and easily repeatable means to optimize group delay dispersion (GDD) compensation through to the sample. Approach Spatial frequency modulation imaging (SPIFI) is used in two domains: the spatial domain (SD) and the wavelength domain (WD). The WD-SPIFI system is an in-line tool enabling GDD optimization that considers all material through to the sample. The SD-SPIFI system follows and enables enhanced resolution imaging. Results The WD-SPIFI dispersion optimization performance is confirmed with independent pulse characterization, enabling rapid optimization of pulses for imaging with the SD-SPIFI system. The SD-SPIFI system demonstrates enhanced resolution imaging without the use of photon counting enabled by signal to noise improvements due to the WD-SPIFI system. Conclusions Implementing SPIFI in-line in two domains enables full-path dispersion compensation optimization through to the sample for enhanced resolution multiphoton microscopy.
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Affiliation(s)
- Daniel Scarbrough
- Colorado School of Mines, Department of Physics, Golden, Colorado, United States
| | - Anna Thomas
- Colorado School of Mines, Department of Physics, Golden, Colorado, United States
| | - Jeff Field
- Colorado State University, Department of Electrical and Computer Engineering, Fort Collins, Colorado, United States
- Colorado State University, Center for Imaging and Surface Science, Fort Collins, Colorado, United States
| | - Randy Bartels
- Colorado State University, Department of Electrical and Computer Engineering, Fort Collins, Colorado, United States
- Colorado State University, School of Biomedical Engineering, Fort Collins, Colorado, United States
| | - Jeff Squier
- Colorado School of Mines, Department of Physics, Golden, Colorado, United States
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7
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Peterson T, Mann S, Sun BL, Peng L, Cai H, Liang R. Motionless volumetric structured light sheet microscopy. BIOMEDICAL OPTICS EXPRESS 2023; 14:2209-2224. [PMID: 37206125 PMCID: PMC10191636 DOI: 10.1364/boe.489280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 05/21/2023]
Abstract
To meet the increasing need for low-cost, compact imaging technology with cellular resolution, we have developed a microLED-based structured light sheet microscope for three-dimensional ex vivo and in vivo imaging of biological tissue in multiple modalities. All the illumination structure is generated directly at the microLED panel-which serves as the source-so light sheet scanning and modulation is completely digital, yielding a system that is simpler and less prone to error than previously reported methods. Volumetric images with optical sectioning are thus achieved in an inexpensive, compact form factor without any moving parts. We demonstrate the unique properties and general applicability of our technique by ex vivo imaging of porcine and murine tissue from the gastrointestinal tract, kidney, and brain.
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Affiliation(s)
- Tyler Peterson
- Wyant College of Optical Sciences,
The University of Arizona, Tucson, Arizona 85721, USA
| | - Shivani Mann
- Department of Neuroscience, The University of Arizona, Tucson, Arizona 85721, USA
| | - Belinda L. Sun
- Department of Pathology, College of Medicine, The University of Arizona, Tucson, Arizona 85721, USA
| | - Leilei Peng
- Wyant College of Optical Sciences,
The University of Arizona, Tucson, Arizona 85721, USA
| | - Haijiang Cai
- Department of Neuroscience, The University of Arizona, Tucson, Arizona 85721, USA
| | - Rongguang Liang
- Wyant College of Optical Sciences,
The University of Arizona, Tucson, Arizona 85721, USA
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8
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Hosu BG, Hill W, Samuel AD, Berg HC. Synchronized strobed phase contrast and fluorescence microscopy: the interlaced standard reimagined. OPTICS EXPRESS 2023; 31:5167-5180. [PMID: 36823805 PMCID: PMC10018787 DOI: 10.1364/oe.474045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/29/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
We propose a simple, cost-effective method for synchronized phase contrast and fluorescence video acquisition in live samples. Counter-phased pulses of phase contrast illumination and fluorescence excitation light are synchronized with the exposure of the two fields of an interlaced camera sensor. This results in a video sequence in which each frame contains both exposure modes, each in half of its pixels. The method allows real-time acquisition and display of synchronized and spatially aligned phase contrast and fluorescence image sequences that can be separated by de-interlacing in two independent videos. The method can be implemented on any fluorescence microscope with a camera port without needing to modify the optical path.
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Affiliation(s)
- Basarab G. Hosu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Winfield Hill
- Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142, USA
| | - Aravinthan D. Samuel
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Howard C. Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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9
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Battistella E, Schniete J, Wesencraft K, Quintana JF, McConnell G. Light-sheet mesoscopy with the Mesolens provides fast sub-cellular resolution imaging throughout large tissue volumes. iScience 2022; 25:104797. [PMID: 36034214 PMCID: PMC9404659 DOI: 10.1016/j.isci.2022.104797] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/27/2022] [Accepted: 07/14/2022] [Indexed: 11/19/2022] Open
Abstract
Rapid imaging of large biological tissue specimens such as ultrathick sections of mouse brain cannot easily be performed with a standard microscope. Optical mesoscopy offers a solution, but thus far imaging has been too slow to be useful for routine use. We have developed two different illuminators for light-sheet mesoscopy with the Mesolens and we demonstrate their use in high-speed optical mesoscale imaging of large tissue specimens. The first light-sheet approach uses Gaussian optics and is straightforward to implement. It provides excellent lateral resolution and high-speed imaging, but the axial resolution is poor. The second light-sheet is a more complex Airy light-sheet that provides sub-cellular resolution in three dimensions that is comparable in quality to point-scanning confocal mesoscopy, but the light-sheet method of illuminating the specimen reduces the imaging time by a factor of 14. This creates new possibilities for high-content, higher-throughput optical bioimaging at the mesoscale.
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Affiliation(s)
- Eliana Battistella
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow G4 0NG, UK
| | - Jan Schniete
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow G4 0NG, UK
| | - Katrina Wesencraft
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow G4 0NG, UK
| | - Juan F. Quintana
- Wellcome Centre for Integrative Parasitology, Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Gail McConnell
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow G4 0NG, UK
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10
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Hu Y, Liang D, Wang J, Xuan Y, Zhao F, Liu J, Li R. Background-free wide-field fluorescence imaging using edge detection combined with HiLo. JOURNAL OF BIOPHOTONICS 2022; 15:e202200031. [PMID: 35488180 DOI: 10.1002/jbio.202200031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/01/2022] [Accepted: 04/28/2022] [Indexed: 06/14/2023]
Abstract
Fluorescence microscopy has been widely used in the field of biological imaging, but the disturbance of background noise has always been an unavoidable phenomenon. To obtain a background free image, a virtual HiLo based on edge detection (V-HiLo-ED) method for background removing is proposed, which is different from the existing popular software algorithms that obtain the background-free image by subtracting the estimated background, but the background-free image is directly reconstructed by estimating the foreground. Compared with two other popular software-based methods, the wavelet-based background and noise subtraction algorithm (WBNS) and the rolling ball algorithm (RBA), the V-HiLo-ED owns a better quality on achieving background-free imaging. Compared with hardware-based method such as HiLo method, V-HiLo-ED exhibits almost the same performance but faster speed. In combination with light sheet microscopy, the V-HiLo-ED further improves the signal-to-noise ratio of images with thick light-sheet. These experiment results indicate that the V-HiLo-ED owns the potentiality in many other image applications such as endoscopy.
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Affiliation(s)
- Yuyao Hu
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- University Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Dong Liang
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- School of Physics Science and Engineering, Tongji University, Shanghai, China
| | - Jing Wang
- Institute of Photonic Chips, University of Shanghai for Science and Technology, Shanghai, China
- Centre for Artificial-Intelligence Nanophotonics, School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yaping Xuan
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- University Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Fu Zhao
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- University Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Jun Liu
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- University Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Ruxin Li
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- University Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
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11
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Image improvement of temporal focusing multiphoton microscopy via superior spatial modulation excitation and Hilbert-Huang transform decomposition. Sci Rep 2022; 12:10079. [PMID: 35710746 PMCID: PMC9203560 DOI: 10.1038/s41598-022-14367-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/06/2022] [Indexed: 11/08/2022] Open
Abstract
Temporal focusing-based multiphoton excitation microscopy (TFMPEM) just provides the advantage of widefield optical sectioning ability with axial resolution of several micrometers. However, under the plane excitation, the photons emitted from the molecules in turbid tissues undergo scattering, resulting in complicated background noise and an impaired widefield image quality. Accordingly, this study constructs a general and comprehensive numerical model of TFMPEM utilizing Fourier optics and performs simulations to determine the superior spatial frequency and orientation of the structured pattern which maximize the axial excitation confinement. It is shown experimentally that the optimized pattern minimizes the intensity of the out-of-focus signal, and hence improves the quality of the image reconstructed using the Hilbert transform (HT). However, the square-like reflection components on digital micromirror device leads to pattern residuals in the demodulated image when applying high spatial frequency of structured pattern. Accordingly, the HT is replaced with Hilbert-Huang transform (HHT) in order to sift out the low-frequency background noise and pattern residuals in the demodulation process. The experimental results obtained using a kidney tissue sample show that the HHT yields a significant improvement in the TFMPEM image quality.
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12
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Hung ST, Cnossen J, Fan D, Siemons M, Jurriens D, Grußmayer K, Soloviev O, Kapitein LC, Smith CS. SOLEIL: single-objective lens inclined light sheet localization microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:3275-3294. [PMID: 35781973 PMCID: PMC9208595 DOI: 10.1364/boe.451634] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
High-NA light sheet illumination can improve the resolution of single-molecule localization microscopy (SMLM) by reducing the background fluorescence. These approaches currently require custom-made sample holders or additional specialized objectives, which makes the sample mounting or the optical system complex and therefore reduces the usability of these approaches. Here, we developed a single-objective lens-inclined light sheet microscope (SOLEIL) that is capable of 2D and 3D SMLM in thick samples. SOLEIL combines oblique illumination with point spread function PSF engineering to enable dSTORM imaging in a wide variety of samples. SOLEIL is compatible with standard sample holders and off-the-shelve optics and standard high NA objectives. To accomplish optimal optical sectioning we show that there is an ideal oblique angle and sheet thickness. Furthermore, to show what optical sectioning delivers for SMLM we benchmark SOLEIL against widefield and HILO microscopy with several biological samples. SOLEIL delivers in 15 μm thick Caco2-BBE cells a 374% higher intensity to background ratio and a 54% improvement in the estimated CRLB compared to widefield illumination, and a 184% higher intensity to background ratio and a 20% improvement in the estimated CRLB compared to HILO illumination.
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Affiliation(s)
- Shih-Te Hung
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Jelmer Cnossen
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Daniel Fan
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Marijn Siemons
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Daphne Jurriens
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Kristin Grußmayer
- Department of Bionanoscience and Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Oleg Soloviev
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
- Flexible Optical B.V., Polakweg 10-11, 2288 GG Rijswijk, Netherlands
| | - Lukas C. Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Carlas S. Smith
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
- Department of Imaging Physics, Delft University of Technology, Delft, Netherlands
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13
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Lee C, Kim HH. Velocity measurement of magnetic particles simultaneously affected by two-phase flow and an external magnetic field using dual-sided SPIM-µPIV. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2021.117278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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14
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Automated computation of nerve fibre inclinations from 3D polarised light imaging measurements of brain tissue. Sci Rep 2022; 12:4328. [PMID: 35288611 PMCID: PMC8921329 DOI: 10.1038/s41598-022-08140-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 03/01/2022] [Indexed: 02/06/2023] Open
Abstract
The method 3D polarised light imaging (3D-PLI) measures the birefringence of histological brain sections to determine the spatial course of nerve fibres (myelinated axons). While the in-plane fibre directions can be determined with high accuracy, the computation of the out-of-plane fibre inclinations is more challenging because they are derived from the amplitude of the birefringence signals, which depends e.g. on the amount of nerve fibres. One possibility to improve the accuracy is to consider the average transmitted light intensity (transmittance weighting). The current procedure requires effortful manual adjustment of parameters and anatomical knowledge. Here, we introduce an automated, optimised computation of the fibre inclinations, allowing for a much faster, reproducible determination of fibre orientations in 3D-PLI. Depending on the degree of myelination, the algorithm uses different models (transmittance-weighted, unweighted, or a linear combination), allowing to account for regionally specific behaviour. As the algorithm is parallelised and GPU optimised, it can be applied to large data sets. Moreover, it only uses images from standard 3D-PLI measurements without tilting, and can therefore be applied to existing data sets from previous measurements. The functionality is demonstrated on unstained coronal and sagittal histological sections of vervet monkey and rat brains.
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15
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Fu Z, Chen J, Liu G, Chen SC. Single-shot optical sectioning microscopy based on structured illumination. OPTICS LETTERS 2022; 47:814-817. [PMID: 35167532 DOI: 10.1364/ol.451267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
In this Letter, we present a single-shot 3D-resolved structured illumination microscopy (SIM) based on a digital micromirror device (DMD), a galvanometric mirror, and the HiLo algorithm. During imaging, the DMD rapidly generates sinusoidal and plane illuminations in the focal region. By synchronizing the DMD with a galvanometric scanner and exploiting the unique data readout process of the camera, the emissions from the specimen under two different illuminations, i.e., structured and uniform illumination, are projected to different regions on a camera, achieving high-resolution single-exposure optical sectioning at the camera's limiting speed, i.e., 200 Hz, without sacrificing the resolution. A model has been developed to guide the design and optimization of the optical system. Imaging experiments on pollen and mouse kidney samples have been performed to verify the predicted performance. The results show that the single-shot SIM with the HiLo algorithm achieves comparable resolution to the standard two-shot HiLo method with a twofold speed enhancement, which may find important applications in biophotonics, e.g., visualizing high-speed biological events in vivo.
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16
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Gagliano G, Nelson T, Saliba N, Vargas-Hernández S, Gustavsson AK. Light Sheet Illumination for 3D Single-Molecule Super-Resolution Imaging of Neuronal Synapses. Front Synaptic Neurosci 2021; 13:761530. [PMID: 34899261 PMCID: PMC8651567 DOI: 10.3389/fnsyn.2021.761530] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/27/2021] [Indexed: 01/02/2023] Open
Abstract
The function of the neuronal synapse depends on the dynamics and interactions of individual molecules at the nanoscale. With the development of single-molecule super-resolution microscopy over the last decades, researchers now have a powerful and versatile imaging tool for mapping the molecular mechanisms behind the biological function. However, imaging of thicker samples, such as mammalian cells and tissue, in all three dimensions is still challenging due to increased fluorescence background and imaging volumes. The combination of single-molecule imaging with light sheet illumination is an emerging approach that allows for imaging of biological samples with reduced fluorescence background, photobleaching, and photodamage. In this review, we first present a brief overview of light sheet illumination and previous super-resolution techniques used for imaging of neurons and synapses. We then provide an in-depth technical review of the fundamental concepts and the current state of the art in the fields of three-dimensional single-molecule tracking and super-resolution imaging with light sheet illumination. We review how light sheet illumination can improve single-molecule tracking and super-resolution imaging in individual neurons and synapses, and we discuss emerging perspectives and new innovations that have the potential to enable and improve single-molecule imaging in brain tissue.
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Affiliation(s)
- Gabriella Gagliano
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Tyler Nelson
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Nahima Saliba
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Sofía Vargas-Hernández
- Department of Chemistry, Rice University, Houston, TX, United States
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
- Department of Biosciences, Rice University, Houston, TX, United States
- Laboratory for Nanophotonics, Rice University, Houston, TX, United States
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17
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Liu C, Yu X, Bai C, Li X, Zhou Y, Yan S, Min J, Dan D, Li R, Gu S, Yao B. Axial resolution enhancement for planar Airy beam light-sheet microscopy via the complementary beam subtraction method. APPLIED OPTICS 2021; 60:10239-10245. [PMID: 34807133 DOI: 10.1364/ao.441070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Airy beam light-sheet illumination can extend the field of view (FOV) of light-sheet fluorescence microscopy due to the unique propagation properties of non-diffraction and self-acceleration. However, the side lobes create undesirable out-of-focus background, leading to poor axial resolution and low image contrast. Here, we propose an Airy complementary beam subtraction (ACBS) method to improve the axial resolution while keeping the extended FOV. By scanning the optimized designed complementary beam that has two main lobes (TML), the generated complementary light-sheet has almost identical intensity distribution to that of the planar Airy light-sheet except for the central lobe. Subtraction of the two images acquired by double exposure respectively using the planar Airy light-sheet and the planar TML light-sheet can effectively suppress the influence of the out-of-focus background. The axial resolution improves from ∼4µm to 1.2 µm. The imaging performance was demonstrated by imaging specimens of aspergillus conidiophores and GFP labeled mouse brain section. The results show that the ACBS method enables the Airy beam light-sheet fluorescence microscopy to obtain better imaging quality.
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18
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Bakas S, Uttamchandani D, Toshiyoshi H, Bauer R. MEMS enabled miniaturized light-sheet microscopy with all optical control. Sci Rep 2021; 11:14100. [PMID: 34238945 PMCID: PMC8266809 DOI: 10.1038/s41598-021-93454-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/16/2021] [Indexed: 11/29/2022] Open
Abstract
We have designed and implemented a compact, cost-efficient miniaturised light-sheet microscopy system based on optical microelectromechanical systems scanners and tunable lenses. The system occupies a footprint of 20 × 28 × 13 cm3 and combines off-the-shelf optics and optomechanics with 3D-printed structural and optical elements, and an economically costed objective lens, excitation laser and camera. All-optical volume scanning enables imaging of 435 × 232 × 60 µm3 volumes with 0.25 vps (volumes per second) and minimum lateral and axial resolution of 1.0 µm and 3.8 µm respectively. An open-top geometry allows imaging of samples on flat bottomed holders, allowing integration with microfluidic devices, multi-well plates and slide mounted samples, with applications envisaged in biomedical research and pre-clinical settings.
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Affiliation(s)
- Spyridon Bakas
- Department of Electronic and Electrical Engineering, University of Strathclyde, Glasgow, UK.
| | - Deepak Uttamchandani
- Department of Electronic and Electrical Engineering, University of Strathclyde, Glasgow, UK
| | | | - Ralf Bauer
- Department of Electronic and Electrical Engineering, University of Strathclyde, Glasgow, UK
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19
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Chen J, Gu S, Meng Y, Fu Z, Chen SC. Holography-based structured light illumination for temporal focusing microscopy. OPTICS LETTERS 2021; 46:3143-3146. [PMID: 34197401 DOI: 10.1364/ol.431161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
In this Letter, we present a holography-based structured light illumination (SLI) method to enhance the resolution of widefield temporal focusing microscopy (TFM). In the system, a digital micromirror device is employed to simultaneously disperse the incoming femtosecond laser to induce temporal focusing at the focal plane and generate designed structured patterns via a Lee hologram. As the generated structured patterns do not contain the zeroth order beam, it improves the contrast and modulation frequency. Mathematical models have been derived to calculate the electric fields at the focal plane and to explain the effects of improved optical cross-sectioning capability. Imaging experiments have been devised and performed on fluorescent beads and mouse kidney sections; the results demonstrate enhanced axial confinement and improved suppression of out-of-focus fluorescence. The new SLI method realizes high-resolution TFM and can be readily applied to other microscopy platforms for biophotonics applications.
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20
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Qiao W, Jin R, Luo T, Li Y, Fan G, Luo Q, Yuan J. Single-scan HiLo with line-illumination strategy for optical section imaging of thick tissues. BIOMEDICAL OPTICS EXPRESS 2021; 12:2373-2383. [PMID: 33996235 PMCID: PMC8086481 DOI: 10.1364/boe.419377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 05/25/2023]
Abstract
Optical sectioning has been widely employed for inhibiting out-of-focus backgrounds in three-dimensional (3D) imaging of biological samples. However, point scanning imaging or multiple acquisitions for wide-field optical sectioning in epi-illumination microscopy remains time-consuming for large-scale imaging. In this paper, we propose a single-scan optical sectioning method based on the hybrid illumination (HiLo) algorithm with a line-illumination strategy. Our method combines HiLo background inhibition with confocal slit detection. It thereby offers a higher optical sectioning capability than wide-field HiLo and line-confocal imaging without extra modulation and multiple data acquisition. To demonstrate the optical-sectioning capability of our system, we imaged a thin fluorescent plane and different fluorescence-labeled mouse tissue. Our method shows an excellent background inhibition in thick tissue and thus potentially provides an alternative tool for 3D imaging of large-scale biological tissue.
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Affiliation(s)
- Wei Qiao
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, 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
- These authors contributed equally
| | - Rui Jin
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, 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
- These authors contributed equally
| | - Tianpeng Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, 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, 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, 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
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, 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
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - Jing Yuan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, 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
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21
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Zhan Y, Wu H, Liu L, Lin J, Zhang S. Organic solvent-based tissue clearing techniques and their applications. JOURNAL OF BIOPHOTONICS 2021; 14:e202000413. [PMID: 33715302 DOI: 10.1002/jbio.202000413] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 02/05/2023]
Abstract
Revealing the true structure of tissues and organs with tissue slicing technology is difficult since images reconstructed in three dimensions are easily distorted. To address the limitations in tissue slicing technology, tissue clearing has been invented and has recently achieved significant progress in three-dimensional imaging. Currently, this technology can mainly be divided into two types: aqueous clearing methods and solvent-based clearing methods. As one of the important parts of this technology, organic solvent-based tissue clearing techniques have been widely applied because of their efficient clearing speed and high clearing intensity. This review introduces the primary organic solvent-based tissue clearing techniques and their applications.
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Affiliation(s)
- Yanjing Zhan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Haoyan Wu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Linfeng Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jie Lin
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shiwen Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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22
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Chai C, Chen C, Liu X, Lei Z. Deep learning based one-shot optically-sectioned structured illumination microscopy for surface measurement. OPTICS EXPRESS 2021; 29:4010-4021. [PMID: 33770989 DOI: 10.1364/oe.415210] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
Optically-sectioned structured illumination microscopy (OS-SIM) is broadly used for biological imaging and engineering surface measurement owing to its simple, low-cost, scanning-free experimental setup and excellent optical sectioning capability. However, the efficiency of current optically-sectioned methods in OS-SIM is yet limited for surface measurement because a set of wide-field images under uniform or structured illumination are needed to derive an optical section at each scanning height. In this paper, a deep-learning-based one-shot optically-sectioned method, called Deep-OS-SIM, is proposed to improve the efficiency of OS-SIM for surface measurement. Specifically, we develop a convolutional neural network (CNN) to learn the statistical invariance of optical sectioning across structured illumination images. By taking full advantage of the high entropy properties of structured illumination images to train the CNN, fast convergence and low training error are achieved in our method even for low-textured surfaces. The well-trained CNN is then applied to a plane mirror for testing, demonstrating the ability of the method to reconstruct high-quality optical sectioning from only one instead of two or three raw structured illumination frames. Further measurement experiments on a standard step and milled surface show that the proposed method has similar accuracy to OS-SIM techniques but with higher imaging speed.
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23
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Fan YJ, Hsieh HY, Tsai SF, Wu CH, Lee CM, Liu YT, Lu CH, Chang SW, Chen BC. Microfluidic channel integrated with a lattice lightsheet microscopic system for continuous cell imaging. LAB ON A CHIP 2021; 21:344-354. [PMID: 33295931 DOI: 10.1039/d0lc01009j] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In this study, a continuous cell-imaging system with subcellular resolution was developed by integrating a microfluidic platform with lattice lightsheet microscopy (LLSM). To reduce aberrations of the lightsheet propagating into the device, a microfluidic channel sealed with a water refractive index-matched thin film was fabricated. When the lightsheet emerged from the water-immersed objectives and penetrated through the water refractive-matched thin film into the microfluidic channel at an incident angle, less light scattering and fewer aberrations were found. Suspended cells flowed across the lattice lightsheet, and an imaging system with the image plane perpendicular to the lightsheet was used to sequentially acquire cell images. By applying a thinner lattice lightsheet, higher-resolution, higher-contrast images were obtained. Furthermore, three-dimensional cell images could be achieved by reconstructing sequential two-dimensional cell images.
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Affiliation(s)
- Yu-Jui Fan
- School of Biomedical Engineering, Taipei Medical University, 250 Wuxing St., Taipei 11031, Taiwan.
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24
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Chia YH, Yeh JA, Huang YY, Luo Y. Simultaneous multi-color optical sectioning fluorescence microscopy with wavelength-coded volume holographic gratings. OPTICS EXPRESS 2020; 28:37177-37187. [PMID: 33379556 DOI: 10.1364/oe.409179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/08/2020] [Indexed: 06/12/2023]
Abstract
Optical sectioning fluorescence microscopy provides high contrast images of volumetric samples and has been widely used for many biological applications. However, simultaneously acquiring multi-color fluorescence images require additional optical elements and devices, which are bulky, wavelength specific, and not cost-effective. In this paper, wavelength-coded volume holographic gratings (WC-VHGs) based optical sectioning fluorescence microscopy is proposed to simultaneously offer multi-color fluorescence images with fine out-of-focus background rejection. Due to wavelength degeneracy, multiplexed WC-VHGs are capable of acquiring multi-wavelength fluorescence images in a single shot, and displaying the laterally separated multi-wavelength images onto CCD. In our system optical sectioning capability is achieved through speckle illumination and HiLo imaging method. To demonstrate imaging characteristics of our system, dual-wavelength fluorescence images of both standard fluorescent microspheres and ex vivo mT/mG mice cardiac tissue are presented. Current results may find important applications in hyperspectral imaging for biomedical research.
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25
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Inamoto J, Fukuda T, Inoue T, Shimizu K, Nishio K, Xia P, Matoba O, Awatsuji Y. Modularized microscope based on parallel phase-shifting digital holography for imaging of living biospecimens. JOURNAL OF BIOMEDICAL OPTICS 2020; 25:JBO-200277SSR. [PMID: 33277888 PMCID: PMC7716092 DOI: 10.1117/1.jbo.25.12.123706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
SIGNIFICANCE Parallel phase-shifting digital holographic microscope (PPSDHM) is powerful for three-dimensional (3D) measurements of dynamic specimens. However, the PPSDHM reported previously was directly fixed on the optical bench and imposed difficulties case, thus it is required to modify the specification of the microscope or transport the microscope to another location. AIM We present a modularized PPSDHM. We construct the proposed PPSDHM and demonstrate the 3D measurement capability of the PPSDHM. APPROACH The PPSDHM was designed as an inverted microscope to record transparent objects and modularized by integrating the optical elements of the PPSDHM on an optical breadboard. To demonstrate the effectiveness of the PPSDHM, we recorded a 3D motion-picture of moving Volvoxes at 1000 frames / s and carried out 3D tracking of the Volvoxes. RESULTS The PPSDHM was practically realized and 3D images of objects were successfully reconstructed from holograms recorded with a single-shot exposure. The 3D trajectories of Volvoxes were obtained from the reconstructed images. CONCLUSIONS We established a modularized PPSDHM that is capable of 3D image acquisition by integrating the optical elements of the PPSDHM on an optical breadboard. The recording capability of 3D motion-pictures of dynamic specimens was experimentally demonstrated by the PPSDHM.
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Affiliation(s)
- Junya Inamoto
- Kyoto Institute of Technology, Graduate School of Science and Technology, Kyoto, Japan
| | - Takahito Fukuda
- Kyoto Institute of Technology, Graduate School of Science and Technology, Kyoto, Japan
| | - Tomoyoshi Inoue
- Kyoto Institute of Technology, Graduate School of Science and Technology, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Kazuki Shimizu
- Kyoto Institute of Technology, Graduate School of Science and Technology, Kyoto, Japan
| | - Kenzo Nishio
- Kyoto Institute of Technology, Graduate School of Science and Technology, Kyoto, Japan
| | - Peng Xia
- National Institute of Advanced Industrial Science and Technology, National Metrology Institute of Japan, Tsukuba, Japan
| | - Osamu Matoba
- Kobe University, Graduate School of System Informatics, Department of Systems Science, Kobe, Japan
| | - Yasuhiro Awatsuji
- Kyoto Institute of Technology, Graduate School of Science and Technology, Kyoto, Japan
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26
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Zhanghao K, Liu W, Li M, Wu Z, Wang X, Chen X, Shan C, Wang H, Chen X, Dai Q, Xi P, Jin D. High-dimensional super-resolution imaging reveals heterogeneity and dynamics of subcellular lipid membranes. Nat Commun 2020; 11:5890. [PMID: 33208737 PMCID: PMC7674432 DOI: 10.1038/s41467-020-19747-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023] Open
Abstract
Lipid membranes are found in most intracellular organelles, and their heterogeneities play an essential role in regulating the organelles' biochemical functionalities. Here we report a Spectrum and Polarization Optical Tomography (SPOT) technique to study the subcellular lipidomics in live cells. Simply using one dye that universally stains the lipid membranes, SPOT can simultaneously resolve the membrane morphology, polarity, and phase from the three optical-dimensions of intensity, spectrum, and polarization, respectively. These high-throughput optical properties reveal lipid heterogeneities of ten subcellular compartments, at different developmental stages, and even within the same organelle. Furthermore, we obtain real-time monitoring of the multi-organelle interactive activities of cell division and successfully reveal their sophisticated lipid dynamics during the plasma membrane separation, tunneling nanotubules formation, and mitochondrial cristae dissociation. This work suggests research frontiers in correlating single-cell super-resolution lipidomics with multiplexed imaging of organelle interactome.
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Affiliation(s)
- Karl Zhanghao
- UTS-SUStech Joint Research Centre for Biomedical Materials & Devices, Department of Biomedical Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, P.R. China.
- Department of Biomedical Engineering, College of Engineering, Peking University, 100871, Beijing, China.
| | - Wenhui Liu
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Meiqi Li
- Department of Biomedical Engineering, College of Engineering, Peking University, 100871, Beijing, China
| | - Zihan Wu
- UTS-SUStech Joint Research Centre for Biomedical Materials & Devices, Department of Biomedical Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, P.R. China
| | - Xiao Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, 100871, Beijing, China
| | - Xingye Chen
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Chunyan Shan
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, 100871, Beijing, China
| | - Haoqian Wang
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Xiaowei Chen
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, 100871, Beijing, China
| | - Qionghai Dai
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Peng Xi
- UTS-SUStech Joint Research Centre for Biomedical Materials & Devices, Department of Biomedical Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, P.R. China.
- Department of Biomedical Engineering, College of Engineering, Peking University, 100871, Beijing, China.
| | - Dayong Jin
- UTS-SUStech Joint Research Centre for Biomedical Materials & Devices, Department of Biomedical Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, P.R. China.
- Institute for Biomedical Materials & Devices (IBMD), University of Technology Sydney, Sydney, NSW 2007, Australia.
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27
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Xiong B, Han X, Wu J, Xie H, Dai Q. Improving axial resolution of Bessel beam light-sheet fluorescence microscopy by photobleaching imprinting. OPTICS EXPRESS 2020; 28:9464-9476. [PMID: 32225553 DOI: 10.1364/oe.388808] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/09/2020] [Indexed: 06/10/2023]
Abstract
Light-sheet microscopy has been widely used in high-speed fluorescence imaging with low phototoxicity, while the trade-off between the field-of-view and optical sectioning capability limits its application in large-scale imaging. Although Bessel beam light-sheet microscopy greatly enhances the light-sheet length with the self-healing ability, it suffers from the strong side-lobe effect. To solve these problems, we introduce the photobleaching imprinting technique in Bessel beam light-sheet microscopy. By extracting the non-linear photobleaching-induced fluorescence decay, we get rid of the large concentric side lobe structures of the Bessel beam to achieve uniform isotropic resolution across a large field-of-view for large-scale fluorescence imaging. Both numerical simulations and experimental results on various samples are demonstrated to show our enhanced resolution and contrast over traditional Bessel-beam light-sheet microscopy.
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28
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Liu P, Mu X, Zhang XD, Ming D. The Near-Infrared-II Fluorophores and Advanced Microscopy Technologies Development and Application in Bioimaging. Bioconjug Chem 2019; 31:260-275. [DOI: 10.1021/acs.bioconjchem.9b00610] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Pengfei Liu
- Academy of Medical Engineering and Translational Medicine, Medical College, Tianjin University, Tianjin 300072, China
| | - Xiaoyu Mu
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, Tianjin 300350, China
| | - Xiao-Dong Zhang
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, Tianjin 300350, China
| | - Dong Ming
- Academy of Medical Engineering and Translational Medicine, Medical College, Tianjin University, Tianjin 300072, China
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29
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Abstract
Light-sheet microscopy is an imaging approach that offers unique advantages for a diverse range of neuroscience applications. Unlike point-scanning techniques such as confocal and two-photon microscopy, light-sheet microscopes illuminate an entire plane of tissue, while imaging this plane onto a camera. Although early implementations of light sheet were optimized for longitudinal imaging of embryonic development in small specimens, emerging implementations are capable of capturing light-sheet images in freely moving, unconstrained specimens and even the intact in vivo mammalian brain. Meanwhile, the unique photobleaching and signal-to-noise benefits afforded by light-sheet microscopy's parallelized detection deliver the ability to perform volumetric imaging at much higher speeds than can be achieved using point scanning. This review describes the basic principles and evolution of light-sheet microscopy, followed by perspectives on emerging applications and opportunities for both imaging large, cleared, and expanded neural tissues and high-speed, functional imaging in vivo.
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Affiliation(s)
- Elizabeth M C Hillman
- Departments of Biomedical Engineering and Radiology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA;
| | - Venkatakaushik Voleti
- Departments of Biomedical Engineering and Radiology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA;
| | - Wenze Li
- Departments of Biomedical Engineering and Radiology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA;
| | - Hang Yu
- Departments of Biomedical Engineering and Radiology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA;
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30
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Ki S, Kwon SH, Eum J, Raslan AA, Kim KN, Hwang BJ, Kee Y. 3D light-sheet assay assessing novel valproate-associated cardiotoxicity and folic acid relief in zebrafish embryogenesis. CHEMOSPHERE 2019; 227:551-560. [PMID: 31004822 DOI: 10.1016/j.chemosphere.2019.04.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 06/09/2023]
Abstract
Precise in vivo toxicological assays to determine the cardiotoxicity of pharmaceuticals and their waste products are essential in order to evaluate their risks to humans and the environment following industrial release. In the present study, we aimed to develop the sensitive imaging-based cardiotoxicity assay and combined 3D light-sheet microscopy with a zebrafish model to identify hidden cardiovascular anomalies induced by valproic acid (VPA) exposure. The zebrafish model is advantageous for this assessment because its embryos remain transparent. The 3D spatial localization of fluorescence-labeled cardiac cells in and around the heart using light-sheet technology revealed dislocalization of the heart from the outflow tract in two-day-old zebrafish embryos treated with 50 μM and 100 μM VPA (P < 0.01) and those embryos exposed to 20 μM VPA presented hypoplastic distal ventricles (P < 0.01). These two observed phenotypes are second heart field-derived cardiac defects. Quantitative analysis of the light-sheet imaging demonstrated that folic acid (FA) supplementation significantly increased the numbers of endocardial and myocardial cells (P < 0.05) and the accretion of second heart field-derived cardiomyocytes to the arterial pole of the outflow tract. The heart rate increased in response to the cellular changes occurring in embryonic heart development (P < 0.05). The present study disclosed the cellular mechanism underlying the role of FA in spontaneous cellular changes in cardiogenesis and in VPA-associated cardiotoxicity. The 3D light-sheet assay may be the next-generation test to evaluate the risks of previously undetected pharmaceutical and environmental cardiotoxicities in both humans and animals.
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Affiliation(s)
- Seoyoung Ki
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea
| | - Seung-Hae Kwon
- Korea Basic Science Institute Chuncheon Center, Chuncheon, South Korea
| | - Juneyong Eum
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea
| | - Ahmed A Raslan
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea
| | - Kil-Nam Kim
- Korea Basic Science Institute Chuncheon Center, Chuncheon, South Korea
| | - Byung Joon Hwang
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea.
| | - Yun Kee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea.
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31
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Colomb W, Osmond M, Durfee C, Krebs MD, Sarkar SK. Imaging and Analysis of Cellular Locations in Three-Dimensional Tissue Models. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2019; 25:753-761. [PMID: 30853032 DOI: 10.1017/s1431927619000102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The absence of quantitative in vitro cell-extracellular matrix models represents an important bottleneck for basic research and human health. Randomness of cellular distributions provides an opportunity for the development of a quantitative in vitro model. However, quantification of the randomness of random cell distributions is still lacking. In this paper, we have imaged cellular distributions in an alginate matrix using a multiview light sheet microscope and developed quantification metrics of randomness by modeling it as a Poisson process, a process that has constant probability of occurring in space or time. We imaged fluorescently labeled human mesenchymal stem cells embedded in an alginate matrix of thickness greater than 5 mm with axial resolution, the mean full width at half maximum of the axial intensity profiles of fluorescent particles. Simulated randomness agrees well with the experiments. Quantification of distributions and validation by simulations will enable quantitative study of cell-matrix interactions in tissue models.
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Affiliation(s)
- Warren Colomb
- Department of Physics,Colorado School of Mines,Golden, Colorado,USA
| | - Matthew Osmond
- Department of Chemical & Biological Engineering,Colorado School of Mines,Golden, Colorado,USA
| | - Charles Durfee
- Department of Physics,Colorado School of Mines,Golden, Colorado,USA
| | - Melissa D Krebs
- Department of Chemical & Biological Engineering,Colorado School of Mines,Golden, Colorado,USA
| | - Susanta K Sarkar
- Department of Physics,Colorado School of Mines,Golden, Colorado,USA
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32
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Wide-Area All-Optical Neurophysiology in Acute Brain Slices. J Neurosci 2019; 39:4889-4908. [PMID: 30952812 DOI: 10.1523/jneurosci.0168-19.2019] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 03/15/2019] [Accepted: 04/01/2019] [Indexed: 11/21/2022] Open
Abstract
Optical tools for simultaneous perturbation and measurement of neural activity open the possibility of mapping neural function over wide areas of brain tissue. However, spectral overlap of actuators and reporters presents a challenge for their simultaneous use, and optical scattering and out-of-focus fluorescence in tissue degrade resolution. To minimize optical crosstalk, we combined an optimized variant (eTsChR) of the most blue-shifted channelrhodopsin reported to-date with a nuclear-localized red-shifted Ca2+ indicator, H2B-jRGECO1a. To perform wide-area optically sectioned imaging in tissue, we designed a structured illumination technique that uses Hadamard matrices to encode spatial information. By combining these molecular and optical approaches we made wide-area functional maps in acute brain slices from mice of both sexes. The maps spanned cortex and striatum and probed the effects of antiepileptic drugs on neural excitability and the effects of AMPA and NMDA receptor blockers on functional connectivity. Together, these tools provide a powerful capability for wide-area mapping of neuronal excitability and functional connectivity in acute brain slices.SIGNIFICANCE STATEMENT A new technique for simultaneous optogenetic stimulation and calcium imaging across wide areas of brain slice enables high-throughput mapping of neuronal excitability and synaptic transmission.
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33
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Macias-Romero C, Teulon C, Didier M, Roke S. Endogenous SHG and 2PEF coherence imaging of substructures in neurons in 3D. OPTICS EXPRESS 2019; 27:2235-2247. [PMID: 30732263 DOI: 10.1364/oe.27.002235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Neuronal morphology, long-distance transport and signalling critically depend on the organization of microtubules in the cytoskeleton. Second harmonic generation (SHG) imaging has been recognized as a potentially powerful tool for in situ label-free neuroimaging with specific sensitivity to microtubules. We study here the structural organization of microtubules in living neurons using a wide-field multiphoton microscope that performs 3D imaging using a structured illumination. This microscope allows label-free high throughput imaging of living mammalian neurons. We show that we can image structural correlations by taking advantage of the structured illumination and the coherence of the emitted light. The result allows us to study the microtubule organization throughout the development of the neuron and to differentiate between the regions of the cytoskeleton in the matured neuron.
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34
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Liu Y, Dale S, Ball R, VanLeuven AJ, Sornborger A, Lauderdale JD, Kner P. Imaging neural events in zebrafish larvae with linear structured illumination light sheet fluorescence microscopy. NEUROPHOTONICS 2019; 6:015009. [PMID: 30854407 PMCID: PMC6400141 DOI: 10.1117/1.nph.6.1.015009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/13/2019] [Indexed: 05/02/2023]
Abstract
Light sheet fluorescence microscopy (LSFM) is a powerful tool for investigating model organisms including zebrafish. However, due to scattering and refractive index variations within the sample, the resulting image often suffers from low contrast. Structured illumination (SI) has been combined with scanned LSFM to remove out-of-focus and scattered light using square-law detection. Here, we demonstrate that the combination of LSFM with linear reconstruction SI can further increase resolution and contrast in the vertical and axial directions compared to the widely adopted root-mean square reconstruction method while using the same input images. We apply this approach to imaging neural activity in 7-day postfertilization zebrafish larvae. We imaged two-dimensional sections of the zebrafish central nervous system in two colors at an effective frame rate of 7 frames per second.
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Affiliation(s)
- Yang Liu
- University of Georgia, College of Engineering, Athens, Georgia, United States
| | - Savannah Dale
- Clemson University, Department of Bioengineering, Clemson, South Carolina, United States
| | - Rebecca Ball
- University of Georgia, Department of Cellular Biology, Athens, Georgia, United States
| | - Ariel J. VanLeuven
- University of Georgia, Department of Cellular Biology, Athens, Georgia, United States
| | - Andrew Sornborger
- Los Alamos National Laboratory, Information Sciences, CCS-3, Los Alamos, New Mexico, United States
| | - James D. Lauderdale
- University of Georgia, Department of Cellular Biology, Athens, Georgia, United States
- University of Georgia, Neuroscience Division of the Biomedical Health Sciences Institute, Athens, Georgia, United States
| | - Peter Kner
- University of Georgia, College of Engineering, Athens, Georgia, United States
- Address all correspondence to Peter Kner, E-mail:
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35
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Yeh CH, Tan CZ, Cheng CHA, Hung JT, Chen SY. Improving resolution of second harmonic generation microscopy via scanning structured illumination. BIOMEDICAL OPTICS EXPRESS 2018; 9:6081-6090. [PMID: 31065414 PMCID: PMC6490992 DOI: 10.1364/boe.9.006081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/03/2018] [Accepted: 11/04/2018] [Indexed: 05/28/2023]
Abstract
Second harmonic generation microscopy (SHGM) is a well-known technique for examining the noncentrosymmetric structures in biomedical research. However, without real-state transitions, fluorescence-based superresolution methods cannot be applied. To improve the resolution, fringe-scanning SHGM (FS-SHGM), which combines SHGM with structured illumination based on point-scanning, is introduced in this paper. The scanning path was modulated to generate illumination patterns. For the coherent parts of SHG signals, a mathematical model of image formation and reconstruction was established. Both simulations and experiments showed a resolution improvement factor of ~1.4 in the lateral and 1.56 in the axial directions for chicken tendons and mouse skin.
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Affiliation(s)
- Chia-Hua Yeh
- Department of Optics and Photonics, National Central University, 300 Jhongda Rd., Jhongli City, Taoyuan County 32001, Taiwan
| | - Cheng-Zn Tan
- Department of Optics and Photonics, National Central University, 300 Jhongda Rd., Jhongli City, Taoyuan County 32001, Taiwan
| | - Ching-hsiao Arthur Cheng
- Department of Mathematics, National Central University, 300 Jhongda Rd., Jhongli City, Taoyuan County 32001, Taiwan
| | - Jui-Ting Hung
- Department of Optics and Photonics, National Central University, 300 Jhongda Rd., Jhongli City, Taoyuan County 32001, Taiwan
| | - Szu-Yu Chen
- Department of Optics and Photonics, National Central University, 300 Jhongda Rd., Jhongli City, Taoyuan County 32001, Taiwan
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36
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Garbellotto C, Taylor JM. Multi-purpose SLM-light-sheet microscope. BIOMEDICAL OPTICS EXPRESS 2018; 9:5419-5436. [PMID: 30460137 PMCID: PMC6238942 DOI: 10.1364/boe.9.005419] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/27/2018] [Accepted: 10/02/2018] [Indexed: 05/16/2023]
Abstract
By integrating a phase-only Spatial Light Modulator (SLM) into the illumination arm of a cylindrical-lens-based Selective Plane Illumination Microscope (SPIM), we have created a versatile system able to deliver high quality images by operating in a wide variety of different imaging modalities. When placed in a Fourier plane, the SLM permits modulation of the microscope's light-sheet to implement imaging techniques such as structured illumination, tiling, pivoting, autofocusing and pencil beam scanning. Previous publications on dedicated microscope setups have shown how these techniques can deliver improved image quality by rejecting out-of-focus light (structured illumination and pencil beam scanning), reducing shadowing (light-sheet pivoting), and obtaining a more uniform illumination by moving the highest-resolution region of the light-sheet across the imaging Field of View (tiling). Our SLM-SPIM configuration is easy to build and use, and has been designed to allow all of these techniques to be employed on an easily reconfigurable optical setup, compatible with the OpenSPIM design. It offers the possibility to choose between three different light-sheets, in thickness and height, which can be selected according to the characteristics of the sample and the imaging technique to be applied. We demonstrate the flexibility and performance of the system with results obtained by applying a variety of different imaging techniques on samples of fluorescent beads, zebrafish embryos, and optically cleared whole mouse brain samples. Thus our approach allows easy implementation of advanced imaging techniques while retaining the simplicity of a cylindrical-lens-based light-sheet microscope.
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37
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Xue Y, Berry KP, Boivin JR, Wadduwage D, Nedivi E, So PTC. Scattering reduction by structured light illumination in line-scanning temporal focusing microscopy. BIOMEDICAL OPTICS EXPRESS 2018; 9:5654-5666. [PMID: 30460153 PMCID: PMC6238912 DOI: 10.1364/boe.9.005654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/26/2018] [Accepted: 10/01/2018] [Indexed: 05/02/2023]
Abstract
Line-scanning temporal focusing microscopy (LineTFM) is capable of imaging biological samples more than 10 times faster than two-photon laser point-scanning microscopy (TPLSM), while achieving nearly the same lateral and axial spatial resolution. However, the image contrast taken by LineTFM is lower than that by TPLSM because LineTFM is severely influenced by biological tissue scattering. To reject the scattered photons, we implemented LineTFM using both structured illumination and uniform illumination combined with the HiLo post-processing algorithm, called HiLL microscopy (HiLo-Line-scanning temporal focusing microscopy). HiLL microscopy significantly reduces tissue scattering and improves image contrast. We demonstrate HiLL microscopy with in vivo brain imaging. This approach could potentially find applications in monitoring fast dynamic events and in mapping high resolution structures over a large volume.
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Affiliation(s)
- Yi Xue
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139,
USA
- Laser Biomedical Research Center, 77 Massachusetts Ave., Cambridge, MA 02139,
USA
| | - Kalen P. Berry
- Department of Biology, 77 Massachusetts Ave., Cambridge MA 02139,
USA
| | - Josiah R. Boivin
- Picower Institute for Learning and Memory,77 Massachusetts Ave., Cambridge, MA 02139,
USA
| | - Dushan Wadduwage
- Laser Biomedical Research Center, 77 Massachusetts Ave., Cambridge, MA 02139,
USA
- Department of Biological Engineering, 77 Massachusetts Ave., Cambridge, MA 02139,
USA
| | - Elly Nedivi
- Department of Biology, 77 Massachusetts Ave., Cambridge MA 02139,
USA
- Picower Institute for Learning and Memory,77 Massachusetts Ave., Cambridge, MA 02139,
USA
- Department of Brain and Cognitive Sciences, 77 Massachusetts Ave., Cambridge, MA 02139,
USA
| | - Peter T. C. So
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139,
USA
- Laser Biomedical Research Center, 77 Massachusetts Ave., Cambridge, MA 02139,
USA
- Department of Biological Engineering, 77 Massachusetts Ave., Cambridge, MA 02139,
USA
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38
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Martin C, Li T, Hegarty E, Zhao P, Mondal S, Ben-Yakar A. Line excitation array detection fluorescence microscopy at 0.8 million frames per second. Nat Commun 2018; 9:4499. [PMID: 30374138 PMCID: PMC6206139 DOI: 10.1038/s41467-018-06775-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/07/2018] [Indexed: 12/20/2022] Open
Abstract
Three-dimensional, fluorescence imaging methods with ~1 MHz frame rates are needed for high-speed, blur-free flow cytometry and capturing volumetric neuronal activity. The frame rates of current imaging methods are limited to kHz by the photon budget, slow camera readout, and/or slow laser beam scanners. Here, we present line excitation array detection (LEAD) fluorescence microscopy, a high-speed imaging method capable of providing 0.8 million frames per second. The method performs 0.8 MHz line-scanning of an excitation laser beam using a chirped signal-driven longitudinal acousto-optic deflector to create a virtual light-sheet, and images the field-of-view with a linear photomultiplier tube array to generate a 66 × 14 pixel frame each scan cycle. We implement LEAD microscopy as a blur-free flow cytometer for Caenorhabditis elegans moving at 1 m s-1 with 3.5-µm resolution and signal-to-background ratios >200. Signal-to-noise measurements indicate future LEAD fluorescence microscopes can reach higher resolutions and pixels per frame without compromising frame rates.
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Affiliation(s)
- Chris Martin
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton St., Austin, TX, 78712, USA
| | - Tianqi Li
- Department of Mechanical Engineering, The University of Texas at Austin, 204 E Dean Keeton St., Austin, TX, 78712, USA
| | - Evan Hegarty
- Department of Mechanical Engineering, The University of Texas at Austin, 204 E Dean Keeton St., Austin, TX, 78712, USA
| | - Peisen Zhao
- Department of Electrical and Computer Engineering, The University of Texas at Austin, 2501 Speedway, Austin, TX, 78712, USA
| | - Sudip Mondal
- Department of Mechanical Engineering, The University of Texas at Austin, 204 E Dean Keeton St., Austin, TX, 78712, USA
| | - Adela Ben-Yakar
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton St., Austin, TX, 78712, USA.
- Department of Mechanical Engineering, The University of Texas at Austin, 204 E Dean Keeton St., Austin, TX, 78712, USA.
- Department of Electrical and Computer Engineering, The University of Texas at Austin, 2501 Speedway, Austin, TX, 78712, USA.
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39
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Ding Y, Ma J, Langenbacher AD, Baek KI, Lee J, Chang CC, Hsu JJ, Kulkarni RP, Belperio J, Shi W, Ranjbarvaziri S, Ardehali R, Tintut Y, Demer LL, Chen JN, Fei P, Packard RRS, Hsiai TK. Multiscale light-sheet for rapid imaging of cardiopulmonary system. JCI Insight 2018; 3:121396. [PMID: 30135307 PMCID: PMC6141183 DOI: 10.1172/jci.insight.121396] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The ability to image tissue morphogenesis in real-time and in 3-dimensions (3-D) remains an optical challenge. The advent of light-sheet fluorescence microscopy (LSFM) has advanced developmental biology and tissue regeneration research. In this review, we introduce a LSFM system in which the illumination lens reshapes a thin light-sheet to rapidly scan across a sample of interest while the detection lens orthogonally collects the imaging data. This multiscale strategy provides deep-tissue penetration, high-spatiotemporal resolution, and minimal photobleaching and phototoxicity, allowing in vivo visualization of a variety of tissues and processes, ranging from developing hearts in live zebrafish embryos to ex vivo interrogation of the microarchitecture of optically cleared neonatal hearts. Here, we highlight multiple applications of LSFM and discuss several studies that have allowed better characterization of developmental and pathological processes in multiple models and tissues. These findings demonstrate the capacity of multiscale light-sheet imaging to uncover cardiovascular developmental and regenerative phenomena.
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Affiliation(s)
- Yichen Ding
- Department of Medicine, David Geffen School of Medicine at UCLA, and
- Department of Bioengineering, UCLA, Los Angeles, California, USA
| | - Jianguo Ma
- Department of Medicine, David Geffen School of Medicine at UCLA, and
- School of Instrumentation Science and Opto-electronics Engineering, Beihang University, Beijing, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beijing, China
| | - Adam D. Langenbacher
- Department of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, California, USA
| | - Kyung In Baek
- Department of Bioengineering, UCLA, Los Angeles, California, USA
| | - Juhyun Lee
- Department of Bioengineering, UCLA, Los Angeles, California, USA
| | | | - Jeffrey J. Hsu
- Department of Medicine, David Geffen School of Medicine at UCLA, and
| | - Rajan P. Kulkarni
- Department of Medicine, David Geffen School of Medicine at UCLA, and
| | - John Belperio
- Department of Medicine, David Geffen School of Medicine at UCLA, and
| | - Wei Shi
- Developmental Biology and Regenerative Medicine Program, Department of Surgery, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | | | - Reza Ardehali
- Department of Medicine, David Geffen School of Medicine at UCLA, and
| | - Yin Tintut
- Department of Medicine, David Geffen School of Medicine at UCLA, and
| | - Linda L. Demer
- Department of Medicine, David Geffen School of Medicine at UCLA, and
| | - Jau-Nian Chen
- Department of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, California, USA
| | - Peng Fei
- Department of Medicine, David Geffen School of Medicine at UCLA, and
- School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, China
| | | | - Tzung K. Hsiai
- Department of Medicine, David Geffen School of Medicine at UCLA, and
- Department of Bioengineering, UCLA, Los Angeles, California, USA
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40
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Kennel P, Teyssedre L, Colombelli J, Plouraboué F. Toward quantitative three-dimensional microvascular networks segmentation with multiview light-sheet fluorescence microscopy. JOURNAL OF BIOMEDICAL OPTICS 2018; 23:1-14. [PMID: 30120828 DOI: 10.1117/1.jbo.23.8.086002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 07/18/2018] [Indexed: 05/08/2023]
Abstract
Three-dimensional (3-D) large-scale imaging of microvascular networks is of interest in various areas of biology and medicine related to structural, functional, developmental, and pathological issues. Light-sheet fluorescence microscopy (LSFM) techniques are rapidly spreading and are now on the way to offer operational solutions for large-scale tissue imaging. This contribution describes how reliable vessel segmentation can be handled from LSFM data in very large tissue volumes using a suitable image analysis workflow. Since capillaries are tubular objects of a few microns scale radius, they represent challenging structures to reliably reconstruct without distortion and artifacts. We provide a systematic analysis of multiview deconvolution image processing workflow to control and evaluate the accuracy of the reconstructed vascular network using various low to high level, metrics. We show that even if low-level structural metrics are sensitive to isotropic imaging enhancement provided by a larger number of views, functional high-level metrics, including perfusion permeability, are less sensitive. Hence, combining deconvolution and registration onto a few number of views appears sufficient for a reliable quantitative 3-D vessel segmentation for their possible use for perfusion modeling.
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Affiliation(s)
- Pol Kennel
- Toulouse University, CNRS, INPT, UPS, Institute of Fluid Mechanics of Toulouse, Toulouse, France
| | - Lise Teyssedre
- ITAV, USR 3505, National Center of Scientific Research, Toulouse, France
| | - Julien Colombelli
- Institute of Science et Technology, Advanced Digital Microscopy Core Facility, Barcelona, Spain
| | - Franck Plouraboué
- Toulouse University, CNRS, INPT, UPS, Institute of Fluid Mechanics of Toulouse, Toulouse, France
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41
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Hillman EM, Voleti V, Patel K, Li W, Yu H, Perez-Campos C, Benezra SE, Bruno RM, Galwaduge PT. High-speed 3D imaging of cellular activity in the brain using axially-extended beams and light sheets. Curr Opin Neurobiol 2018; 50:190-200. [PMID: 29642044 PMCID: PMC6002850 DOI: 10.1016/j.conb.2018.03.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/19/2018] [Accepted: 03/21/2018] [Indexed: 10/17/2022]
Abstract
As optical reporters and modulators of cellular activity have become increasingly sophisticated, the amount that can be learned about the brain via high-speed cellular imaging has increased dramatically. However, despite fervent innovation, point-scanning microscopy is facing a fundamental limit in achievable 3D imaging speeds and fields of view. A range of alternative approaches are emerging, some of which are moving away from point-scanning to use axially-extended beams or sheets of light, for example swept confocally aligned planar excitation (SCAPE) microscopy. These methods are proving effective for high-speed volumetric imaging of the nervous system of small organisms such as Drosophila (fruit fly) and D. Rerio (Zebrafish), and are showing promise for imaging activity in the living mammalian brain using both single and two-photon excitation. This article describes these approaches and presents a simple model that demonstrates key advantages of axially-extended illumination over point-scanning strategies for high-speed volumetric imaging, including longer integration times per voxel, improved photon efficiency and reduced photodamage.
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Affiliation(s)
- Elizabeth Mc Hillman
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
| | - Venkatakaushik Voleti
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Kripa Patel
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Wenze Li
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Hang Yu
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Citlali Perez-Campos
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Sam E Benezra
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA; Bruno Lab, Department of Neuroscience, Columbia University, New York, NY, USA
| | - Randy M Bruno
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA; Bruno Lab, Department of Neuroscience, Columbia University, New York, NY, USA
| | - Pubudu T Galwaduge
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
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42
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Gustavsson AK, Petrov PN, Moerner WE. Light sheet approaches for improved precision in 3D localization-based super-resolution imaging in mammalian cells [Invited]. OPTICS EXPRESS 2018; 26:13122-13147. [PMID: 29801343 PMCID: PMC6005674 DOI: 10.1364/oe.26.013122] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/30/2018] [Indexed: 05/08/2023]
Abstract
The development of imaging techniques beyond the diffraction limit has paved the way for detailed studies of nanostructures and molecular mechanisms in biological systems. Imaging thicker samples, such as mammalian cells and tissue, in all three dimensions, is challenging due to increased background and volumes to image. Light sheet illumination is a method that allows for selective irradiation of the image plane, and its inherent optical sectioning capability allows for imaging of biological samples with reduced background, photobleaching, and photodamage. In this review, we discuss the advantage of combining single-molecule imaging with light sheet illumination. We begin by describing the principles of single-molecule localization microscopy and of light sheet illumination. Finally, we present examples of designs that successfully have married single-molecule super-resolution imaging with light sheet illumination for improved precision in mammalian cells.
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Gould EA, Busquet N, Shepherd D, Dietz RM, Herson PS, Simoes de Souza FM, Li A, George NM, Restrepo D, Macklin WB. Mild myelin disruption elicits early alteration in behavior and proliferation in the subventricular zone. eLife 2018; 7:34783. [PMID: 29436368 PMCID: PMC5828668 DOI: 10.7554/elife.34783] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/01/2018] [Indexed: 11/16/2022] Open
Abstract
Myelin, the insulating sheath around axons, supports axon function. An important question is the impact of mild myelin disruption. In the absence of the myelin protein proteolipid protein (PLP1), myelin is generated but with age, axonal function/maintenance is disrupted. Axon disruption occurs in Plp1-null mice as early as 2 months in cortical projection neurons. High-volume cellular quantification techniques revealed a region-specific increase in oligodendrocyte density in the olfactory bulb and rostral corpus callosum that increased during adulthood. A distinct proliferative response of progenitor cells was observed in the subventricular zone (SVZ), while the number and proliferation of parenchymal oligodendrocyte progenitor cells was unchanged. This SVZ proliferative response occurred prior to evidence of axonal disruption. Thus, a novel SVZ response contributes to the region-specific increase in oligodendrocytes in Plp1-null mice. Young adult Plp1-null mice exhibited subtle but substantial behavioral alterations, indicative of an early impact of mild myelin disruption.
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Affiliation(s)
- Elizabeth A Gould
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, United States.,Rocky Mountain Taste and Smell Center, University of Colorado Anschutz Medical Campus, Aurora, United States.,Neuroscience Program, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Nicolas Busquet
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Douglas Shepherd
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, United States.,Pediatric Heart Lung Center, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Robert M Dietz
- Department of Anesthesiology, University of Colorado School of Medicine, Aurora, United States
| | - Paco S Herson
- Department of Anesthesiology, University of Colorado School of Medicine, Aurora, United States
| | | | - Anan Li
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Research Center for Biochemistry and Molecular Biology, Xuzhou Medical University, Xuzhou, China
| | - Nicholas M George
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, United States.,Rocky Mountain Taste and Smell Center, University of Colorado Anschutz Medical Campus, Aurora, United States.,Neuroscience Program, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Diego Restrepo
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, United States.,Rocky Mountain Taste and Smell Center, University of Colorado Anschutz Medical Campus, Aurora, United States.,Neuroscience Program, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Wendy B Macklin
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, United States.,Rocky Mountain Taste and Smell Center, University of Colorado Anschutz Medical Campus, Aurora, United States.,Neuroscience Program, University of Colorado Anschutz Medical Campus, Aurora, United States
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44
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Silva SF, Domingues JP, Morgado AM. Accurate Rapid Lifetime Determination on Time-Gated FLIM Microscopy with Optical Sectioning. JOURNAL OF HEALTHCARE ENGINEERING 2018; 2018:1371386. [PMID: 29599938 PMCID: PMC5823430 DOI: 10.1155/2018/1371386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/21/2017] [Accepted: 12/03/2017] [Indexed: 11/18/2022]
Abstract
Time-gated fluorescence lifetime imaging microscopy (FLIM) is a powerful technique to assess the biochemistry of cells and tissues. When applied to living thick samples, it is hampered by the lack of optical sectioning and the need of acquiring many images for an accurate measurement of fluorescence lifetimes. Here, we report on the use of processing techniques to overcome these limitations, minimizing the acquisition time, while providing optical sectioning. We evaluated the application of the HiLo and the rapid lifetime determination (RLD) techniques for accurate measurement of fluorescence lifetimes with optical sectioning. HiLo provides optical sectioning by combining the high-frequency content from a standard image, obtained with uniform illumination, with the low-frequency content of a second image, acquired using structured illumination. Our results show that HiLo produces optical sectioning on thick samples without degrading the accuracy of the measured lifetimes. We also show that instrument response function (IRF) deconvolution can be applied with the RLD technique on HiLo images, improving greatly the accuracy of the measured lifetimes. These results open the possibility of using the RLD technique with pulsed diode laser sources to determine accurately fluorescence lifetimes in the subnanosecond range on thick multilayer samples, providing that offline processing is allowed.
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Affiliation(s)
- Susana F. Silva
- Institute for Biomedical Imaging and Life Sciences (IBILI), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - José Paulo Domingues
- Institute for Biomedical Imaging and Life Sciences (IBILI), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Department of Physics, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - António Miguel Morgado
- Institute for Biomedical Imaging and Life Sciences (IBILI), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Department of Physics, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
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45
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Chang CY, Lin CH, Lin CY, Sie YD, Hu YY, Tsai SF, Chen SJ. Temporal focusing-based widefield multiphoton microscopy with spatially modulated illumination for biotissue imaging. JOURNAL OF BIOPHOTONICS 2018; 11:e201600287. [PMID: 28464488 DOI: 10.1002/jbio.201600287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/29/2017] [Accepted: 03/14/2017] [Indexed: 06/07/2023]
Abstract
A developed temporal focusing-based multiphoton excitation microscope (TFMPEM) has a digital micromirror device (DMD) which is adopted not only as a blazed grating for light spatial dispersion but also for patterned illumination simultaneously. Herein, the TFMPEM has been extended to implement spatially modulated illumination at structured frequency and orientation to increase the beam coverage at the back-focal aperture of the objective lens. The axial excitation confinement (AEC) of TFMPEM can be condensed from 3.0 μm to 1.5 μm for a 50 % improvement. By using the TFMPEM with HiLo technique as two structured illuminations at the same spatial frequency but different orientation, reconstructed biotissue images according to the condensed AEC structured illumination are shown obviously superior in contrast and better scattering suppression. Picture: TPEF images of the eosin-stained mouse cerebellar cortex by conventional TFMPEM (left), and the TFMPEM with HiLo technique as 1.09 μm-1 spatially modulated illumination at 90° (center) and 0° (right) orientations.
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Affiliation(s)
- Chia-Yuan Chang
- Center for Micro/Nano Science and Technology, National Cheng Kung University, 701, Tainan, Taiwan
- Department of Engineering Science, National Cheng Kung University, 701, Tainan, Taiwan
| | - Cheng-Han Lin
- Department of Engineering Science, National Cheng Kung University, 701, Tainan, Taiwan
| | - Chun-Yu Lin
- Advanced Optoelectronic Technology Center, National Cheng Kung University, 701, Tainan, Taiwan
| | - Yong-Da Sie
- Department of Engineering Science, National Cheng Kung University, 701, Tainan, Taiwan
| | - Yvonne Yuling Hu
- Department of Photonics, National Cheng Kung University, 701, Tainan, Taiwan
| | - Sheng-Feng Tsai
- Institute of Basic Medical Sciences, National Cheng Kung University, 701, Tainan, Taiwan
| | - Shean-Jen Chen
- Advanced Optoelectronic Technology Center, National Cheng Kung University, 701, Tainan, Taiwan
- College of Photonics, National Chiao Tung University, 711 Tainan, Taiwan
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46
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Ding Y, Abiri A, Abiri P, Li S, Chang CC, Baek KI, Hsu JJ, Sideris E, Li Y, Lee J, Segura T, Nguyen TP, Bui A, Sevag Packard RR, Fei P, Hsiai TK. Integrating light-sheet imaging with virtual reality to recapitulate developmental cardiac mechanics. JCI Insight 2017; 2:97180. [PMID: 29202458 PMCID: PMC5752380 DOI: 10.1172/jci.insight.97180] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/12/2017] [Indexed: 11/17/2022] Open
Abstract
Currently, there is a limited ability to interactively study developmental cardiac mechanics and physiology. We therefore combined light-sheet fluorescence microscopy (LSFM) with virtual reality (VR) to provide a hybrid platform for 3D architecture and time-dependent cardiac contractile function characterization. By taking advantage of the rapid acquisition, high axial resolution, low phototoxicity, and high fidelity in 3D and 4D (3D spatial + 1D time or spectra), this VR-LSFM hybrid methodology enables interactive visualization and quantification otherwise not available by conventional methods, such as routine optical microscopes. We hereby demonstrate multiscale applicability of VR-LSFM to (a) interrogate skin fibroblasts interacting with a hyaluronic acid-based hydrogel, (b) navigate through the endocardial trabecular network during zebrafish development, and (c) localize gene therapy-mediated potassium channel expression in adult murine hearts. We further combined our batch intensity normalized segmentation algorithm with deformable image registration to interface a VR environment with imaging computation for the analysis of cardiac contraction. Thus, the VR-LSFM hybrid platform demonstrates an efficient and robust framework for creating a user-directed microenvironment in which we uncovered developmental cardiac mechanics and physiology with high spatiotemporal resolution.
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Affiliation(s)
- Yichen Ding
- Department of Medicine
- Department of Bioengineering, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Arash Abiri
- Department of Medicine
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, USA
| | - Parinaz Abiri
- Department of Medicine
- Department of Bioengineering, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Shuoran Li
- Chemical and Biomolecular Engineering Department
| | - Chih-Chiang Chang
- Department of Bioengineering, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Kyung In Baek
- Department of Bioengineering, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | | | | | - Yilei Li
- Electrical Engineering Department, and
| | - Juhyun Lee
- Department of Bioengineering, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Tatiana Segura
- Department of Bioengineering, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
- Chemical and Biomolecular Engineering Department
| | | | - Alexander Bui
- Department of Bioengineering, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
- Medical Imaging Informatics Group, Department of Radiological Sciences, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | | | - Peng Fei
- School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, China
| | - Tzung K. Hsiai
- Department of Medicine
- Department of Bioengineering, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
- Medical Engineering, California Institute of Technology, Pasadena, California, USA
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47
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Automatic and adaptive heterogeneous refractive index compensation for light-sheet microscopy. Nat Commun 2017; 8:612. [PMID: 28931809 PMCID: PMC5606987 DOI: 10.1038/s41467-017-00514-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 06/30/2017] [Indexed: 11/17/2022] Open
Abstract
Optical tissue clearing has revolutionized researchers’ ability to perform fluorescent measurements of molecules, cells, and structures within intact tissue. One common complication to all optically cleared tissue is a spatially heterogeneous refractive index, leading to light scattering and first-order defocus. We designed C-DSLM (cleared tissue digital scanned light-sheet microscopy) as a low-cost method intended to automatically generate in-focus images of cleared tissue. We demonstrate the flexibility and power of C-DSLM by quantifying fluorescent features in tissue from multiple animal models using refractive index matched and mismatched microscope objectives. This includes a unique measurement of myelin tracks within intact tissue using an endogenous fluorescent reporter where typical clearing approaches render such structures difficult to image. For all measurements, we provide independent verification using standard serial tissue sectioning and quantification methods. Paired with advancements in volumetric image processing, C-DSLM provides a robust methodology to quantify sub-micron features within large tissue sections. Optical clearing of tissue has enabled optical imaging deeper into tissue due to significantly reduced light scattering. Here, Ryan et al. tackle first-order defocus, an artefact of a non-uniform refractive index, extending light-sheet microscopy to partially cleared samples.
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48
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Kim DH, Kim J, Marques JC, Grama A, Hildebrand DGC, Gu W, Li JM, Robson DN. Pan-neuronal calcium imaging with cellular resolution in freely swimming zebrafish. Nat Methods 2017; 14:1107-1114. [DOI: 10.1038/nmeth.4429] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 07/29/2017] [Indexed: 12/15/2022]
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49
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Duchi S, Piccinini F, Pierini M, Bevilacqua A, Torre ML, Lucarelli E, Santi S. A new holistic 3D non-invasive analysis of cellular distribution and motility on fibroin-alginate microcarriers using light sheet fluorescent microscopy. PLoS One 2017; 12:e0183336. [PMID: 28817694 PMCID: PMC5560673 DOI: 10.1371/journal.pone.0183336] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/02/2017] [Indexed: 12/12/2022] Open
Abstract
Cell interaction with biomaterials is one of the keystones to developing medical devices for tissue engineering applications. Biomaterials are the scaffolds that give three-dimensional support to the cells, and are vectors that deliver the cells to the injured tissue requiring repair. Features of biomaterials can influence the behaviour of the cells and consequently the efficacy of the tissue-engineered product. The adhesion, distribution and motility of the seeded cells onto the scaffold represent key aspects, and must be evaluated in vitro during the product development, especially when the efficacy of a specific tissue-engineered product depends on viable and functional cell loading. In this work, we propose a non-invasive and non-destructive imaging analysis for investigating motility, viability and distribution of Mesenchymal Stem Cells (MSCs) on silk fibroin-based alginate microcarriers, to test the adhesion capacity of the fibroin coating onto alginate which is known to be unsuitable for cell adhesion. However, in depth characterization of the biomaterial is beyond the scope of this paper. Scaffold-loaded MSCs were stained with Calcein-AM and Ethidium homodimer-1 to detect live and dead cells, respectively, and counterstained with Hoechst to label cell nuclei. Time-lapse Light Sheet Fluorescent Microscopy (LSFM) was then used to produce three-dimensional images of the entire cells-loaded fibroin/alginate microcarriers. In order to quantitatively track the cell motility over time, we also developed an open source user friendly software tool called Fluorescent Cell Tracker in Three-Dimensions (F-Tracker3D). Combining LSFM with F-Tracker3D we were able for the first time to assess the distribution and motility of stem cells in a non-invasive, non-destructive, quantitative, and three-dimensional analysis of the entire surface of the cell-loaded scaffold. We therefore propose this imaging technique as an innovative holistic tool for monitoring cell-biomaterial interactions, and as a tool for the design, fabrication and functionalization of a scaffold as a medical device.
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Affiliation(s)
- Serena Duchi
- Osteoarticolar Regeneration Laboratory, Rizzoli Orthopaedic Institute, Bologna, Italy
- Department of Surgery, St Vincent’s Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Filippo Piccinini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Meldola (FC), Italy
| | - Michela Pierini
- Osteoarticolar Regeneration Laboratory, Rizzoli Orthopaedic Institute, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences (DIBINEM), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Alessandro Bevilacqua
- Advanced Research Center on Electronic Systems “Ercole De Castro” (ARCES), Alma Mater Studiorum University of Bologna, Bologna, Italy
- Department of Computer Science and Engineering (DISI), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Maria Luisa Torre
- Cell Delivery System Lab, Department of Drug Sciences, University of Pavia, Pavia, Italy
| | - Enrico Lucarelli
- Osteoarticolar Regeneration Laboratory, Rizzoli Orthopaedic Institute, Bologna, Italy
| | - Spartaco Santi
- Institute of Molecular Genetics (CNR), Bologna, Italy
- SC Laboratory of Musculoskeletal Cell Biology, Rizzoli Orthopaedic Institute, Bologna, Italy
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50
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Macias-Romero C, Nahalka I, Okur HI, Roke S. Optical imaging of surface chemistry and dynamics in confinement. Science 2017; 357:784-788. [PMID: 28729352 DOI: 10.1126/science.aal4346] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 04/05/2017] [Accepted: 06/30/2017] [Indexed: 12/23/2022]
Abstract
We imaged the interfacial structure and dynamics of water in a microscopically confined geometry, in three dimensions and on millisecond time scales, with a structurally illuminated wide-field second harmonic microscope. The second harmonic images reported on the orientational order of interfacial water, induced by charge-dipole interactions between water molecules and surface charges. The images were converted into surface potential maps. Spatially resolved surface acid dissociation constant (pKa,s) values were determined for the silica deprotonation reaction by following pH-induced chemical changes on the curved and confined surfaces of a glass microcapillary immersed in aqueous solutions. These values ranged from 2.3 to 10.7 along the wall of a single capillary because of surface heterogeneities. Water molecules that rotate along an oscillating external electric field were also imaged.
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Affiliation(s)
- Carlos Macias-Romero
- Laboratory for Fundamental BioPhotonics, Institute of Bioengineering, and Institute of Materials Science, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Igor Nahalka
- Laboratory for Fundamental BioPhotonics, Institute of Bioengineering, and Institute of Materials Science, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Halil I Okur
- Laboratory for Fundamental BioPhotonics, Institute of Bioengineering, and Institute of Materials Science, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sylvie Roke
- Laboratory for Fundamental BioPhotonics, Institute of Bioengineering, and Institute of Materials Science, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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