1
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Subash P, Gray A, Boswell M, Cohen SL, Garner R, Salehi S, Fisher C, Hobel S, Ghosh S, Halchenko Y, Dichter B, Poldrack RA, Markiewicz C, Hermes D, Delorme A, Makeig S, Behan B, Sparks A, Arnott SR, Wang Z, Magnotti J, Beauchamp MS, Pouratian N, Toga AW, Duncan D. A comparison of neuroelectrophysiology databases. Sci Data 2023; 10:719. [PMID: 37857685 PMCID: PMC10587056 DOI: 10.1038/s41597-023-02614-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023] Open
Abstract
As data sharing has become more prevalent, three pillars - archives, standards, and analysis tools - have emerged as critical components in facilitating effective data sharing and collaboration. This paper compares four freely available intracranial neuroelectrophysiology data repositories: Data Archive for the BRAIN Initiative (DABI), Distributed Archives for Neurophysiology Data Integration (DANDI), OpenNeuro, and Brain-CODE. The aim of this review is to describe archives that provide researchers with tools to store, share, and reanalyze both human and non-human neurophysiology data based on criteria that are of interest to the neuroscientific community. The Brain Imaging Data Structure (BIDS) and Neurodata Without Borders (NWB) are utilized by these archives to make data more accessible to researchers by implementing a common standard. As the necessity for integrating large-scale analysis into data repository platforms continues to grow within the neuroscientific community, this article will highlight the various analytical and customizable tools developed within the chosen archives that may advance the field of neuroinformatics.
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Affiliation(s)
- Priyanka Subash
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles, CA, 90033, USA
| | - Alex Gray
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles, CA, 90033, USA
| | - Misque Boswell
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles, CA, 90033, USA
| | - Samantha L Cohen
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles, CA, 90033, USA
| | - Rachael Garner
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles, CA, 90033, USA
| | - Sana Salehi
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles, CA, 90033, USA
| | - Calvary Fisher
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles, CA, 90033, USA
| | - Samuel Hobel
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles, CA, 90033, USA
| | - Satrajit Ghosh
- McGovern Institute for Brain Research, MIT Brain and Cognitive Sciences, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Yaroslav Halchenko
- Department of Psychological & Brain Sciences, Center for Cognitive Neuroscience, Dartmouth Brain Imaging Center, Dartmouth College, 6207 Moore Hall, Hanover, NH, 03755, USA
| | | | - Russell A Poldrack
- Department of Psychology, Stanford University, 450 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Chris Markiewicz
- Department of Psychology, Stanford University, 450 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Dora Hermes
- Mayo Clinic, Department of Physiology & Biomedical Engineering, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Arnaud Delorme
- Swartz Center of Computational Neuroscience, INC, University of California San Diego, La Jolla, CA, 92093, USA
| | - Scott Makeig
- Swartz Center of Computational Neuroscience, INC, University of California San Diego, La Jolla, CA, 92093, USA
| | - Brendan Behan
- Ontario Brain Institute, 1 Richmond Street West, Toronto, ON, M5H 3W4, Canada
| | | | | | - Zhengjia Wang
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA, 19104, USA
| | - John Magnotti
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA, 19104, USA
| | - Michael S Beauchamp
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA, 19104, USA
| | - Nader Pouratian
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, 5303 Harry Hines Blvd, Dallas, TX, 75390, USA
| | - Arthur W Toga
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles, CA, 90033, USA
| | - Dominique Duncan
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles, CA, 90033, USA.
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2
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Barroso M, Monaghan MG, Niesner R, Dmitriev RI. Probing organoid metabolism using fluorescence lifetime imaging microscopy (FLIM): The next frontier of drug discovery and disease understanding. Adv Drug Deliv Rev 2023; 201:115081. [PMID: 37647987 PMCID: PMC10543546 DOI: 10.1016/j.addr.2023.115081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/20/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023]
Abstract
Organoid models have been used to address important questions in developmental and cancer biology, tissue repair, advanced modelling of disease and therapies, among other bioengineering applications. Such 3D microenvironmental models can investigate the regulation of cell metabolism, and provide key insights into the mechanisms at the basis of cell growth, differentiation, communication, interactions with the environment and cell death. Their accessibility and complexity, based on 3D spatial and temporal heterogeneity, make organoids suitable for the application of novel, dynamic imaging microscopy methods, such as fluorescence lifetime imaging microscopy (FLIM) and related decay time-assessing readouts. Several biomarkers and assays have been proposed to study cell metabolism by FLIM in various organoid models. Herein, we present an expert-opinion discussion on the principles of FLIM and PLIM, instrumentation and data collection and analysis protocols, and general and emerging biosensor-based approaches, to highlight the pioneering work being performed in this field.
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Affiliation(s)
- Margarida Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Michael G Monaghan
- Department of Mechanical, Manufacturing and Biomedical Engineering, Trinity College Dublin, Dublin 02, Ireland
| | - Raluca Niesner
- Dynamic and Functional In Vivo Imaging, Freie Universität Berlin and Biophysical Analytics, German Rheumatism Research Center, Berlin, Germany
| | - Ruslan I Dmitriev
- Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium; Ghent Light Microscopy Core, Ghent University, 9000 Ghent, Belgium.
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3
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Subash P, Gray A, Boswell M, Cohen SL, Garner R, Salehi S, Fisher C, Hobel S, Ghosh S, Halchenko Y, Dichter B, Poldrack RA, Markiewicz C, Hermes D, Delorme A, Makeig S, Behan B, Sparks A, Arnott SR, Wang Z, Magnotti J, Beauchamp MS, Pouratian N, Toga AW, Duncan D. A Comparison of Neuroelectrophysiology Databases. ARXIV 2023:arXiv:2306.15041v2. [PMID: 37426452 PMCID: PMC10327244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
As data sharing has become more prevalent, three pillars - archives, standards, and analysis tools - have emerged as critical components in facilitating effective data sharing and collaboration. This paper compares four freely available intracranial neuroelectrophysiology data repositories: Data Archive for the BRAIN Initiative (DABI), Distributed Archives for Neurophysiology Data Integration (DANDI), OpenNeuro, and Brain-CODE. The aim of this review is to describe archives that provide researchers with tools to store, share, and reanalyze both human and non-human neurophysiology data based on criteria that are of interest to the neuroscientific community. The Brain Imaging Data Structure (BIDS) and Neurodata Without Borders (NWB) are utilized by these archives to make data more accessible to researchers by implementing a common standard. As the necessity for integrating large-scale analysis into data repository platforms continues to grow within the neuroscientific community, this article will highlight the various analytical and customizable tools developed within the chosen archives that may advance the field of neuroinformatics.
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Affiliation(s)
- Priyanka Subash
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles CA 90033
| | - Alex Gray
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles CA 90033
| | - Misque Boswell
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles CA 90033
| | - Samantha L Cohen
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles CA 90033
| | - Rachael Garner
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles CA 90033
| | - Sana Salehi
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles CA 90033
| | - Calvary Fisher
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles CA 90033
| | - Samuel Hobel
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles CA 90033
| | - Satrajit Ghosh
- McGovern Institute for Brain Research, MIT Brain and Cognitive Sciences, 77 Massachusetts Avenue, Cambridge MA 02139
| | - Yaroslav Halchenko
- Department of Psychological & Brain Sciences, Center for Cognitive Neuroscience, Dartmouth Brain Imaging Center, Dartmouth College, 6207 Moore Hall, Hanover NH 03755
| | | | - Russell A Poldrack
- Department of Psychology, Stanford University, 450 Jane Stanford Way, Stanford CA 94305
| | - Chris Markiewicz
- Department of Psychology, Stanford University, 450 Jane Stanford Way, Stanford CA 94305
| | - Dora Hermes
- Mayo Clinic, Department of Physiology & Biomedical Engineering, 200 1st Street SW, Rochester MN 55905
| | - Arnaud Delorme
- Swartz Center of Computational Neuroscience, INC, University of California San Diego, La Jolla CA 92093
| | - Scott Makeig
- Swartz Center of Computational Neuroscience, INC, University of California San Diego, La Jolla CA 92093
| | - Brendan Behan
- Ontario Brain Institute, 1 Richmond Street West, Toronto ON M5H 3W4, Canada
| | | | | | - Zhengjia Wang
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia PA 19104
| | - John Magnotti
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia PA 19104
| | - Michael S Beauchamp
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia PA 19104
| | - Nader Pouratian
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, 5303 Harry Hines Blvd, Dallas TX 75390
| | - Arthur W Toga
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles CA 90033
| | - Dominique Duncan
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, 2025 Zonal Avenue, Los Angeles CA 90033
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4
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Liu Y, Liu B, Green J, Duffy C, Song M, Lauderdale JD, Kner P. Volumetric light sheet imaging with adaptive optics correction. BIOMEDICAL OPTICS EXPRESS 2023; 14:1757-1771. [PMID: 37078033 PMCID: PMC10110302 DOI: 10.1364/boe.473237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 05/02/2023]
Abstract
Light sheet microscopy has developed quickly over the past decades and become a popular method for imaging live model organisms and other thick biological tissues. For rapid volumetric imaging, an electrically tunable lens can be used to rapidly change the imaging plane in the sample. For larger fields of view and higher NA objectives, the electrically tunable lens introduces aberrations in the system, particularly away from the nominal focus and off-axis. Here, we describe a system that employs an electrically tunable lens and adaptive optics to image over a volume of 499 × 499 × 192 μm3 with close to diffraction-limited resolution. Compared to the system without adaptive optics, the performance shows an increase in signal to background ratio by a factor of 3.5. While the system currently requires 7s/volume, it should be straightforward to increase the imaging speed to under 1s per volume.
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Affiliation(s)
- Yang Liu
- School of Electrical and Computer Engineering, University of Georgia, Athens, GA 30602, USA
| | - Bingxi Liu
- School of Electrical and Computer Engineering, University of Georgia, Athens, GA 30602, USA
| | - John Green
- School of Electrical and Computer Engineering, University of Georgia, Athens, GA 30602, USA
| | - Carly Duffy
- Dept. of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Ming Song
- School of Electrical and Computer Engineering, University of Georgia, Athens, GA 30602, USA
| | - James D. Lauderdale
- Dept. of Cellular Biology, University of Georgia, Athens, GA 30602, USA
- Neuroscience Division of the Biomedical Health Sciences Institute, University of Georgia, Athens, GA 30602, USA
| | - Peter Kner
- School of Electrical and Computer Engineering, University of Georgia, Athens, GA 30602, USA
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5
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Tong A, Voronov R. A Minireview of Microfluidic Scaffold Materials in Tissue Engineering. Front Mol Biosci 2022; 8:783268. [PMID: 35087865 PMCID: PMC8787357 DOI: 10.3389/fmolb.2021.783268] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 12/14/2021] [Indexed: 01/09/2023] Open
Abstract
In 2020, nearly 107,000 people in the U.S needed a lifesaving organ transplant, but due to a limited number of donors, only ∼35% of them have actually received it. Thus, successful bio-manufacturing of artificial tissues and organs is central to satisfying the ever-growing demand for transplants. However, despite decades of tremendous investments in regenerative medicine research and development conventional scaffold technologies have failed to yield viable tissues and organs. Luckily, microfluidic scaffolds hold the promise of overcoming the major challenges associated with generating complex 3D cultures: 1) cell death due to poor metabolite distribution/clearing of waste in thick cultures; 2) sacrificial analysis due to inability to sample the culture non-invasively; 3) product variability due to lack of control over the cell action post-seeding, and 4) adoption barriers associated with having to learn a different culturing protocol for each new product. Namely, their active pore networks provide the ability to perform automated fluid and cell manipulations (e.g., seeding, feeding, probing, clearing waste, delivering drugs, etc.) at targeted locations in-situ. However, challenges remain in developing a biomaterial that would have the appropriate characteristics for such scaffolds. Specifically, it should ideally be: 1) biocompatible—to support cell attachment and growth, 2) biodegradable—to give way to newly formed tissue, 3) flexible—to create microfluidic valves, 4) photo-crosslinkable—to manufacture using light-based 3D printing and 5) transparent—for optical microscopy validation. To that end, this minireview summarizes the latest progress of the biomaterial design, and of the corresponding fabrication method development, for making the microfluidic scaffolds.
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Affiliation(s)
- Anh Tong
- Otto H. York Department of Chemical and Materials Engineering, Newark College of Engineering, New Jersey Institute of Technology, Newark, NJ, United States
- *Correspondence: Roman Voronov, ; Anh Tong,
| | - Roman Voronov
- Otto H. York Department of Chemical and Materials Engineering, Newark College of Engineering, New Jersey Institute of Technology, Newark, NJ, United States
- Department of Biomedical Engineering, Newark College of Engineering, New Jersey Institute of Technology, Newark, NJ, United States
- *Correspondence: Roman Voronov, ; Anh Tong,
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6
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Bowman AJ, Kasevich MA. Resonant Electro-Optic Imaging for Microscopy at Nanosecond Resolution. ACS NANO 2021; 15:16043-16054. [PMID: 34546704 DOI: 10.1021/acsnano.1c04470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We demonstrate an electro-optic wide-field method to enable fluorescence lifetime microscopy (FLIM) with high throughput and single-molecule sensitivity. Resonantly driven Pockels cells are used to efficiently gate images at 39 MHz, allowing fluorescence lifetime to be captured on standard camera sensors. Lifetime imaging of single molecules is enabled in wide field with exposure times of less than 100 ms. This capability allows combination of wide-field FLIM with single-molecule super-resolution localization microscopy. Fast single-molecule dynamics such as FRET and molecular binding events are captured from wide-field images without prior spatial knowledge. A lifetime sensitivity of 1.9 times the photon shot-noise limit is achieved, and high throughput is shown by acquiring wide-field FLIM images with millisecond exposure and >108 photons per frame. Resonant electro-optic FLIM allows lifetime contrast in any wide-field microscopy method.
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Affiliation(s)
- Adam J Bowman
- Physics Department, Stanford University, 382 Via Pueblo Mall, Stanford, California 94305, United States
| | - Mark A Kasevich
- Physics Department, Stanford University, 382 Via Pueblo Mall, Stanford, California 94305, United States
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7
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Efstathiou C, Draviam VM. Electrically tunable lenses - eliminating mechanical axial movements during high-speed 3D live imaging. J Cell Sci 2021; 134:271866. [PMID: 34409445 DOI: 10.1242/jcs.258650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The successful investigation of photosensitive and dynamic biological events, such as those in a proliferating tissue or a dividing cell, requires non-intervening high-speed imaging techniques. Electrically tunable lenses (ETLs) are liquid lenses possessing shape-changing capabilities that enable rapid axial shifts of the focal plane, in turn achieving acquisition speeds within the millisecond regime. These human-eye-inspired liquid lenses can enable fast focusing and have been applied in a variety of cell biology studies. Here, we review the history, opportunities and challenges underpinning the use of cost-effective high-speed ETLs. Although other, more expensive solutions for three-dimensional imaging in the millisecond regime are available, ETLs continue to be a powerful, yet inexpensive, contender for live-cell microscopy.
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Affiliation(s)
- Christoforos Efstathiou
- School of Biological and Chemical Sciences , Queen Mary University of London, London, E1 4NS, UK
| | - Viji M Draviam
- School of Biological and Chemical Sciences , Queen Mary University of London, London, E1 4NS, UK
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8
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Dmitriev RI, Intes X, Barroso MM. Luminescence lifetime imaging of three-dimensional biological objects. J Cell Sci 2021; 134:1-17. [PMID: 33961054 PMCID: PMC8126452 DOI: 10.1242/jcs.254763] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A major focus of current biological studies is to fill the knowledge gaps between cell, tissue and organism scales. To this end, a wide array of contemporary optical analytical tools enable multiparameter quantitative imaging of live and fixed cells, three-dimensional (3D) systems, tissues, organs and organisms in the context of their complex spatiotemporal biological and molecular features. In particular, the modalities of luminescence lifetime imaging, comprising fluorescence lifetime imaging (FLI) and phosphorescence lifetime imaging microscopy (PLIM), in synergy with Förster resonance energy transfer (FRET) assays, provide a wealth of information. On the application side, the luminescence lifetime of endogenous molecules inside cells and tissues, overexpressed fluorescent protein fusion biosensor constructs or probes delivered externally provide molecular insights at multiple scales into protein-protein interaction networks, cellular metabolism, dynamics of molecular oxygen and hypoxia, physiologically important ions, and other physical and physiological parameters. Luminescence lifetime imaging offers a unique window into the physiological and structural environment of cells and tissues, enabling a new level of functional and molecular analysis in addition to providing 3D spatially resolved and longitudinal measurements that can range from microscopic to macroscopic scale. We provide an overview of luminescence lifetime imaging and summarize key biological applications from cells and tissues to organisms.
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Affiliation(s)
- Ruslan I. Dmitriev
- Tissue Engineering and Biomaterials Group, Department of
Human Structure and Repair, Faculty of Medicine and Health Sciences,
Ghent University, Ghent 9000,
Belgium
| | - Xavier Intes
- Department of Biomedical Engineering, Center for
Modeling, Simulation and Imaging for Medicine (CeMSIM),
Rensselaer Polytechnic Institute, Troy, NY
12180-3590, USA
| | - Margarida M. Barroso
- Department of Molecular and Cellular
Physiology, Albany Medical College,
Albany, NY 12208, USA
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9
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Hsieh TY, Vyas S, Wu JC, Luo Y. Volume holographic optical element for light sheet fluorescence microscopy. OPTICS LETTERS 2020; 45:6478-6481. [PMID: 33258841 DOI: 10.1364/ol.413204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 06/12/2023]
Abstract
Three-dimensional (3D) imaging of living organisms requires fine optical sectioning and high-speed image acquisition, which can be achieved by light sheet fluorescence microscopy (LSFM). However, orthogonal illumination and detection arms in the LSFM system make it bulky. Here, we propose and demonstrate the application of a volume holographic optical element (photopolymer-based volume holographic grating) for designing a compact LSFM system, called a volume holographic LSFM (VHLSFM). Using the VHLSFM, we performed in vivo imaging of Caenorhabditis elegans (C. elegans) and observed high-contrast optically sectioned fluorescence images of the oocytes and embryonic development in real time for 3D imaging.
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10
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Li R, Liu A, Wu T, Xiao W, Tang LI, Chen L. Digital scanned laser light-sheet fluorescence lifetime microscopy with wide-field time-gated imaging. J Microsc 2020; 279:69-76. [PMID: 32307699 DOI: 10.1111/jmi.12898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/21/2020] [Accepted: 04/14/2020] [Indexed: 01/01/2023]
Abstract
We develop a multidimensional fluorescence imaging technique by implementing a wide-field time-gated fluorescence lifetime imaging into digital scanned laser light-sheet microscopy (FLIM-DSLM) to measure 3D fluorescence lifetime distribution in mesoscopic specimens with high resolution. This is achieved by acquiring a series of time-gated images at different relative time delays with respect of excitation pulses at different depths. The lifetime is determined for each voxel by iteratively fitting to single exponential decay. The performance of the developed system is evaluated with the measurements of a lifetime reference Rhodamine 6G solution and a subresolution fluorescent bead phantom. We also demonstrate the application performances of this system to ex vivo and in vivo imaging of Tg(kdrl:EGFP) transgenic zebrafish embryos, illustrating the lifetime differences between the GFP signal and the autofluorescence signal. The results show that FLIM-DSLM can be used for sample size up to a few millimetres and can be utilised as a powerful and robust method for biomedical research, for example as a readout of protein-protein interactions via Förster resonance energy transfer.
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Affiliation(s)
- R Li
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China.,College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
| | - A Liu
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China.,College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
| | - T Wu
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China.,College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
| | - W Xiao
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China.,College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
| | - L I Tang
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China.,College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
| | - Lingling Chen
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China.,College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
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11
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Hirvonen LM, Nedbal J, Almutairi N, Phillips TA, Becker W, Conneely T, Milnes J, Cox S, Stürzenbaum S, Suhling K. Lightsheet fluorescence lifetime imaging microscopy with wide-field time-correlated single photon counting. JOURNAL OF BIOPHOTONICS 2020; 13:e201960099. [PMID: 31661595 PMCID: PMC7065631 DOI: 10.1002/jbio.201960099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 05/22/2023]
Abstract
We report on wide-field time-correlated single photon counting (TCSPC)-based fluorescence lifetime imaging microscopy (FLIM) with lightsheet illumination. A pulsed diode laser is used for excitation, and a crossed delay line anode image intensifier, effectively a single-photon sensitive camera, is used to record the position and arrival time of the photons with picosecond time resolution, combining low illumination intensity of microwatts with wide-field data collection. We pair this detector with the lightsheet illumination technique, and apply it to 3D FLIM imaging of dye gradients in human cancer cell spheroids, and C. elegans.
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Affiliation(s)
- Liisa M. Hirvonen
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
| | - Jakub Nedbal
- Department of PhysicsKing's College LondonLondonUK
| | - Norah Almutairi
- School of Population Health & Environmental Sciences, Faculty of Life Sciences & MedicineKing's College LondonLondonUK
| | - Thomas A. Phillips
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
| | | | | | | | - Susan Cox
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
| | - Stephen Stürzenbaum
- School of Population Health & Environmental Sciences, Faculty of Life Sciences & MedicineKing's College LondonLondonUK
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12
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Steuwe C, Vaeyens MM, Jorge-Peñas A, Cokelaere C, Hofkens J, Roeffaers MBJ, Van Oosterwyck H. Fast quantitative time lapse displacement imaging of endothelial cell invasion. PLoS One 2020; 15:e0227286. [PMID: 31910228 PMCID: PMC6946139 DOI: 10.1371/journal.pone.0227286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 12/16/2019] [Indexed: 11/18/2022] Open
Abstract
In order to unravel rapid mechano-chemical feedback mechanisms in sprouting angiogenesis, we combine selective plane illumination microscopy (SPIM) and tailored image registration algorithms - further referred to as SPIM-based displacement microscopy - with an in vitro model of angiogenesis. SPIM successfully tackles the problem of imaging large volumes while upholding the spatial resolution required for the analysis of matrix displacements at a subcellular level. Applied to in vitro angiogenic sprouts, this unique methodological combination relates subcellular activity - minute to second time scale growing and retracting of protrusions - of a multicellular systems to the surrounding matrix deformations with an exceptional temporal resolution of 1 minute for a stack with multiple sprouts simultaneously or every 4 seconds for a single sprout, which is 20 times faster than with a conventional confocal setup. Our study reveals collective but non-synchronised, non-continuous activity of adjacent sprouting cells along with correlations between matrix deformations and protrusion dynamics.
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Affiliation(s)
- Christian Steuwe
- Centre for Membrane Separations, Adsorption, Catalysis and Spectroscopy for Sustainable Solutions (cMACS), Department of Microbial and Molecular Systems (MS), KU Leuven, Leuven, Belgium
| | - Marie-Mo Vaeyens
- Biomechanics Section (BMe), Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
| | - Alvaro Jorge-Peñas
- Biomechanics Section (BMe), Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
| | - Célie Cokelaere
- Centre for Membrane Separations, Adsorption, Catalysis and Spectroscopy for Sustainable Solutions (cMACS), Department of Microbial and Molecular Systems (MS), KU Leuven, Leuven, Belgium
| | - Johan Hofkens
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Maarten B. J. Roeffaers
- Centre for Membrane Separations, Adsorption, Catalysis and Spectroscopy for Sustainable Solutions (cMACS), Department of Microbial and Molecular Systems (MS), KU Leuven, Leuven, Belgium
| | - Hans Van Oosterwyck
- Biomechanics Section (BMe), Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
- Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium
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Okkelman IA, Papkovsky DB, Dmitriev RI. Estimation of the Mitochondrial Membrane Potential Using Fluorescence Lifetime Imaging Microscopy. Cytometry A 2019; 97:471-482. [PMID: 31486581 DOI: 10.1002/cyto.a.23886] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/11/2019] [Accepted: 08/19/2019] [Indexed: 12/19/2022]
Abstract
Monitoring of cell metabolism represents an important application area for fluorescence lifetime imaging microscopy (FLIM). In particular, assessment of mitochondrial membrane potential (MMP) in complex three-dimensional multicellular in vitro, ex vivo, and in vivo models would enable improved segmentation and functional discrimination of cell types, directly report on the mitochondrial function and complement the quenched-phosphorescence detection of cellular O2 and two-photon excited FLIM of endogenous NAD(P)H. Here, we report the green and orange-emitting fluorescent dyes SYTO and tetramethylrhodamine methyl ester (TMRM) as potential FLIM probes for MMP. In addition to nuclear, SYTO 16 and 24 dyes also display mitochondrial accumulation. FLIM with the culture of human colon cancer HCT116 cells allowed observation of the heterogeneity of mitochondrial polarization during the cell cycle progression. The dyes also demonstrated good performance with 3D cultures of Lgr5-GFP mouse intestinal organoids, providing efficient and quick cell staining and compatibility with two-photon excitation. Multiplexed imaging of Lgr5-GFP, proliferating cells (Hoechst 33342-aided FLIM), and TMRM-FLIM allowed us to identify the population of metabolically active cells in stem cell niche. TMRM-FLIM enabled to visualize the differences in membrane potential between Lgr5-positive and other proliferating and differentiated cell types. Altogether, SYTO 24 and TMRM dyes represent promising markers for advanced FLIM-based studies of cell bioenergetics with complex 3D and in vivo models. © 2019 International Society for Advancement of Cytometry.
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Affiliation(s)
- Irina A Okkelman
- Laboratory of Biophysics and Bioanalysis, ABCRF, School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Dmitri B Papkovsky
- Laboratory of Biophysics and Bioanalysis, ABCRF, School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ruslan I Dmitriev
- Laboratory of Biophysics and Bioanalysis, ABCRF, School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.,Institute for Regenerative Medicine, I.M. Sechenov First Moscow State University, Moscow, Russian Federation
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McCarthy ME, Birtwistle MR. Highly Multiplexed, Quantitative Tissue Imaging at Cellular Resolution. CURRENT PATHOBIOLOGY REPORTS 2019. [DOI: 10.1007/s40139-019-00203-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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