1
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Bae S, Sung K, Kim SK. Linear spectral unmixing analysis in single-molecule FRET spectroscopy for fluorophores with large spectral overlap. Phys Chem Chem Phys 2024; 26:16561-16566. [PMID: 38832676 DOI: 10.1039/d4cp00736k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Fluorescence resonance energy transfer (FRET) is a highly useful tool to investigate biomolecular interactions and dynamics in single-molecule spectroscopy and nanoscopy. However, the use of spectrally overlapping dye pairs results in various artifact signals that prevent accurate determination of FRET values. In this paper, an algorithmic method of spectral unmixing was devised to extract FRET values of spectrally overlapping dye pairs at the single molecule level. Application of this method allows the determination of both the donor-acceptor composition and the FRET efficiency of the samples labelled with spectrally overlapping dye pairs.
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Affiliation(s)
- Sohyeon Bae
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Keewon Sung
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
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2
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Bentahar S, Gómez-Gaviro MV, Desco M, Ripoll J, Fernández R. Multispectral imaging for characterizing autofluorescent tissues. Sci Rep 2024; 14:12084. [PMID: 38802477 PMCID: PMC11130125 DOI: 10.1038/s41598-024-61020-7] [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: 11/24/2023] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
Selective Plane Illumination Microscopy (SPIM) has become an emerging technology since its first application for 3D in-vivo imaging of the development of a living organism. An extensive number of works have been published, improving both the speed of acquisition and the resolution of the systems. Furthermore, multispectral imaging allows the effective separation of overlapping signals associated with different fluorophores from the spectrum over the whole field-of-view of the analyzed sample. To eliminate the need of using fluorescent dyes, this technique can also be applied to autofluorescence imaging. However, the effective separation of the overlapped spectra in autofluorescence imaging necessitates the use of mathematical tools. In this work, we explore the application of a method based on Principal Component Analysis (PCA) that enables tissue characterization upon spectral autofluorescence data without the use of fluorophores. Thus, enabling the separation of different tissue types in fixed and living samples with no need of staining techniques. Two procedures are described for acquiring spectral data, including a single excitation based method and a multi-excitation scanning approach. In both cases, we demonstrate the effective separation of various tissue types based on their unique autofluorescence spectra.
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Affiliation(s)
- Sara Bentahar
- Departamento de Bioingeniería, Universidad Carlos III de Madrid, Madrid, Spain
| | | | - Manuel Desco
- Departamento de Bioingeniería, Universidad Carlos III de Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Jorge Ripoll
- Departamento de Bioingeniería, Universidad Carlos III de Madrid, Madrid, Spain.
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.
| | - Roberto Fernández
- Departamento de Bioingeniería, Universidad Carlos III de Madrid, Madrid, Spain.
- Departamento de Física, Ingeniería de Sistemas y Teoría de la Señal, Universidad de Alicante, Alicante, Spain.
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3
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Liu S, Zou W, Sha H, Feng X, Chen B, Zhang J, Han S, Li X, Zhang Y. Deep learning-enhanced snapshot hyperspectral confocal microscopy imaging system. OPTICS EXPRESS 2024; 32:13918-13931. [PMID: 38859350 DOI: 10.1364/oe.519045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/17/2024] [Indexed: 06/12/2024]
Abstract
Laser-scanning confocal hyperspectral microscopy is a powerful technique to identify the different sample constituents and their spatial distribution in three-dimensional (3D). However, it suffers from low imaging speed because of the mechanical scanning methods. To overcome this challenge, we propose a snapshot hyperspectral confocal microscopy imaging system (SHCMS). It combined coded illumination microscopy based on a digital micromirror device (DMD) with a snapshot hyperspectral confocal neural network (SHCNet) to realize single-shot confocal hyperspectral imaging. With SHCMS, high-contrast 160-bands confocal hyperspectral images of potato tuber autofluorescence can be collected by only single-shot, which is almost 5 times improvement in the number of spectral channels than previously reported methods. Moreover, our approach can efficiently record hyperspectral volumetric imaging due to the optical sectioning capability. This fast high-resolution hyperspectral imaging method may pave the way for real-time highly multiplexed biological imaging.
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4
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Zhou C, Martin OJF, Charbon E. Planar 16-band metasurface-enhanced spectral filter for integrated image sensing. OPTICS EXPRESS 2024; 32:7463-7472. [PMID: 38439425 DOI: 10.1364/oe.515675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/02/2024] [Indexed: 03/06/2024]
Abstract
We study theoretically and demonstrate experimentally a 16-band narrow band wavelength selective filter in the near-infrared range. The combination of a pair of distributed Bragg reflectors with a sub-wavelength grating metasurface embedded in the intra-cavity provides a narrow response which can be tuned by adjusting the geometry of the sub-wavelength grating metasurface. The key advantage of this approach is its ease of fabrication, where the spectral response is tuned by merely changing the grating period, resulting in a perfectly planar geometry that can be easily integrated with a broad variety of photodetectors, thus enabling attractive applications such as bio-imaging, time-of-flight sensors and LiDAR. The experimental results are supported by numerical simulations and effective medium theory that unveil the mechanisms that lead to the optical response of the device. It is also shown how the polarization dependence of the structure can be used to determine very accurately the polarization of incoming light.
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5
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Han X, Lu X, Li PH, Wang S, Schalek R, Meirovitch Y, Lin Z, Adhinarta J, Berger D, Wu Y, Fang T, Meral ES, Asraf S, Ploegh H, Pfister H, Wei D, Jain V, Trimmer JS, Lichtman JW. Multiplexed volumetric CLEM enabled by antibody derivatives provides new insights into the cytology of the mouse cerebellar cortex. RESEARCH SQUARE 2023:rs.3.rs-3121892. [PMID: 37461609 PMCID: PMC10350204 DOI: 10.21203/rs.3.rs-3121892/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Mapping neuronal networks that underlie behavior has become a central focus in neuroscience. While serial section electron microscopy (ssEM) can reveal the fine structure of neuronal networks (connectomics), it does not provide the molecular information that helps identify cell types or their functional properties. Volumetric correlated light and electron microscopy (vCLEM) combines ssEM and volumetric fluorescence microscopy to incorporate molecular labeling into ssEM datasets. We developed an approach that uses small fluorescent single-chain variable fragment (scFv) immuno-probes to perform multiplexed detergent-free immuno-labeling and ssEM on the same samples. We generated eight such fluorescent scFvs that targeted useful markers for brain studies (green fluorescent protein, glial fibrillary acidic protein, calbindin, parvalbumin, voltage-gated potassium channel subfamily A member 2, vesicular glutamate transporter 1, postsynaptic density protein 95, and neuropeptide Y). To test the vCLEM approach, six different fluorescent probes were imaged in a sample of the cortex of a cerebellar lobule (Crus 1), using confocal microscopy with spectral unmixing, followed by ssEM imaging of the same sample. The results show excellent ultrastructure with superimposition of the multiple fluorescence channels. Using this approach we could document a poorly described cell type in the cerebellum, two types of mossy fiber terminals, and the subcellular localization of one type of ion channel. Because scFvs can be derived from existing monoclonal antibodies, hundreds of such probes can be generated to enable molecular overlays for connectomic studies.
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Affiliation(s)
- Xiaomeng Han
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
| | - Xiaotang Lu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
| | | | - Shuohong Wang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
| | - Richard Schalek
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
| | - Yaron Meirovitch
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
| | - Zudi Lin
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Jason Adhinarta
- Computer Science Department, Boston College, Chestnut Hill, MA
| | - Daniel Berger
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
| | - Yuelong Wu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
| | - Tao Fang
- Program of Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
| | | | - Shadnan Asraf
- School of Public Health, University of Massachusetts Amherst, Amherst, MA
| | - Hidde Ploegh
- Program of Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
| | - Hanspeter Pfister
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Donglai Wei
- Computer Science Department, Boston College, Chestnut Hill, MA
| | | | - James S. Trimmer
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA
| | - Jeff W. Lichtman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
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6
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Han X, Lu X, Li PH, Wang S, Schalek R, Meirovitch Y, Lin Z, Adhinarta J, Berger D, Wu Y, Fang T, Meral ES, Asraf S, Ploegh H, Pfister H, Wei D, Jain V, Trimmer JS, Lichtman JW. Multiplexed Volumetric CLEM enabled by antibody derivatives provides new insights into the cytology of the mouse cerebellar cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.20.540091. [PMID: 37292964 PMCID: PMC10245788 DOI: 10.1101/2023.05.20.540091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mapping neuronal networks that underlie behavior has become a central focus in neuroscience. While serial section electron microscopy (ssEM) can reveal the fine structure of neuronal networks (connectomics), it does not provide the molecular information that helps identify cell types or their functional properties. Volumetric correlated light and electron microscopy (vCLEM) combines ssEM and volumetric fluorescence microscopy to incorporate molecular labeling into ssEM datasets. We developed an approach that uses small fluorescent single-chain variable fragment (scFv) immuno-probes to perform multiplexed detergent-free immuno-labeling and serial electron microscopy on the same samples. We generated eight such fluorescent scFvs that targeted useful markers for brain studies (GFP, GFAP, calbindin, parvalbumin, Kv1.2, VGluT1, PSD-95, and neuropeptide Y). To test the vCLEM approach, six different fluorescent probes were imaged in a sample of the cortex of a cerebellar lobule (Crus 1), using confocal microscopy with linear unmixing, followed by ssEM imaging of the same sample. The results show excellent ultrastructure and superimposition of the different fluorescence channels. We document a poorly described cell type in the cerebellum, two types of mossy fiber terminals, and the subcellular localization of ion channels. Because scFvs can be derived from existing monoclonal antibodies, hundreds of such probes can be generated to enable a wide range of connectomic studies.
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7
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Wang P, Kitano M, Keomanee-Dizon K, Truong TV, Fraser SE, Cutrale F. A single-shot hyperspectral phasor camera for fast, multi-color fluorescence microscopy. CELL REPORTS METHODS 2023; 3:100441. [PMID: 37159674 PMCID: PMC10162951 DOI: 10.1016/j.crmeth.2023.100441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 11/16/2022] [Accepted: 03/09/2023] [Indexed: 05/11/2023]
Abstract
Hyperspectral fluorescence imaging improves multiplexed observations of biological samples by utilizing multiple color channels across the spectral range to compensate for spectral overlap between labels. Typically, spectral resolution comes at a cost of decreased detection efficiency, which both hampers imaging speed and increases photo-toxicity to the samples. Here, we present a high-speed, high-efficiency snapshot spectral acquisition method, based on optical compression of the fluorescence spectra via Fourier transform, that overcomes the challenges of discrete spectral sampling: single-shot hyperspectral phasor camera (SHy-Cam). SHy-Cam captures fluorescence spatial and spectral information in a single exposure with a standard scientific CMOS camera, with photon efficiency of over 80%, easily and with acquisition rates exceeding 30 datasets per second, making it a powerful tool for multi-color in vivo imaging. Its simple design, using readily available optical components, and its easy integration provide a low-cost solution for multi-color fluorescence imaging with increased efficiency and speed.
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Affiliation(s)
- Pu Wang
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Masahiro Kitano
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Kevin Keomanee-Dizon
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Thai V. Truong
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Scott E. Fraser
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Francesco Cutrale
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
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8
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Chen L, Li R, Zhang Y, Xu Y, Chen J, Wang L, Zhu H, Zhang M, Zhang H. In Situ Visualization of Membrane Fouling Evolution during Ultrafiltration Using Label-Free Hyperspectral Light Sheet Fluorescence Imaging. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4533-4542. [PMID: 36869003 DOI: 10.1021/acs.est.2c08731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Profound understanding of fouling behaviors and underlying mechanisms is fundamentally important for fouling control in membrane-based environmental applications. Therefore, it entails novel noninvasive analytical approaches for in situ characterizing the formation and development of membrane fouling processes. This work presents a characterization approach based on hyperspectral light sheet fluorescence microscopy (HSPEC-LSFM), which is capable of discriminating various foulants and providing their 2-dimensional/3-dimensional spatial distributions on/in membranes in a label-free manner. A fast, highly sensitive and noninvasive imaging platform was established by developing a HSPEC-LSFM system and further extending it to incorporate a laboratory-scale pressure-driven membrane filtration system. Hyperspectral data sets with a spectral resolution of ∼1.1 nm and spatial resolution of ∼3 μm as well as the temporal resolution of ∼8 s/plane were obtained, and the fouling formation and development process of foulants onto membrane surfaces, within the pores and on the pore walls were clearly observed during the ultrafiltration of protein and humic substances solutions. Pore blocking/constriction at short times while cake growth/concentration polarization at longer times was found to have coupled effects for the flux decline in these filtration tests, and yet the contribution of each effect as well as the transition of the governing mechanisms was found distinct. These results demonstrate in situ label-free characterization of membrane fouling evolution with the recognition of foulant species during filtration and provide new insights into membrane fouling. This work offers a powerful tool to investigate dynamic processes for a wide range of membrane-based explorations.
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Affiliation(s)
- Lingling Chen
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118, China
| | - Renjian Li
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118, China
- School of Electronic and Information Engineering, Beihang University, Beijing, 100191, China
| | - Yang Zhang
- State Key Laboratory of Separation Membranes and Membrane Processes, School of Environmental Science and Engineering, Tiangong University, Tianjin, 300387, China
| | - Yizhi Xu
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118, China
| | - Jiajun Chen
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118, China
| | - Lili Wang
- Beijing Memtech Environmental Technology Ltd. Co, Beijing, 100102, China
| | - Haiou Zhu
- College of New Materials and New Energies, Shenzhen Technology University, Shenzhen, 518118, China
| | - Meng Zhang
- School of Electronic and Information Engineering, Beihang University, Beijing, 100191, China
| | - Hongwei Zhang
- State Key Laboratory of Separation Membranes and Membrane Processes, School of Environmental Science and Engineering, Tiangong University, Tianjin, 300387, China
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9
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Chiang HJ, Koo DES, Kitano M, Burkitt S, Unruh JR, Zavaleta C, Trinh LA, Fraser SE, Cutrale F. HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence. Nat Methods 2023; 20:248-258. [PMID: 36658278 PMCID: PMC9911352 DOI: 10.1038/s41592-022-01751-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/13/2022] [Indexed: 01/21/2023]
Abstract
The expansion of fluorescence bioimaging toward more complex systems and geometries requires analytical tools capable of spanning widely varying timescales and length scales, cleanly separating multiple fluorescent labels and distinguishing these labels from background autofluorescence. Here we meet these challenging objectives for multispectral fluorescence microscopy, combining hyperspectral phasors and linear unmixing to create Hybrid Unmixing (HyU). HyU is efficient and robust, capable of quantitative signal separation even at low illumination levels. In dynamic imaging of developing zebrafish embryos and in mouse tissue, HyU was able to cleanly and efficiently unmix multiple fluorescent labels, even in demanding volumetric timelapse imaging settings. HyU permits high dynamic range imaging, allowing simultaneous imaging of bright exogenous labels and dim endogenous labels. This enables coincident studies of tagged components, cellular behaviors and cellular metabolism within the same specimen, providing more accurate insights into the orchestrated complexity of biological systems.
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Affiliation(s)
- Hsiao Ju Chiang
- grid.42505.360000 0001 2156 6853Translational Imaging Center, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Department of Biomedical Engineering, University of Southern California, Los Angeles, CA USA
| | - Daniel E. S. Koo
- grid.42505.360000 0001 2156 6853Translational Imaging Center, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Department of Biomedical Engineering, University of Southern California, Los Angeles, CA USA
| | - Masahiro Kitano
- grid.42505.360000 0001 2156 6853Translational Imaging Center, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Molecular and Computational Biology, University of Southern California, Los Angeles, CA USA
| | - Sean Burkitt
- grid.42505.360000 0001 2156 6853Department of Biomedical Engineering, University of Southern California, Los Angeles, CA USA
| | - Jay R. Unruh
- grid.250820.d0000 0000 9420 1591Stowers Institute for Medical Research, Kansas City, MO USA
| | - Cristina Zavaleta
- grid.42505.360000 0001 2156 6853Department of Biomedical Engineering, University of Southern California, Los Angeles, CA USA
| | - Le A. Trinh
- grid.42505.360000 0001 2156 6853Translational Imaging Center, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Molecular and Computational Biology, University of Southern California, Los Angeles, CA USA
| | - Scott E. Fraser
- grid.42505.360000 0001 2156 6853Translational Imaging Center, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Department of Biomedical Engineering, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Molecular and Computational Biology, University of Southern California, Los Angeles, CA USA
| | - Francesco Cutrale
- Translational Imaging Center, University of Southern California, Los Angeles, CA, USA. .,Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA.
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10
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Cui Q, Park J, Lee J, Wang Z, Gao L. Tunable image projection spectrometry. BIOMEDICAL OPTICS EXPRESS 2022; 13:6457-6469. [PMID: 36589580 PMCID: PMC9774845 DOI: 10.1364/boe.477752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/05/2022] [Accepted: 11/06/2022] [Indexed: 06/17/2023]
Abstract
We present tunable image projection spectrometry (TIPS), a Fourier-domain line-scan spectral imager with a tunable compression ratio. Compared to state-of-the-art spatial-domain pushbroom hyperspectral cameras, TIPS requires much fewer measurements and provides a higher light throughput. Using a rotating Dove prism and a cylindrical field lens, TIPS scans an input scene in the Fourier domain and captures a subset of multi-angled one-dimensional (1D) en face projections of the input scene, allowing a tailored data compression ratio for a given scene. We demonstrate the spectral imaging capability of TIPS with a hematoxylin and eosin (H&E) stained pathology slide. Moreover, we showed the spectral information obtained can be further converted to depths when combining TIPS with a low-coherence full-field spectral-domain interferometer.
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11
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Chen K, Li W, Xu K. Super-multiplexing excitation spectral microscopy with multiple fluorescence bands. BIOMEDICAL OPTICS EXPRESS 2022; 13:6048-6060. [PMID: 36733753 PMCID: PMC9872899 DOI: 10.1364/boe.473241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 06/18/2023]
Abstract
Fluorescence microscopy, with high molecular specificity and selectivity, is a valuable tool for studying complex biological systems and processes. However, the ability to distinguish a large number of distinct subcellular structures in a single sample is impeded by the broad spectra of molecular fluorescence. We have recently shown that excitation spectral microscopy provides a powerful means to unmix up to six fluorophores in a single fluorescence band. Here, by working with multiple fluorescence bands, we extend this approach to the simultaneous imaging of up to ten targets, with the potential for further expansions. By covering the excitation/emission bandwidth across the full visible range, an ultra-broad 24-wavelength excitation scheme is established through frame-synchronized scanning of the excitation wavelength from a white lamp via an acousto-optic tunable filter (AOTF), so that full-frame excitation-spectral images are obtained every 24 camera frames, offering superior spectral information and multiplexing capability. With numerical simulations, we validate the concurrent imaging of 10 fluorophores spanning the visible range to achieve exceptionally low (∼0.5%) crosstalks. For cell imaging experiments, we demonstrate unambiguous identification of up to eight different intracellular structures labeled by common fluorophores of substantial spectral overlap with minimal color crosstalks. We thus showcase an easy-to-implement, cost-effective microscopy system for visualizing complex cellular components with more colors and lower crosstalks.
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Affiliation(s)
- Kun Chen
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Wan Li
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ke Xu
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
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12
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van Ineveld RL, Collot R, Román MB, Pagliaro A, Bessler N, Ariese HCR, Kleinnijenhuis M, Kool M, Alieva M, Chuva de Sousa Lopes SM, Wehrens EJ, Rios AC. Multispectral confocal 3D imaging of intact healthy and tumor tissue using mLSR-3D. Nat Protoc 2022; 17:3028-3055. [PMID: 36180532 DOI: 10.1038/s41596-022-00739-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 06/16/2022] [Indexed: 11/09/2022]
Abstract
Revealing the 3D composition of intact tissue specimens is essential for understanding cell and organ biology in health and disease. State-of-the-art 3D microscopy techniques aim to capture tissue volumes on an ever-increasing scale, while also retaining sufficient resolution for single-cell analysis. Furthermore, spatial profiling through multi-marker imaging is fast developing, providing more context and better distinction between cell types. Following these lines of technological advance, we here present a protocol based on FUnGI (fructose, urea and glycerol clearing solution for imaging) optical clearing of tissue before multispectral large-scale single-cell resolution 3D (mLSR-3D) imaging, which implements 'on-the-fly' linear unmixing of up to eight fluorophores during a single acquisition. Our protocol removes the need for repetitive illumination, thereby allowing larger volumes to be scanned with better image quality in less time, also reducing photo-bleaching and file size. To aid in the design of multiplex antibody panels, we provide a fast and manageable intensity equalization assay with automated analysis to design a combination of markers with balanced intensities suitable for mLSR-3D. We demonstrate effective mLSR-3D imaging of various tissues, including patient-derived organoids and xenografted tumors, and, furthermore, describe an optimized workflow for mLSR-3D imaging of formalin-fixed paraffin-embedded samples. Finally, we provide essential steps for 3D image data processing, including shading correction that does not require pre-acquired shading references and 3D inhomogeneity correction to correct fluorescence artefacts often afflicting 3D datasets. Together, this provides a one-week protocol for eight-fluorescent-marker 3D visualization and exploration of intact tissue of various origins at single-cell resolution.
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Affiliation(s)
- Ravian L van Ineveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Raphaël Collot
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Mario Barrera Román
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Anna Pagliaro
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Nils Bessler
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Hendrikus C R Ariese
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Michiel Kleinnijenhuis
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center DKFZ and German Cancer Consortium DKTK, Heidelberg, Germany
| | - Maria Alieva
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | | | - Ellen J Wehrens
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands. .,Oncode Institute, Utrecht, the Netherlands.
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13
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Pterygium and Ocular Surface Squamous Neoplasia: Optical Biopsy Using a Novel Autofluorescence Multispectral Imaging Technique. Cancers (Basel) 2022; 14:cancers14061591. [PMID: 35326744 PMCID: PMC8946656 DOI: 10.3390/cancers14061591] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
In this study, differentiation of pterygium vs. ocular surface squamous neoplasia based on multispectral autofluorescence imaging technique was investigated. Fifty (N = 50) patients with histopathological diagnosis of pterygium (PTG) and/or ocular surface squamous neoplasia (OSSN) were recruited. Fixed unstained biopsy specimens were imaged by multispectral microscopy. Tissue autofluorescence images were obtained with a custom-built fluorescent microscope with 59 spectral channels, each with specific excitation and emission wavelength ranges, suitable for the most abundant tissue fluorophores such as elastin, flavins, porphyrin, and lipofuscin. Images were analyzed using a new classification framework called fused-classification, designed to minimize interpatient variability, as an established support vector machine learning method. Normal, PTG, and OSSN regions were automatically detected and delineated, with accuracy evaluated against expert assessment by a specialist in OSSN pathology. Signals from spectral channels yielding signals from elastin, flavins, porphyrin, and lipofuscin were significantly different between regions classified as normal, PTG, and OSSN (p < 0.01). Differential diagnosis of PTG/OSSN and normal tissue had accuracy, sensitivity, and specificity of 88 ± 6%, 84 ± 10% and 91 ± 6%, respectively. Our automated diagnostic method generated maps of the reasonably well circumscribed normal/PTG and OSSN interface. PTG and OSSN margins identified by our automated analysis were in close agreement with the margins found in the H&E sections. Such a map can be rapidly generated on a real time basis and potentially used for intraoperative assessment.
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14
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Crombez S, Leclerc P, Ray C, Ducros N. Computational hyperspectral light-sheet microscopy. OPTICS EXPRESS 2022; 30:4856-4866. [PMID: 35209458 DOI: 10.1364/oe.442043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
We describe a computational light-sheet microscope designed for hyperspectral acquisition at high spectral resolution. The fluorescence light emitted from the full field-of-view is focused along the entrance slit of an imaging spectrometer using a cylindrical lens. To acquire the spatial dimension orthogonal to the slit of the spectrometer, we propose to illuminate the specimen with a sequence of structured light patterns and to solve the image reconstruction problem. Beam shaping is obtained simply using a digital micromirror device in conjunction with a traditional selective plane illumination microscopy setup. We demonstrate the feasibility of this method and report the first results in vivo in hydra specimens labeled using two fluorophores.
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15
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Delgado-Rodriguez P, Brooks CJ, Vaquero JJ, Muñoz-Barrutia A. Innovations in ex vivo Light Sheet Fluorescence Microscopy. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 168:37-51. [PMID: 34293338 DOI: 10.1016/j.pbiomolbio.2021.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Light Sheet Fluorescence Microscopy (LSFM) has revolutionized how optical imaging of biological specimens can be performed as this technique allows to produce 3D fluorescence images of entire samples with a high spatiotemporal resolution. In this manuscript, we aim to provide readers with an overview of the field of LSFM on ex vivo samples. Recent advances in LSFM architectures have made the technique widely accessible and have improved its acquisition speed and resolution, among other features. These developments are strongly supported by quantitative analysis of the huge image volumes produced thanks to the boost in computational capacities, the advent of Deep Learning techniques, and by the combination of LSFM with other imaging modalities. Namely, LSFM allows for the characterization of biological structures, disease manifestations and drug effectivity studies. This information can ultimately serve to develop novel diagnostic procedures, treatments and even to model the organs physiology in healthy and pathological conditions.
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Affiliation(s)
- Pablo Delgado-Rodriguez
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain
| | - Claire Jordan Brooks
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain
| | - Juan José Vaquero
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Arrate Muñoz-Barrutia
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.
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16
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Williams GOS, Williams E, Finlayson N, Erdogan AT, Wang Q, Fernandes S, Akram AR, Dhaliwal K, Henderson RK, Girkin JM, Bradley M. Full spectrum fluorescence lifetime imaging with 0.5 nm spectral and 50 ps temporal resolution. Nat Commun 2021; 12:6616. [PMID: 34785666 PMCID: PMC8595732 DOI: 10.1038/s41467-021-26837-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 10/15/2021] [Indexed: 11/23/2022] Open
Abstract
The use of optical techniques to interrogate wide ranging samples from semiconductors to biological tissue for rapid analysis and diagnostics has gained wide adoption over the past decades. The desire to collect ever more spatially, spectrally and temporally detailed optical signatures for sample characterization has specifically driven a sharp rise in new optical microscopy technologies. Here we present a high-speed optical scanning microscope capable of capturing time resolved images across 512 spectral and 32 time channels in a single acquisition with the potential for ~0.2 frames per second (256 × 256 image pixels). Each pixel in the resulting images contains a detailed data cube for the study of diverse time resolved light driven phenomena. This is enabled by integration of system control electronics and on-chip processing which overcomes the challenges presented by high data volume and low imaging speed, often bottlenecks in previous systems. High data volumes from multidimensional imaging techniques can lead to slow collection and processing times. Here, the authors implement multispectral fluorescence lifetime imaging microscopy (FLIM) that uses time-correlated photon counting technology to reach simultaneously high imaging rates combined with high spectral and temporal resolution.
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Affiliation(s)
- Gareth O S Williams
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Elvira Williams
- Centre for Advanced Instrumentation, Department of Physics, Durham University, South Road, Durham, DH1 3LE, UK
| | - Neil Finlayson
- School of Engineering, Institute for Integrated Micro and Nano Systems, University of Edinburgh, King's Buildings, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK
| | - Ahmet T Erdogan
- School of Engineering, Institute for Integrated Micro and Nano Systems, University of Edinburgh, King's Buildings, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK
| | - Qiang Wang
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Susan Fernandes
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Ahsan R Akram
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Kev Dhaliwal
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Robert K Henderson
- School of Engineering, Institute for Integrated Micro and Nano Systems, University of Edinburgh, King's Buildings, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK
| | - John M Girkin
- Centre for Advanced Instrumentation, Department of Physics, Durham University, South Road, Durham, DH1 3LE, UK.
| | - Mark Bradley
- School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
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17
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Dorozynska K, Ek S, Kornienko V, Andersson D, Andersson A, Ehn A, Kristensson E. Snapshot multicolor fluorescence imaging using double multiplexing of excitation and emission on a single detector. Sci Rep 2021; 11:20454. [PMID: 34650144 PMCID: PMC8517015 DOI: 10.1038/s41598-021-99670-6] [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: 06/22/2021] [Accepted: 09/27/2021] [Indexed: 12/02/2022] Open
Abstract
Fluorescence-based multispectral imaging of rapidly moving or dynamic samples requires both fast two-dimensional data acquisition as well as sufficient spectral sensitivity for species separation. As the number of fluorophores in the experiment increases, meeting both these requirements becomes technically challenging. Although several solutions for fast imaging of multiple fluorophores exist, they all have one main restriction; they rely solely on spectrally resolving either the excitation- or the emission characteristics of the fluorophores. This inability directly limits how many fluorophores existing methods can simultaneously distinguish. Here we present a snapshot multispectral imaging approach that not only senses the excitation and emission characteristics of the probed fluorophores but also all cross term combinations of excitation and emission. To the best of the authors’ knowledge, this is the only snapshot multispectral imaging method that has this ability, allowing us to even sense and differentiate between light of equal wavelengths emitted from the same fluorescing species but where the signal components stem from different excitation sources. The current implementation of the technique allows us to simultaneously gather 24 different spectral images on a single detector, from which we demonstrate the ability to visualize and distinguish up to nine fluorophores within the visible wavelength range.
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Affiliation(s)
| | - Simon Ek
- Department of Combustion Physics, Lund University, 22363, Lund, Sweden
| | - Vassily Kornienko
- Department of Combustion Physics, Lund University, 22363, Lund, Sweden
| | - David Andersson
- Department of Combustion Physics, Lund University, 22363, Lund, Sweden
| | | | - Andreas Ehn
- Department of Combustion Physics, Lund University, 22363, Lund, Sweden
| | - Elias Kristensson
- Department of Combustion Physics, Lund University, 22363, Lund, Sweden.
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18
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Out-of-Phase Imaging after Optical Modulation (OPIOM) for Multiplexed Fluorescence Imaging Under Adverse Optical Conditions. Methods Mol Biol 2021; 2350:191-227. [PMID: 34331287 DOI: 10.1007/978-1-0716-1593-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescence imaging has become a powerful tool for observations in biology. Yet it has also encountered limitations to overcome optical interferences of ambient light, autofluorescence, and spectrally interfering fluorophores. In this account, we first examine the current approaches which address these limitations. Then we more specifically report on Out-of-Phase Imaging after Optical Modulation (OPIOM), which has proved attractive for highly selective multiplexed fluorescence imaging even under adverse optical conditions. After exposing the OPIOM principle, we detail the protocols for successful OPIOM implementation.
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19
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Hedde PN, Cinco R, Malacrida L, Kamaid A, Gratton E. Phasor-based hyperspectral snapshot microscopy allows fast imaging of live, three-dimensional tissues for biomedical applications. Commun Biol 2021; 4:721. [PMID: 34117344 PMCID: PMC8195998 DOI: 10.1038/s42003-021-02266-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/26/2021] [Indexed: 01/31/2023] Open
Abstract
Hyperspectral imaging is highly sought after in many fields including mineralogy and geology, environment and agriculture, astronomy and, importantly, biomedical imaging and biological fluorescence. We developed ultrafast phasor-based hyperspectral snapshot microscopy based on sine/cosine interference filters for biomedical imaging not feasible with conventional hyperspectral detection methods. Current approaches rely on slow spatial or spectral scanning limiting their application in living biological tissues, while faster snapshot methods such as image mapping spectrometry and multispectral interferometry are limited in spatial and/or spectral resolution, are computationally demanding, and imaging devices are very expensive to manufacture. Leveraging light sheet microscopy, phasor-based hyperspectral snapshot microscopy improved imaging speed 10-100 fold which, combined with minimal light exposure and high detection efficiency, enabled hyperspectral metabolic imaging of live, three-dimensional mouse tissues not feasible with other methods. As a fit-free method that does not require any a priori information often unavailable in complex and evolving biological systems, the rule of linear combinations of the phasor could spectrally resolve subtle differences between cell types in the developing zebrafish retina and spectrally separate and track multiple organelles in 3D cultured cells over time. The sine/cosine snapshot method is adaptable to any microscope or imaging device thus making hyperspectral imaging and fit-free analysis based on linear combinations broadly available to researchers and the public.
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Affiliation(s)
- Per Niklas Hedde
- grid.266093.80000 0001 0668 7243Laboratory for Fluorescence Dynamics, University of California, Irvine, CA USA ,grid.266093.80000 0001 0668 7243Department of Pharmaceutical Sciences, University of California, Irvine, CA USA ,grid.266093.80000 0001 0668 7243Beckman Laser Institute & Medical Clinic, University of California, Irvine, CA USA
| | - Rachel Cinco
- grid.266093.80000 0001 0668 7243Laboratory for Fluorescence Dynamics, University of California, Irvine, CA USA
| | - Leonel Malacrida
- grid.11630.350000000121657640Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay ,grid.11630.350000000121657640Advanced Bioimaging Unit, Institut Pasteur of Montevideo and Universidad de la República, Montevideo, Uruguay
| | - Andrés Kamaid
- grid.11630.350000000121657640Advanced Bioimaging Unit, Institut Pasteur of Montevideo and Universidad de la República, Montevideo, Uruguay
| | - Enrico Gratton
- grid.266093.80000 0001 0668 7243Laboratory for Fluorescence Dynamics, University of California, Irvine, CA USA ,grid.266093.80000 0001 0668 7243Beckman Laser Institute & Medical Clinic, University of California, Irvine, CA USA
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20
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Juntunen C, Woller IM, Sung Y. Hyperspectral Three-Dimensional Fluorescence Imaging Using Snapshot Optical Tomography. SENSORS 2021; 21:s21113652. [PMID: 34073956 PMCID: PMC8197295 DOI: 10.3390/s21113652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/14/2021] [Accepted: 05/21/2021] [Indexed: 12/18/2022]
Abstract
Hyperspectral three-dimensional (3D) imaging can provide both 3D structural and functional information of a specimen. The imaging throughput is typically very low due to the requirement of scanning mechanisms for different depths and wavelengths. Here we demonstrate hyperspectral 3D imaging using Snapshot projection optical tomography (SPOT) and Fourier-transform spectroscopy (FTS). SPOT allows us to instantaneously acquire the projection images corresponding to different viewing angles, while FTS allows us to perform hyperspectral imaging at high spectral resolution. Using fluorescent beads and sunflower pollens, we demonstrate the imaging performance of the developed system.
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Affiliation(s)
- Cory Juntunen
- College of Engineering and Applied Science, University of Wisconsin-Milwaukee, 3200 N Cramer St, Milwaukee, WI 53211, USA;
| | - Isabel M. Woller
- College of Health Sciences, University of Wisconsin-Milwaukee, 2025 E Newport Ave, Milwaukee, WI 53211, USA;
| | - Yongjin Sung
- College of Engineering and Applied Science, University of Wisconsin-Milwaukee, 3200 N Cramer St, Milwaukee, WI 53211, USA;
- Correspondence:
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21
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Mishra D, Hurbon H, Wang J, Wang ST, Du T, Wu Q, Kim D, Basir S, Cao Q, Zhang H, Xu K, Yu A, Zhang Y, Huang Y, Garnett R, Gerasimchuk-Djordjevic M, Berezin MY. IDCube Lite: Free Interactive Discovery Cube software for multi- and hyperspectral applications. JOURNAL OF SPECTRAL IMAGING 2021; 10:a1. [PMID: 34484655 PMCID: PMC8409277 DOI: 10.1255/jsi.2021.a1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Multi- and hyperspectral imaging modalities encompass a growing number of spectral techniques that find many applications in geospatial, biomedical, machine vision and other fields. The rapidly increasing number of applications requires convenient easy-to-navigate software that can be used by new and experienced users to analyse data, and develop, apply and deploy novel algorithms. Herein, we present our platform, IDCube Lite, an Interactive Discovery Cube that performs essential operations in hyperspectral data analysis to realise the full potential of spectral imaging. The strength of the software lies in its interactive features that enable the users to optimise parameters and obtain visual input for the user in a way not previously accessible with other software packages. The entire software can be operated without any prior programming skills allowing interactive sessions of raw and processed data. IDCube Lite, a free version of the software described in the paper, has many benefits compared to existing packages and offers structural flexibility to discover new, hidden features that allow users to integrate novel computational methods.
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Affiliation(s)
- Deependra Mishra
- Department of Radiology, Washington University School of Medicine, 4515 McKinley Ave, St Louis, MO 63110, USA
| | - Helena Hurbon
- Department of Radiology, Washington University School of Medicine, 4515 McKinley Ave, St Louis, MO 63110, USA
- HSpeQ LLC, 4340 Duncan Ave, St Louis, MO 63110, USA
| | - John Wang
- Department of Radiology, Washington University School of Medicine, 4515 McKinley Ave, St Louis, MO 63110, USA
- HSpeQ LLC, 4340 Duncan Ave, St Louis, MO 63110, USA
| | - Steven T Wang
- Department of Radiology, Washington University School of Medicine, 4515 McKinley Ave, St Louis, MO 63110, USA
- HSpeQ LLC, 4340 Duncan Ave, St Louis, MO 63110, USA
| | - Tommy Du
- Department of Radiology, Washington University School of Medicine, 4515 McKinley Ave, St Louis, MO 63110, USA
| | - Qian Wu
- Department of Radiology, Washington University School of Medicine, 4515 McKinley Ave, St Louis, MO 63110, USA
| | - David Kim
- Department of Radiology, Washington University School of Medicine, 4515 McKinley Ave, St Louis, MO 63110, USA
| | - Shiva Basir
- Department of Radiology, Washington University School of Medicine, 4515 McKinley Ave, St Louis, MO 63110, USA
| | - Qian Cao
- Department of Radiology, Washington University School of Medicine, 4515 McKinley Ave, St Louis, MO 63110, USA
| | - Hairong Zhang
- Department of Radiology, Washington University School of Medicine, 4515 McKinley Ave, St Louis, MO 63110, USA
| | - Kathleen Xu
- Department of Radiology, Washington University School of Medicine, 4515 McKinley Ave, St Louis, MO 63110, USA
| | - Andy Yu
- Department of Radiology, Washington University School of Medicine, 4515 McKinley Ave, St Louis, MO 63110, USA
| | - Yifan Zhang
- Department of Radiology, Washington University School of Medicine, 4515 McKinley Ave, St Louis, MO 63110, USA
| | - Yunshen Huang
- Department of Radiology, Washington University School of Medicine, 4515 McKinley Ave, St Louis, MO 63110, USA
| | - Roman Garnett
- Department of Computer Science and Engineering, Washington University, 1 Brookings Hall, St Louis, MO 63110, USA
| | | | - Mikhail Y Berezin
- Department of Radiology, Washington University School of Medicine, 4515 McKinley Ave, St Louis, MO 63110, USA
- HSpeQ LLC, 4340 Duncan Ave, St Louis, MO 63110, USA
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22
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Hugelier S, Van den Eynde R, Vandenberg W, Dedecker P. Fluorophore unmixing based on bleaching and recovery kinetics using MCR-ALS. Talanta 2021; 226:122117. [PMID: 33676672 DOI: 10.1016/j.talanta.2021.122117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 02/03/2023]
Abstract
Fluorescence microscopy is a key technology in the life sciences, though its performance is constrained by the number of labels that can be recorded. We propose to use the kinetics of fluorophore photodestruction and subsequent fluorescence recovery to distinguish multiple spectrally-overlapping emitters in fixed cells, thus enhancing the information that can be obtained from a single measurement. We show that the data can be directly processed using multivariate curve resolution - alternating least squares (MCR-ALS) to deliver distinct images for each fluorophore in their local environment, and apply this methodology to membrane imaging using DiBAC4(3) and concanavalin A - Alexa Fluor 488 as the fluorophores. We find that the DiBAC4(3) displays two distinct degradation/recovery kinetics that correspond to two different label distributions, allowing us to simultaneously distinguish three different fluorescence distributions from two spectrally overlapping fluorophores. We expect that our approach will scale to other dynamically-binding dyes, leading to similarly increased multiplexing capability.
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Affiliation(s)
- S Hugelier
- Laboratory for Nanobiology, KU Leuven, B-3001 Leuven, Belgium.
| | - R Van den Eynde
- Laboratory for Nanobiology, KU Leuven, B-3001 Leuven, Belgium
| | - W Vandenberg
- Laboratory for Nanobiology, KU Leuven, B-3001 Leuven, Belgium; Univ. Lille, CNRS, Laboratoire de Spectroscopie pour Les Interactions, La Réactivité et L'Environnement (LASIRE), F-59000 Lille, France
| | - P Dedecker
- Laboratory for Nanobiology, KU Leuven, B-3001 Leuven, Belgium
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23
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A versatile deep learning architecture for classification and label-free prediction of hyperspectral images. NAT MACH INTELL 2021; 3:306-315. [PMID: 34676358 PMCID: PMC8528004 DOI: 10.1038/s42256-021-00309-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hyperspectral imaging is a technique that provides rich chemical or compositional information not regularly available to traditional imaging modalities such as intensity imaging or color imaging based on the reflection, transmission, or emission of light. Analysis of hyperspectral imaging often relies on machine learning methods to extract information. Here, we present a new flexible architecture, the U-within-U-Net, that can perform classification, segmentation, and prediction of orthogonal imaging modalities on a variety of hyperspectral imaging techniques. Specifically, we demonstrate feature segmentation and classification on the Indian Pines hyperspectral dataset and simultaneous location prediction of multiple drugs in mass spectrometry imaging of rat liver tissue. We further demonstrate label-free fluorescence image prediction from hyperspectral stimulated Raman scattering microscopy images. The applicability of the U-within-U-Net architecture on diverse datasets with widely varying input and output dimensions and data sources suggest that it has great potential in advancing the use of hyperspectral imaging across many different application areas ranging from remote sensing, to medical imaging, to microscopy.
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24
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Dong X, Tong G, Song X, Xiao X, Yu Y. DMD-based hyperspectral microscopy with flexible multiline parallel scanning. MICROSYSTEMS & NANOENGINEERING 2021; 7:68. [PMID: 34567780 PMCID: PMC8433375 DOI: 10.1038/s41378-021-00299-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 05/16/2023]
Abstract
As one of the most common hyperspectral microscopy (HSM) techniques, line-scanning HSM is currently utilized in many fields. However, its scanning efficiency is still considered to be inadequate since many biological and chemical processes occur too rapidly to be captured. Accordingly, in this work, a digital micromirror device (DMD) based on microelectromechanical systems (MEMS) is utilized to demonstrate a flexible multiline scanning HSM system. To the best of our knowledge, this is the first line-scanning HSM system in which the number of scanning lines N can be tuned by simply changing the DMD's parallel scanning units according to diverse applications. This brilliant strategy of effortless adjustability relies only on on-chip scanning methods and totally exploits the benefits of parallelization, aiming to achieve nearly an N-time improvement in the detection efficiency and an N-time decrease in the scanning time and data volume compared with the single-line method under the same operating conditions. To validate this, we selected a few samples of different spectral wavebands to perform reflection imaging, transmission imaging, and fluorescence imaging with varying numbers of scanning lines. The results show the great potential of our DMD-based HSM system for the rapid development of cellular biology, material analysis, and so on. In addition, its on-chip scanning process eliminates the inherent microscopic architecture, making the whole system compact, lightweight, portable, and not subject to site constraints.
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Affiliation(s)
- Xue Dong
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen, 518057 China
- Ningbo Institute of Northwestern Polytechnical University, Ningbo, 315103 China
- Key Laboratory of Micro/Nano Systems for Aerospace (Ministry of Education), Northwestern Polytechnical University, Xi’an, 710072 China
- Shaanxi Province Key Laboratory of Micro and Nano Electro-Mechanical Systems, Northwestern Polytechnical University, Xi’an, 710072 China
| | - Geng Tong
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen, 518057 China
- Ningbo Institute of Northwestern Polytechnical University, Ningbo, 315103 China
- Key Laboratory of Micro/Nano Systems for Aerospace (Ministry of Education), Northwestern Polytechnical University, Xi’an, 710072 China
- Shaanxi Province Key Laboratory of Micro and Nano Electro-Mechanical Systems, Northwestern Polytechnical University, Xi’an, 710072 China
| | - Xuankun Song
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen, 518057 China
- Ningbo Institute of Northwestern Polytechnical University, Ningbo, 315103 China
- Key Laboratory of Micro/Nano Systems for Aerospace (Ministry of Education), Northwestern Polytechnical University, Xi’an, 710072 China
- Shaanxi Province Key Laboratory of Micro and Nano Electro-Mechanical Systems, Northwestern Polytechnical University, Xi’an, 710072 China
| | - Xingchen Xiao
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen, 518057 China
- Ningbo Institute of Northwestern Polytechnical University, Ningbo, 315103 China
- Key Laboratory of Micro/Nano Systems for Aerospace (Ministry of Education), Northwestern Polytechnical University, Xi’an, 710072 China
- Shaanxi Province Key Laboratory of Micro and Nano Electro-Mechanical Systems, Northwestern Polytechnical University, Xi’an, 710072 China
| | - Yiting Yu
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen, 518057 China
- Ningbo Institute of Northwestern Polytechnical University, Ningbo, 315103 China
- Key Laboratory of Micro/Nano Systems for Aerospace (Ministry of Education), Northwestern Polytechnical University, Xi’an, 710072 China
- Shaanxi Province Key Laboratory of Micro and Nano Electro-Mechanical Systems, Northwestern Polytechnical University, Xi’an, 710072 China
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25
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Ochoa M, Rudkouskaya A, Yao R, Yan P, Barroso M, Intes X. High compression deep learning based single-pixel hyperspectral macroscopic fluorescence lifetime imaging in vivo. BIOMEDICAL OPTICS EXPRESS 2020; 11:5401-5424. [PMID: 33149959 PMCID: PMC7587256 DOI: 10.1364/boe.396771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/02/2020] [Accepted: 07/15/2020] [Indexed: 05/05/2023]
Abstract
Single pixel imaging frameworks facilitate the acquisition of high-dimensional optical data in biological applications with photon starved conditions. However, they are still limited to slow acquisition times and low pixel resolution. Herein, we propose a convolutional neural network for fluorescence lifetime imaging with compressed sensing at high compression (NetFLICS-CR), which enables in vivo applications at enhanced resolution, acquisition and processing speeds, without the need for experimental training datasets. NetFLICS-CR produces intensity and lifetime reconstructions at 128 × 128 pixel resolution over 16 spectral channels while using only up to 1% of the required measurements, therefore reducing acquisition times from ∼2.5 hours at 50% compression to ∼3 minutes at 99% compression. Its potential is demonstrated in silico, in vitro and for mice in vivo through the monitoring of receptor-ligand interactions in liver and bladder and further imaging of intracellular delivery of the clinical drug Trastuzumab to HER2-positive breast tumor xenografts. The data acquisition time and resolution improvement through NetFLICS-CR, facilitate the translation of single pixel macroscopic flurorescence lifetime imaging (SP-MFLI) for in vivo monitoring of lifetime properties and drug uptake.
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Affiliation(s)
- M. Ochoa
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - A. Rudkouskaya
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - R. Yao
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - P. Yan
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - M. Barroso
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - X. Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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26
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Totero Gongora JS, Olivieri L, Peters L, Tunesi J, Cecconi V, Cutrona A, Tucker R, Kumar V, Pasquazi A, Peccianti M. Route to Intelligent Imaging Reconstruction via Terahertz Nonlinear Ghost Imaging. MICROMACHINES 2020; 11:mi11050521. [PMID: 32443881 DOI: 10.1364/optica.381035] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/30/2020] [Accepted: 05/17/2020] [Indexed: 05/26/2023]
Abstract
Terahertz (THz) imaging is a rapidly emerging field, thanks to many potential applications in diagnostics, manufacturing, medicine and material characterisation. However, the relatively coarse resolution stemming from the large wavelength limits the deployment of THz imaging in micro- and nano-technologies, keeping its potential benefits out-of-reach in many practical scenarios and devices. In this context, single-pixel techniques are a promising alternative to imaging arrays, in particular when targeting subwavelength resolutions. In this work, we discuss the key advantages and practical challenges in the implementation of time-resolved nonlinear ghost imaging (TIMING), an imaging technique combining nonlinear THz generation with time-resolved time-domain spectroscopy detection. We numerically demonstrate the high-resolution reconstruction of semi-transparent samples, and we show how the Walsh-Hadamard reconstruction scheme can be optimised to significantly reduce the reconstruction time. We also discuss how, in sharp contrast with traditional intensity-based ghost imaging, the field detection at the heart of TIMING enables high-fidelity image reconstruction via low numerical-aperture detection. Even more striking-and to the best of our knowledge, an issue never tackled before-the general concept of "resolution" of the imaging system as the "smallest feature discernible" appears to be not well suited to describing the fidelity limits of nonlinear ghost-imaging systems. Our results suggest that the drop in reconstruction accuracy stemming from non-ideal detection conditions is complex and not driven by the attenuation of high-frequency spatial components (i.e., blurring) as in standard imaging. On the technological side, we further show how achieving efficient optical-to-terahertz conversion in extremely short propagation lengths is crucial regarding imaging performance, and we propose low-bandgap semiconductors as a practical framework to obtain THz emission from quasi-2D structures, i.e., structure in which the interaction occurs on a deeply subwavelength scale. Our results establish a comprehensive theoretical and experimental framework for the development of a new generation of terahertz hyperspectral imaging devices.
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Affiliation(s)
- Juan S Totero Gongora
- Emergent Photonics (EPic) Laboratory, Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
| | - Luana Olivieri
- Emergent Photonics (EPic) Laboratory, Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
| | - Luke Peters
- Emergent Photonics (EPic) Laboratory, Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
| | - Jacob Tunesi
- Emergent Photonics (EPic) Laboratory, Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
| | - Vittorio Cecconi
- Emergent Photonics (EPic) Laboratory, Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
| | - Antonio Cutrona
- Emergent Photonics (EPic) Laboratory, Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
| | - Robyn Tucker
- Emergent Photonics (EPic) Laboratory, Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
| | - Vivek Kumar
- Emergent Photonics (EPic) Laboratory, Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
| | - Alessia Pasquazi
- Emergent Photonics (EPic) Laboratory, Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
| | - Marco Peccianti
- Emergent Photonics (EPic) Laboratory, Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
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27
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Xu Z, Forsberg E, Guo Y, Cai F, He S. Light-Sheet Microscopy for Surface Topography Measurements and Quantitative Analysis. SENSORS 2020; 20:s20102842. [PMID: 32429437 PMCID: PMC7288151 DOI: 10.3390/s20102842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/06/2020] [Accepted: 05/13/2020] [Indexed: 12/13/2022]
Abstract
A novel light-sheet microscopy (LSM) system that uses the laser triangulation method to quantitatively calculate and analyze the surface topography of opaque samples is discussed. A spatial resolution of at least 10 μm in z-direction, 10 μm in x-direction and 25 μm in y-direction with a large field-of-view (FOV) is achieved. A set of sample measurements that verify the system′s functionality in various applications are presented. The system has a simple mechanical structure, such that the spatial resolution is easily improved by replacement of the objective, and a linear calibration formula, which enables convenient system calibration. As implemented, the system has strong potential for, e.g., industrial sample line inspections, however, since the method utilizes reflected/scattered light, it also has the potential for three-dimensional analysis of translucent and layered structures.
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Affiliation(s)
- Zhanpeng Xu
- Centre for Optical and Electromagnetic Research, National Engineering Research Center for Optical Instruments, Zhejiang Provincial Key Laboratory for Sensing Technologies, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310058, China; (Z.X.); (E.F.); (Y.G.)
| | - Erik Forsberg
- Centre for Optical and Electromagnetic Research, National Engineering Research Center for Optical Instruments, Zhejiang Provincial Key Laboratory for Sensing Technologies, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310058, China; (Z.X.); (E.F.); (Y.G.)
| | - Yang Guo
- Centre for Optical and Electromagnetic Research, National Engineering Research Center for Optical Instruments, Zhejiang Provincial Key Laboratory for Sensing Technologies, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310058, China; (Z.X.); (E.F.); (Y.G.)
| | - Fuhong Cai
- School of Biomedical Engineering, Hainan University, Haikou 570228, China;
| | - Sailing He
- Centre for Optical and Electromagnetic Research, National Engineering Research Center for Optical Instruments, Zhejiang Provincial Key Laboratory for Sensing Technologies, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310058, China; (Z.X.); (E.F.); (Y.G.)
- Correspondence: ; Tel.: +86-571-8820-6525
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28
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Keomanee-Dizon K, Fraser SE, Truong TV. A versatile, multi-laser twin-microscope system for light-sheet imaging. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:053703. [PMID: 32486724 PMCID: PMC7255815 DOI: 10.1063/1.5144487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/28/2020] [Indexed: 05/25/2023]
Abstract
Light-sheet microscopy offers faster imaging and reduced phototoxicity in comparison to conventional point-scanning microscopy, making it a preferred technique for imaging biological dynamics for durations of hours or days. Such extended imaging sessions pose a challenge, as it reduces the number of specimens that can be imaged in a given day. Here, we present a versatile light-sheet imaging instrument that combines two independently controlled microscope-twins, built so that they can share an ultrafast near-infrared laser and a bank of continuous-wave visible lasers, increasing the throughput and decreasing the cost. To permit a wide variety of specimens to be imaged, each microscope-twin provides flexible imaging parameters, including (i) operation in one-photon and/or two-photon excitation modes, (ii) delivery of one to three light-sheets via a trio of orthogonal excitation arms, (iii) sub-micron to micron imaging resolution, (iv) multicolor compatibility, and (v) upright (with provision for inverted) detection geometry. We offer a detailed description of the twin-microscope design to aid instrument builders who wish to construct and use similar systems. We demonstrate the instrument's versatility for biological investigation by performing fast imaging of the beating heart in an intact zebrafish embryo, deep imaging of thick patient-derived tumor organoids, and gentle whole-brain imaging of neural activity in behaving larval zebrafish.
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Affiliation(s)
- Kevin Keomanee-Dizon
- Translational Imaging Center, Dornsife College of Letters, Arts and Sciences, and Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA
| | - Scott E. Fraser
- Translational Imaging Center, Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Thai V. Truong
- Translational Imaging Center, Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
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29
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Yoon J, Grigoroiu A, Bohndiek SE. A background correction method to compensate illumination variation in hyperspectral imaging. PLoS One 2020; 15:e0229502. [PMID: 32168335 PMCID: PMC7069652 DOI: 10.1371/journal.pone.0229502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/09/2020] [Indexed: 12/12/2022] Open
Abstract
Hyperspectral imaging (HSI) can measure both spatial (morphological) and spectral (biochemical) information from biological tissues. While HSI appears promising for biomedical applications, interpretation of hyperspectral images can be challenging when data is acquired in complex biological environments. Variations in surface topology or optical power distribution at the sample, encountered for example during endoscopy, can lead to errors in post-processing of the HSI data, compromising disease diagnostic capabilities. Here, we propose a background correction method to compensate for such variations, which estimates the optical properties of illumination at the target based on the normalised spectral profile of the light source and the measured HSI intensity values at a fixed wavelength where the absorption characteristics of the sample are relatively low (in this case, 800 nm). We demonstrate the feasibility of the proposed method by imaging blood samples, tissue-mimicking phantoms, and ex vivo chicken tissue. Moreover, using synthetic HSI data composed from experimentally measured spectra, we show the proposed method would improve statistical analysis of HSI data. The proposed method could help the implementation of HSI techniques in practical clinical applications, where controlling the illumination pattern and power is difficult.
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Affiliation(s)
- Jonghee Yoon
- Department of Physics, University of Cambridge, Cambridge, England, United Kingdom
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, England, United Kingdom
| | - Alexandru Grigoroiu
- Department of Physics, University of Cambridge, Cambridge, England, United Kingdom
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, England, United Kingdom
| | - Sarah E. Bohndiek
- Department of Physics, University of Cambridge, Cambridge, England, United Kingdom
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, England, United Kingdom
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30
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Chouket R, Pellissier-Tanon A, Lemarchand A, Espagne A, Le Saux T, Jullien L. Dynamic contrast with reversibly photoswitchable fluorescent labels for imaging living cells. Chem Sci 2020; 11:2882-2887. [PMID: 34122788 PMCID: PMC8157520 DOI: 10.1039/d0sc00182a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 02/23/2020] [Indexed: 12/20/2022] Open
Abstract
Interrogating living cells requires sensitive imaging of a large number of components in real time. The state-of-the-art of multiplexed imaging is usually limited to a few components. This review reports on the promise and the challenges of dynamic contrast to overcome this limitation.
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Affiliation(s)
- Raja Chouket
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS 24, rue Lhomond 75005 Paris France +33 4432 3333
| | - Agnès Pellissier-Tanon
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS 24, rue Lhomond 75005 Paris France +33 4432 3333
| | - Annie Lemarchand
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Théorique de la Matière Condensée (LPTMC) 4 Place Jussieu, Case Courrier 121 75252 Paris Cedex 05 France
| | - Agathe Espagne
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS 24, rue Lhomond 75005 Paris France +33 4432 3333
| | - Thomas Le Saux
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS 24, rue Lhomond 75005 Paris France +33 4432 3333
| | - Ludovic Jullien
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS 24, rue Lhomond 75005 Paris France +33 4432 3333
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31
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Shi W, Koo DES, Kitano M, Chiang HJ, Trinh LA, Turcatel G, Steventon B, Arnesano C, Warburton D, Fraser SE, Cutrale F. Pre-processing visualization of hyperspectral fluorescent data with Spectrally Encoded Enhanced Representations. Nat Commun 2020; 11:726. [PMID: 32024828 PMCID: PMC7002680 DOI: 10.1038/s41467-020-14486-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/12/2020] [Indexed: 11/09/2022] Open
Abstract
Hyperspectral fluorescence imaging is gaining popularity for it enables multiplexing of spatio-temporal dynamics across scales for molecules, cells and tissues with multiple fluorescent labels. This is made possible by adding the dimension of wavelength to the dataset. The resulting datasets are high in information density and often require lengthy analyses to separate the overlapping fluorescent spectra. Understanding and visualizing these large multi-dimensional datasets during acquisition and pre-processing can be challenging. Here we present Spectrally Encoded Enhanced Representations (SEER), an approach for improved and computationally efficient simultaneous color visualization of multiple spectral components of hyperspectral fluorescence images. Exploiting the mathematical properties of the phasor method, we transform the wavelength space into information-rich color maps for RGB display visualization. We present multiple biological fluorescent samples and highlight SEER’s enhancement of specific and subtle spectral differences, providing a fast, intuitive and mathematical way to interpret hyperspectral images during collection, pre-processing and analysis. Spectral phasor analysis allows unmixing fluorescence microscopy images, but it requires user involvement and has a limited number of labels that can be analyzed and displayed. Here the authors present a semi-automated solution to visualise multiple spectral components of hyperspectral fluorescence images, simultaneously.
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Affiliation(s)
- Wen Shi
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - Daniel E S Koo
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - Masahiro Kitano
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - Hsiao J Chiang
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - Le A Trinh
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Gianluca Turcatel
- Developmental Biology and Regenerative Medicine Program, Saban Research Institute, Children's Hospital, 4661 Sunset Blvd, Los Angeles, CA, 90089, USA.,Keck School of Medicine and Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
| | - Benjamin Steventon
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Cosimo Arnesano
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - David Warburton
- Developmental Biology and Regenerative Medicine Program, Saban Research Institute, Children's Hospital, 4661 Sunset Blvd, Los Angeles, CA, 90089, USA.,Keck School of Medicine and Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
| | - Scott E Fraser
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - Francesco Cutrale
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA. .,Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA. .,Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.
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32
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Cui Q, Park J, Smith RT, Gao L. Snapshot hyperspectral light field imaging using image mapping spectrometry. OPTICS LETTERS 2020; 45:772-775. [PMID: 32004308 PMCID: PMC7472785 DOI: 10.1364/ol.382088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 11/23/2019] [Indexed: 05/22/2023]
Abstract
In this Letter, we present a snapshot hyperspectral light field imaging system using a single camera. By integrating an unfocused light field camera with a snapshot hyperspectral imager, the image mapping spectrometer, we captured a five-dimensional (5D) ($x,y,u,v,\lambda $x,y,u,v,λ) ($x,y,$x,y, spatial coordinates; $u,v,$u,v, emittance angles; $\lambda ,$λ, wavelength) datacube in a single camera exposure. The corresponding volumetric image ($x,y,z$x,y,z) at each wavelength is then computed through a scale-depth space transform. We demonstrated the snapshot advantage of our system by imaging the spectral-volumetric scenes in real time.
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Affiliation(s)
- Qi Cui
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405N Mathews Avenue, Urbana, Illinois 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 306N Wright St., Urbana, Illinois 61801, USA
| | - Jongchan Park
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405N Mathews Avenue, Urbana, Illinois 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 306N Wright St., Urbana, Illinois 61801, USA
| | - R. Theodore Smith
- Department of Ophthalmology, New York Eye and Ear Infirmary of Mount Sinai, New York, New York 10003, USA
| | - Liang Gao
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405N Mathews Avenue, Urbana, Illinois 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 306N Wright St., Urbana, Illinois 61801, USA
- Corresponding author:
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33
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Elsayad K. Optical imaging spectroscopy for plant research: more than a colorful picture. CURRENT OPINION IN PLANT BIOLOGY 2019; 52:77-85. [PMID: 31520788 DOI: 10.1016/j.pbi.2019.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 05/24/2023]
Abstract
Optical imaging is a routine and indispensable tool in plant research. Here we review different emerging spectrally resolved optical imaging approaches and the wealth of information they can be used to obtain pertaining to the underlying chemistry, structure and mechanics of plants.
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Affiliation(s)
- Kareem Elsayad
- Advanced Microscopy, VBCF, Vienna Biocenter, Dr. Bohr-Gasse 3, Vienna A-1030, Austria.
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34
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Abstract
Embryonic development is highly complex and dynamic, requiring the coordination of numerous molecular and cellular events at precise times and places. Advances in imaging technology have made it possible to follow developmental processes at cellular, tissue, and organ levels over time as they take place in the intact embryo. Parallel innovations of in vivo probes permit imaging to report on molecular, physiological, and anatomical events of embryogenesis, but the resulting multidimensional data sets pose significant challenges for extracting knowledge. In this review, we discuss recent and emerging advances in imaging technologies, in vivo labeling, and data processing that offer the greatest potential for jointly deciphering the intricate cellular dynamics and the underlying molecular mechanisms. Our discussion of the emerging area of “image-omics” highlights both the challenges of data analysis and the promise of more fully embracing computation and data science for rapidly advancing our understanding of biology.
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Affiliation(s)
- Francesco Cutrale
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, USA
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, USA
| | - Scott E. Fraser
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, USA
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, USA
- Division of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Le A. Trinh
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, USA
- Division of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
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35
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Belthangady C, Royer LA. Applications, promises, and pitfalls of deep learning for fluorescence image reconstruction. Nat Methods 2019; 16:1215-1225. [DOI: 10.1038/s41592-019-0458-z] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 05/22/2019] [Indexed: 02/06/2023]
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36
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Dong X, Xiao X, Pan Y, Wang G, Yu Y. DMD-based hyperspectral imaging system with tunable spatial and spectral resolution. OPTICS EXPRESS 2019; 27:16995-17006. [PMID: 31252917 DOI: 10.1364/oe.27.016995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/20/2019] [Indexed: 05/28/2023]
Abstract
Pushbroom hyperspectral imaging (HSI) has been used in many areas from air to land. However, its inherent operational drawback of the bulky slit leads to a limited field of view (FOV) and high energy consumption. Accordingly, a new and versatile HSI system is proposed by employing a smart digital micromirror device (DMD) to replace the mechanical scanning component. Moreover, tunable spatial and spectral resolution is implemented through adjusting the on-chip scanning linewidth and adopting the pixel fusion method, respectively. Meanwhile, three scanning modes including rough scanning, fine scanning, and regional scanning are achieved. These multiple choices increase the system's flexibility, universality, and intelligence, which is attractive for practically different applications, especially for military and remote sensing fields in need of a large FOV, and medical and food fields in need of tunable resolution for various samples.
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37
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Yoon J, Joseph J, Waterhouse DJ, Luthman AS, Gordon GSD, di Pietro M, Januszewicz W, Fitzgerald RC, Bohndiek SE. A clinically translatable hyperspectral endoscopy (HySE) system for imaging the gastrointestinal tract. Nat Commun 2019; 10:1902. [PMID: 31015458 PMCID: PMC6478902 DOI: 10.1038/s41467-019-09484-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/12/2019] [Indexed: 02/06/2023] Open
Abstract
Hyperspectral imaging (HSI) enables visualisation of morphological and biochemical information, which could improve disease diagnostic accuracy. Unfortunately, the wide range of image distortions that arise during flexible endoscopy in the clinic have made integration of HSI challenging. To address this challenge, we demonstrate a hyperspectral endoscope (HySE) that simultaneously records intrinsically co-registered hyperspectral and standard-of-care white light images, which allows image distortions to be compensated computationally and an accurate hyperspectral data cube to be reconstructed as the endoscope moves in the lumen. Evaluation of HySE performance shows excellent spatial, spectral and temporal resolution and high colour fidelity. Application of HySE enables: quantification of blood oxygenation levels in tissue mimicking phantoms; differentiation of spectral profiles from normal and pathological ex vivo human tissues; and recording of hyperspectral data under freehand motion within an intact ex vivo pig oesophagus model. HySE therefore shows potential for enabling HSI in clinical endoscopy.
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Affiliation(s)
- Jonghee Yoon
- Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - James Joseph
- Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Dale J Waterhouse
- Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - A Siri Luthman
- Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - George S D Gordon
- Department of Engineering, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0FA, UK
| | - Massimiliano di Pietro
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Wladyslaw Januszewicz
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Rebecca C Fitzgerald
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Sarah E Bohndiek
- Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
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38
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Chen L, Li G, Tang L, Zhang M, Liu L, Liu A, McGinty J, Ruan S. Hyperspectral scanning laser optical tomography. JOURNAL OF BIOPHOTONICS 2019; 12:e201800221. [PMID: 30187691 DOI: 10.1002/jbio.201800221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 09/04/2018] [Indexed: 06/08/2023]
Abstract
In order to study physical relationships within tissue volumes or even organism-level systems, the spatial distribution of multiple fluorescent markers needs to be resolved efficiently in three dimensions. Here, rather than acquiring discrete spectral images sequentially using multiple emission filters, a hyperspectral scanning laser optical tomography system is developed to obtain hyperspectral volumetric data sets with 2-nm spectral resolution of optically transparent mesoscopic (millimeter-centimeter) specimens. This is achieved by acquiring a series of point-scanning hyperspectral extended depth of field images at different angles and subsequently tomographically reconstructing the 3D intensity distribution for each wavelength. This technique is demonstrated to provide robust measurements via the comparison of spectral and intensity profiles of fluorescent bead phantoms. Due to its enhanced spectral resolving ability, this technique is also demonstrated to resolve largely overlapping fluorophores, as demonstrated by the 3D fluorescence hyperspectral reconstruction of a dual-labeled mouse thymus gland sample and the ability to distinguish tumorous and normal tissues of an unlabeled mouse intestine sample.
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Affiliation(s)
- Lingling Chen
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China
- College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
- Key Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Higher Education Institutes, Shenzhen Technology University, Shenzhen, China
| | - Guiye Li
- College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
- Key Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Higher Education Institutes, Shenzhen Technology University, Shenzhen, China
| | - Li Tang
- College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
- Department of Medicine, Shenzhen University, Shenzhen, China
| | - Meng Zhang
- School of Electronics and information Engineering, Beihang University, Beijing, China
| | - Lina Liu
- College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
| | - Ang Liu
- College of Optoelectronics Engineering, Shenzhen University, Shenzhen, China
| | - James McGinty
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Shuangchen Ruan
- Key Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Higher Education Institutes, Shenzhen Technology University, Shenzhen, China
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Habibalahi A, Bala C, Allende A, Anwer AG, Goldys EM. Novel automated non invasive detection of ocular surface squamous neoplasia using multispectral autofluorescence imaging. Ocul Surf 2019; 17:540-550. [PMID: 30904597 DOI: 10.1016/j.jtos.2019.03.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/28/2019] [Accepted: 03/12/2019] [Indexed: 12/20/2022]
Abstract
PURPOSE Diagnosing Ocular surface squamous neoplasia (OSSN) using newly designed multispectral imaging technique. METHODS Eighteen patients with histopathological diagnosis of Ocular Surface Squamous Neoplasia (OSSN) were recruited. Their previously collected biopsy specimens of OSSN were reprocessed without staining to obtain auto fluorescence multispectral microscopy images. This technique involved a custom-built spectral imaging system with 38 spectral channels. Inter and intra-patient frameworks were deployed to automatically detect and delineate OSSN using machine learning methods. Different machine learning methods were evaluated, with K nearest neighbor and Support Vector Machine chosen as preferred classifiers for intra- and inter-patient frameworks, respectively. The performance of the technique was evaluated against a pathological assessment. RESULTS Quantitative analysis of the spectral images provided a strong multispectral signature of a relative difference between neoplastic and normal tissue both within each patient (at p < 0.0005) and between patients (at p < 0.001). Our fully automated diagnostic method based on machine learning produces maps of the relatively well circumscribed neoplastic-non neoplastic interface. Such maps can be rapidly generated in quasi-real time and used for intraoperative assessment. Generally, OSSN could be detected using multispectral analysis in all patients investigated here. The cancer margins detected by multispectral analysis were in close and reasonable agreement with the margins observed in the H&E sections in intra- and inter-patient classification, respectively. CONCLUSIONS This study shows the feasibility of using multispectral auto-fluorescence imaging to detect and find the boundary of human OSSN. Fully automated analysis of multispectral images based on machine learning methods provides a promising diagnostic tool for OSSN which can be translated to future clinical applications.
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Affiliation(s)
- Abbas Habibalahi
- ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, North Ryde, NSW, 2109, Australia; School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia; Graduate School of Biomedical Engineering, University of New South Wales, Sydney, 2032, NSW, Australia.
| | - Chandra Bala
- Department of Ophthalmology, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Alexandra Allende
- Douglass Hanly Moir Pathology, Macquarie Park, Sydney, NSW, 2113, Australia; Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ayad G Anwer
- ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, North Ryde, NSW, 2109, Australia; Graduate School of Biomedical Engineering, University of New South Wales, Sydney, 2032, NSW, Australia
| | - Ewa M Goldys
- ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, North Ryde, NSW, 2109, Australia; Graduate School of Biomedical Engineering, University of New South Wales, Sydney, 2032, NSW, Australia.
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40
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Imaging Flies by Fluorescence Microscopy: Principles, Technologies, and Applications. Genetics 2019; 211:15-34. [PMID: 30626639 PMCID: PMC6325693 DOI: 10.1534/genetics.118.300227] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/05/2018] [Indexed: 02/07/2023] Open
Abstract
The development of fluorescent labels and powerful imaging technologies in the last two decades has revolutionized the field of fluorescence microscopy, which is now widely used in diverse scientific fields from biology to biomedical and materials science. Fluorescence microscopy has also become a standard technique in research laboratories working on Drosophila melanogaster as a model organism. Here, we review the principles of fluorescence microscopy technologies from wide-field to Super-resolution microscopy and its application in the Drosophila research field.
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Wang Y, Yang B, Feng S, Pessino V, Huang B. Multicolor fluorescent imaging by space-constrained computational spectral imaging. OPTICS EXPRESS 2019; 27:5393-5402. [PMID: 30876144 PMCID: PMC6410920 DOI: 10.1364/oe.27.005393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/12/2019] [Accepted: 01/13/2019] [Indexed: 05/31/2023]
Abstract
Spectral imaging is a powerful technique used to simultaneously study multiple fluorophore labels with overlapping emissions. Here, we present a computational spectral imaging method, which uses sample spatial fluorescence information as a reconstruction constraint. Our method addresses both the under-sampling issue of compressive spectral imaging and the low throughput issue of scanning spectral imaging. With simulated and experimental data, we have demonstrated the reconstruction precision of our method in two and three-color imaging. We have experimentally validated this method for differentiating cellular structures labeled with two red-colored fluorescent proteins, tdTomato and mCherry, which have highly overlapping emission spectra. Our method has the advantage of totally free wavelength choice and can also be combined with conventional filter-based sequential multi-color imaging to further improve multiplexing capability.
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Affiliation(s)
- Y. Wang
- Department of Pharmaceutical Chemistry, University of California in San Francisco, San Francisco, CA 94143, USA
| | - B. Yang
- Department of Pharmaceutical Chemistry, University of California in San Francisco, San Francisco, CA 94143, USA
| | - S. Feng
- The UC Berkeley-UCSF Graduate Program in Bioengineering, San Francisco, CA 94143, USA
| | - V. Pessino
- Department of Pharmaceutical Chemistry, University of California in San Francisco, San Francisco, CA 94143, USA
- Graduate Program of Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - B. Huang
- Department of Pharmaceutical Chemistry, University of California in San Francisco, San Francisco, CA 94143, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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42
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Licea-Rodriguez J, Figueroa-Melendez A, Falaggis K, Plata-Sanchez M, Riquelme M, Rocha-Mendoza I. Multicolor fluorescence microscopy using static light sheets and a single-channel detection. JOURNAL OF BIOMEDICAL OPTICS 2019; 24:1-8. [PMID: 30612379 PMCID: PMC6985699 DOI: 10.1117/1.jbo.24.1.016501] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/06/2018] [Indexed: 05/25/2023]
Abstract
We present a multicolor fluorescence microscope system, under a selective plane illumination microscopy (SPIM) configuration, using three continuous wave-lasers and a single-channel-detection camera. The laser intensities are modulated with three time-delayed pulse trains that operate synchronously at one third of the camera frame rate, allowing a sequential excitation and an image acquisition of up to three different biomarkers. The feasibility of this imaging acquisition mode is demonstrated by acquiring single-plane multicolor images of living hyphae of Neurospora crassa. This allows visualizing simultaneously the localization and dynamics of different cellular components involved in apical growth in living hyphae. The configuration presented represents a noncommercial, cost-effective alternative microscopy system for the rapid and simultaneous acquisition of multifluorescent images and can be potentially useful for three-dimensional imaging of large biological samples.
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Affiliation(s)
- Jacob Licea-Rodriguez
- Centro de Investigación Científica y de Educación Superior de Ensenada, Department of Optics, Ensenada, Baja California, Mexico
- Cátedras Conacyt, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Alfredo Figueroa-Melendez
- Centro de Investigación Científica y de Educación Superior de Ensenada, Department of Microbiology, Ensenada, Baja California, Mexico
| | - Konstantinos Falaggis
- Cátedras Conacyt, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
- University of North Carolina, Department of Mechanical Engineering and Engineering Science, Charlotte, North Carolina, United States
| | - Marcos Plata-Sanchez
- Centro de Investigación Científica y de Educación Superior de Ensenada, Department of Optics, Ensenada, Baja California, Mexico
| | - Meritxell Riquelme
- Centro de Investigación Científica y de Educación Superior de Ensenada, Department of Microbiology, Ensenada, Baja California, Mexico
| | - Israel Rocha-Mendoza
- Centro de Investigación Científica y de Educación Superior de Ensenada, Department of Optics, Ensenada, Baja California, Mexico
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43
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Joshi P, Kang SY, Datar A, Lee MY. High-Throughput Assessment of Mechanistic Toxicity of Chemicals in Miniaturized 3D Cell Culture. ACTA ACUST UNITED AC 2018; 79:e66. [PMID: 30387930 DOI: 10.1002/cptx.66] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High-content imaging (HCI) assays on two-dimensional (2D) cell cultures often do not represent in vivo characteristics accurately, thus reducing the predictability of drug toxicity/efficacy in vivo. On the other hand, conventional 3D cell cultures are relatively low throughput and possess difficulty in cell imaging. To address these limitations, a miniaturized 3D cell culture has been developed on a micropillar/microwell chip platform with human cells encapsulated in biomimetic hydrogels. Model compounds are used to validate human cell microarrays for high-throughput assessment of mechanistic toxicity. Main mechanisms of toxicity of compounds can be investigated by analyzing multiple parameters such as DNA damage, mitochondrial impairment, intracellular glutathione level, and cell membrane integrity. IC50 values of these parameters can be determined and compared for the compounds to investigate the main mechanism of toxicity. This paper describes miniaturized HCI assays on 3D-cultured cell microarrays for high-throughput assessment of mechanistic profiles of compound-induced toxicity. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Pranav Joshi
- Department of Chemical and Biomedical Engineering, Cleveland State University, Cleveland, Ohio
| | - Soo-Yeon Kang
- Department of Chemical and Biomedical Engineering, Cleveland State University, Cleveland, Ohio
| | - Akshata Datar
- Department of Chemical and Biomedical Engineering, Cleveland State University, Cleveland, Ohio
| | - Moo-Yeal Lee
- Department of Chemical and Biomedical Engineering, Cleveland State University, Cleveland, Ohio
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Zhu S, Gao L, Zhang Y, Lin J, Jin P. Complete plenoptic imaging using a single detector. OPTICS EXPRESS 2018; 26:26495-26510. [PMID: 30469735 DOI: 10.1364/oe.26.026495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/12/2018] [Indexed: 06/09/2023]
Abstract
Multi-dimensional imaging is a powerful technique for many applications, such as biological analysis, remote sensing, and object recognition. Most existing multi-dimensional imaging systems rely on scanning or camera array, which make the system bulky and unstable. To some extent, these problems can be mitigated by employing compressed sensing algorithms. However, they are computationally expensive and highly rely on the ill-posed assumption that the information is sparse in a given domain. Here, we propose a snapshot spectral-volumetric imaging (SSVI) system by introducing the paradigm of light-field imaging into Fourier transform imaging spectroscopy. We demonstrate that SSVI can reconstruct a complete plenoptic function, P(x,y,z,θ,φ,λ,t), of the incoming light rays using a single detector. Compared with other multidimensional imagers, SSVI features prominent advantages in compactness, robustness, and low cost.
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45
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Ovečka M, von Wangenheim D, Tomančák P, Šamajová O, Komis G, Šamaj J. Multiscale imaging of plant development by light-sheet fluorescence microscopy. NATURE PLANTS 2018; 4:639-650. [PMID: 30185982 DOI: 10.1038/s41477-018-0238-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/31/2018] [Indexed: 05/21/2023]
Abstract
Light-sheet fluorescence microscopy (LSFM) methods collectively represent the major breakthrough in developmental bio-imaging of living multicellular organisms. They are becoming a mainstream approach through the development of both commercial and custom-made LSFM platforms that are adjusted to diverse biological applications. Based on high-speed acquisition rates under conditions of low light exposure and minimal photo-damage of the biological sample, these methods provide ideal means for long-term and in-depth data acquisition during organ imaging at single-cell resolution. The introduction of LSFM methods into biology extended our understanding of pattern formation and developmental progress of multicellular organisms from embryogenesis to adult body. Moreover, LSFM imaging allowed the dynamic visualization of biological processes under almost natural conditions. Here, we review the most important, recent biological applications of LSFM methods in developmental studies of established and emerging plant model species, together with up-to-date methods of data editing and evaluation for modelling of complex biological processes. Recent applications in animal models push LSFM into the forefront of current bio-imaging approaches. Since LSFM is now the single most effective method for fast imaging of multicellular organisms, allowing quantitative analyses of their long-term development, its broader use in plant developmental biology will likely bring new insights.
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Affiliation(s)
- Miroslav Ovečka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - Daniel von Wangenheim
- Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Pavel Tomančák
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Olga Šamajová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - George Komis
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic.
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Garbacik ET, Sanz-Paz M, Borgman KJE, Campelo F, Garcia-Parajo MF. Frequency-Encoded Multicolor Fluorescence Imaging with Single-Photon-Counting Color-Blind Detection. Biophys J 2018; 115:725-736. [PMID: 30037496 PMCID: PMC6104530 DOI: 10.1016/j.bpj.2018.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/25/2018] [Accepted: 07/09/2018] [Indexed: 02/06/2023] Open
Abstract
Standard fluorescence microscopy relies on filter-based detection of emitted photons after fluorophore excitation at the appropriate wavelength. Although of enormous utility to the biological community, the implementation of approaches for simultaneous multicolor fluorescence imaging is commonly challenged by the large spectral overlap between different fluorophores. Here, we describe an alternative multicolor fluorescence imaging methodology that exclusively relies on the absorption spectra of the fluorophores instead of their fluorescence emissions. The method is based on multiplexing optical excitation signals in the frequency domain and using single color-blind detection. Because the spectral information is fully encoded during excitation, the method requires minimal spectral filtering on detection. This enables the simultaneous identification of multiple color channels in a single measurement with only one color-blind detector. We demonstrate simultaneous three-color confocal imaging of individual molecules and of four-target imaging on cells with excellent discrimination. Moreover, we have implemented a non-negative matrix factorization algorithm for spectral unmixing to extend the number of color targets that can be discriminated in a single measurement. Using this algorithm, we resolve six spectrally and spatially overlapping fluorophores on fixed cells using four excitation wavelengths. The methodology is fully compatible with live imaging of biological samples and can be easily extended to other imaging modalities, including super-resolution microscopy, making simultaneous multicolor imaging more accessible to the biological research community.
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Affiliation(s)
- Erik T Garbacik
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Maria Sanz-Paz
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Kyra J E Borgman
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Maria F Garcia-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain; ICREA, Barcelona, Spain.
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47
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Experimental Demonstration of Remote and Compact Imaging Spectrometer Based on Mobile Devices. SENSORS 2018; 18:s18071989. [PMID: 29933615 PMCID: PMC6068658 DOI: 10.3390/s18071989] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 06/03/2018] [Accepted: 06/20/2018] [Indexed: 12/30/2022]
Abstract
Imaging spectrometers show great potential for environmental and biomedical sensing applications. Selfie sticks, which are tools used to take photographs or videos, have gained global popularity in recent years. Few people have connected these two objects, and few people have researched the application of imaging spectrometers to perform scientific monitoring in point-of-use scenarios. In this paper, we develop a compact imaging spectrometer (35 g in weight, 18 mm in diameter, and 72 mm in length) that can be equipped on a motorized selfie stick to perform remote sensing. We applied this system to perform environmental and facial remote sensing via motorized scanning. The absorption of chlorophyll and hemoglobin can be found in the reflectance spectra, indicating that our system can be used in urban greening monitoring and point-of-care testing. In addition, this compact imaging spectrometer was also easily attached to an underwater dome port and a quad-rotor unmanned aerial vehicle to perform underwater and airborne spectral detection. Our system offers a route toward mobile imaging spectrometers used in daily life.
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48
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Parthasarathy R. Monitoring microbial communities using light sheet fluorescence microscopy. Curr Opin Microbiol 2018; 43:31-37. [PMID: 29175679 PMCID: PMC5963963 DOI: 10.1016/j.mib.2017.11.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/10/2017] [Accepted: 11/06/2017] [Indexed: 01/20/2023]
Abstract
Microbes often live in dense, dynamic, multi-species communities whose architecture and function are intimately intertwined. Imaging these complex, three-dimensional ensembles presents considerable technical challenges, however. In this review, I describe light sheet fluorescence microscopy, a technique that enables rapid acquisition of three-dimensional images over large fields of view and over long durations, and I highlight recent applications of this method to microbial systems that include artificial closed ecosystems, bacterial biofilms, and gut microbiota. I comment also on the history of light sheet imaging and the many variants of the method. Light sheet techniques have tremendous potential for illuminating the workings of microbial communities, a potential that is just beginning to be realized.
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49
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Liao J, Jiang S, Zhang Z, Guo K, Bian Z, Jiang Y, Zhong J, Zheng G. Terapixel hyperspectral whole-slide imaging via slit-array detection and projection. JOURNAL OF BIOMEDICAL OPTICS 2018; 23:1-7. [PMID: 29959834 PMCID: PMC8357323 DOI: 10.1117/1.jbo.23.6.066503] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/13/2018] [Indexed: 05/06/2023]
Abstract
Digital pathology via whole-slide imaging (WSI) systems has recently been approved for the primary diagnostic use in the US. Acquiring whole-slide images with spectral information at each pixel permits the use of multiplexed antibody labeling and allow for the measurement of cellularly resolved chemical information. Here, we report the development of a high-throughput terapixel hyperspectral WSI system using prism-based slit-array dispersion. We demonstrate a slit-array detection scheme for absorption-based measurements and a slit-array projection scheme for fluorescence-based measurements. The spectral resolution and spectral range in the reported schemes can be adjusted by changing the orientation of the slit-array mask. We use our system to acquire 74 5-megapixel brightfield images at different wavelengths in ∼1 s, corresponding to a throughput of 0.375 gigapixels / s. A terapixel whole-slide spatial-spectral data cube can be obtained in ∼45 min. The reported system is compatible with existing WSI systems and can be developed as an add-on module for whole-slide spectral imaging. It may find broad applications in high-throughput chemical imaging with multiple antibody labeling. The use of slit array for structured illumination may also provide insights for developing high-throughput hyperspectral confocal imaging systems.
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Affiliation(s)
- Jun Liao
- University of Connecticut, Department of Biomedical Engineering, Storrs, Connecticut, United States
| | - Shaowei Jiang
- University of Connecticut, Department of Biomedical Engineering, Storrs, Connecticut, United States
| | - Zibang Zhang
- Jinan University, Department of Optoelectronic Engineering, Guangzhou, China
| | - Kaikai Guo
- University of Connecticut, Department of Biomedical Engineering, Storrs, Connecticut, United States
| | - Zichao Bian
- University of Connecticut, Department of Biomedical Engineering, Storrs, Connecticut, United States
| | - Yutong Jiang
- University of Connecticut, Department of Biomedical Engineering, Storrs, Connecticut, United States
| | - Jingang Zhong
- Jinan University, Department of Optoelectronic Engineering, Guangzhou, China
| | - Guoan Zheng
- University of Connecticut, Department of Biomedical Engineering, Storrs, Connecticut, United States
- University of Connecticut, Department of Electrical and Computer Engineering, Storrs, Connecticut, United States
- Address all correspondence to: Guoan Zheng, E-mail:
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50
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Chen Z, Deán-Ben XL, Gottschalk S, Razansky D. Performance of optoacoustic and fluorescence imaging in detecting deep-seated fluorescent agents. BIOMEDICAL OPTICS EXPRESS 2018; 9:2229-2239. [PMID: 29760983 PMCID: PMC5946784 DOI: 10.1364/boe.9.002229] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/08/2018] [Accepted: 03/09/2018] [Indexed: 05/03/2023]
Abstract
Fluorescent contrast agents are widely employed in biomedical research. While many studies have reported deep tissue imaging of fluorescent moieties using either fluorescence-based or absorption-based (optoacoustic) imaging systems, no systematic comparison has been performed regarding the actual performance of these imaging modalities in detecting deep-seated fluorescent agents. Herein, an integrated imager combining epi-fluorescence and volumetric optoacoustic imaging capabilities has been employed in order to evaluate image degradation with depth for several commonly-used near-infrared dyes in both modes. We performed controlled experiments in tissue-mimicking phantoms containing deeply embedded targets filled with different concentrations of Alexa Fluor 700, Alexa Fluor 750, indocyanine green (ICG) and IRDye 800CW. The results are further corroborated by multi-modal imaging of ICG through mouse tissues in vivo. It is shown that optoacoustics consistently provides better sensitivity in differentiating fluorescent targets located at depths beyond 2 mm in turbid tissues, as quantified by evaluating image contrast, signal to noise ratio and spatial resolution performance.
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Affiliation(s)
- Zhenyue Chen
- Institute for Biological and Medical Imaging (IBMI), Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Xosé Luís Deán-Ben
- Institute for Biological and Medical Imaging (IBMI), Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Sven Gottschalk
- Institute for Biological and Medical Imaging (IBMI), Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Daniel Razansky
- Institute for Biological and Medical Imaging (IBMI), Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- Faculty of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
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