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Daetwyler S, Fiolka RP. Light-sheets and smart microscopy, an exciting future is dawning. Commun Biol 2023; 6:502. [PMID: 37161000 PMCID: PMC10169780 DOI: 10.1038/s42003-023-04857-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 04/20/2023] [Indexed: 05/11/2023] Open
Abstract
Light-sheet fluorescence microscopy has transformed our ability to visualize and quantitatively measure biological processes rapidly and over long time periods. In this review, we discuss current and future developments in light-sheet fluorescence microscopy that we expect to further expand its capabilities. This includes smart and adaptive imaging schemes to overcome traditional imaging trade-offs, i.e., spatiotemporal resolution, field of view and sample health. In smart microscopy, a microscope will autonomously decide where, when, what and how to image. We further assess how image restoration techniques provide avenues to overcome these tradeoffs and how "open top" light-sheet microscopes may enable multi-modal imaging with high throughput. As such, we predict that light-sheet microscopy will fulfill an important role in biomedical and clinical imaging in the future.
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Affiliation(s)
- Stephan Daetwyler
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Reto Paul Fiolka
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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2
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Power RM, Schlaeppi A, Huisken J. Compact, high-speed multi-directional selective plane illumination microscopy. BIOMEDICAL OPTICS EXPRESS 2023; 14:1445-1459. [PMID: 37078034 PMCID: PMC10110309 DOI: 10.1364/boe.476217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 05/03/2023]
Abstract
We present an elegant scheme for providing multi-directional illumination in selective plane illumination microscopy (SPIM). Light sheets can be delivered from one of two opposed directions at a time and pivoted about their center for efficient stripe artifact suppression using only a single galvanometric scanning mirror to perform both functions. The scheme results in a much smaller instrument footprint and allows multi-directional illumination with reduced expense compared with comparable schemes. Switching between the illumination paths is near instantaneous and the whole-plane illumination scheme of SPIM maintains the lowest rates of photodamage, which is often sacrificed by other recently reported destriping strategies. The ease of synchronization allows this scheme to be used at higher speeds than resonant mirrors typically used in this regard. We provide validation of this approach in the dynamic environment of the zebrafish beating heart, where imaging at up to 800 frames per second is demonstrated alongside efficient suppression of artifacts.
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Affiliation(s)
- Rory M. Power
- Morgridge Institute for Research, 330 N Orchard St, Madison, WI 53715, USA
- EMBL Imaging Centre EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Anjalie Schlaeppi
- Morgridge Institute for Research, 330 N Orchard St, Madison, WI 53715, USA
- Bioimaging and Optics Platform, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
| | - Jan Huisken
- Morgridge Institute for Research, 330 N Orchard St, Madison, WI 53715, USA
- Department of Integrative Biology, University of Wisconsin, Madison, 250 N Mills St, Madison, WI 53706, USA
- Department of Biology and Psychology, Georg-August-University Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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3
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Cao Y, Lee S, Kim K, Kang SH. Minimizing the Optical Illusion of Nanoparticles in Single Cells Using Four-Dimensional Cuboid Multiangle Illumination-Based Light-Sheet Super-Resolution Imaging. Anal Chem 2022; 94:17877-17884. [PMID: 36509731 DOI: 10.1021/acs.analchem.2c03729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although light-sheet-based super-resolution microscopy is an excellent detection technique for biological samples because of minimal photodamage, uneven light paths due to solid-angle illumination limits it, resulting in an optical illusion. Furthermore, the optical illusion limits the observations of individual molecules in diffraction. In this study, a four-dimensional cuboid multiangle illumination-based light-sheet super-resolution (4D CMLS) imaging system was developed to minimize optical illusions in cells. The lab-built 4D CMLS imaging system was integrated with total internal reflection fluorescence and a differential interference contrast microscope. A specially designed rotatable cuboid prism simply overcame the optical illusion by rotating a specimen on the prism to change the direction of light coming from an illumination lens. 4D CMLS reconstructed images of nanoparticles of different sizes were acquired in multi-illumination angles of 0°, 90°, 180°, and 270°. Additionally, a 4D multiangle illumination-based algorithm was created to select the optimal illumination angle by combining three-dimensional super-resolution imaging with multiangle observation, even in the presence of obstacles. The 4D CMLS imaging method demonstrates the in-depth 4D observation of samples at an optimum angle that can be used in various applications, such as single-molecule and subcellular organelle observations in single cells at subdiffraction limit resolutions that describe the scenario of nature.
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Affiliation(s)
- Yingying Cao
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
| | - Seungah Lee
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
| | - Kyungsoo Kim
- Department of Applied Mathematics, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
| | - Seong Ho Kang
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea.,Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
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Haynes EM, Ulland TK, Eliceiri KW. A Model of Discovery: The Role of Imaging Established and Emerging Non-mammalian Models in Neuroscience. Front Mol Neurosci 2022; 15:867010. [PMID: 35493325 PMCID: PMC9046975 DOI: 10.3389/fnmol.2022.867010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/18/2022] [Indexed: 11/24/2022] Open
Abstract
Rodents have been the dominant animal models in neurobiology and neurological disease research over the past 60 years. The prevalent use of rats and mice in neuroscience research has been driven by several key attributes including their organ physiology being more similar to humans, the availability of a broad variety of behavioral tests and genetic tools, and widely accessible reagents. However, despite the many advances in understanding neurobiology that have been achieved using rodent models, there remain key limitations in the questions that can be addressed in these and other mammalian models. In particular, in vivo imaging in mammals at the cell-resolution level remains technically difficult and demands large investments in time and cost. The simpler nervous systems of many non-mammalian models allow for precise mapping of circuits and even the whole brain with impressive subcellular resolution. The types of non-mammalian neuroscience models available spans vertebrates and non-vertebrates, so that an appropriate model for most cell biological questions in neurodegenerative disease likely exists. A push to diversify the models used in neuroscience research could help address current gaps in knowledge, complement existing rodent-based bodies of work, and bring new insight into our understanding of human disease. Moreover, there are inherent aspects of many non-mammalian models such as lifespan and tissue transparency that can make them specifically advantageous for neuroscience studies. Crispr/Cas9 gene editing and decreased cost of genome sequencing combined with advances in optical microscopy enhances the utility of new animal models to address specific questions. This review seeks to synthesize current knowledge of established and emerging non-mammalian model organisms with advances in cellular-resolution in vivo imaging techniques to suggest new approaches to understand neurodegeneration and neurobiological processes. We will summarize current tools and in vivo imaging approaches at the single cell scale that could help lead to increased consideration of non-mammalian models in neuroscience research.
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Affiliation(s)
- Elizabeth M. Haynes
- Morgridge Institute for Research, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
| | - Tyler K. Ulland
- Department of Pathology, University of Wisconsin-Madison, Madison, WI, United States
| | - Kevin W. Eliceiri
- Morgridge Institute for Research, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
- Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, United States
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Pursuit of precision medicine: Systems biology approaches in Alzheimer's disease mouse models. Neurobiol Dis 2021; 161:105558. [PMID: 34767943 PMCID: PMC10112395 DOI: 10.1016/j.nbd.2021.105558] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's disease (AD) is a complex disease that is mediated by numerous factors and manifests in various forms. A systems biology approach to studying AD involves analyses of various body systems, biological scales, environmental elements, and clinical outcomes to understand the genotype to phenotype relationship that potentially drives AD development. Currently, there are many research investigations probing how modifiable and nonmodifiable factors impact AD symptom presentation. This review specifically focuses on how imaging modalities can be integrated into systems biology approaches using model mouse populations to link brain level functional and structural changes to disease onset and progression. Combining imaging and omics data promotes the classification of AD into subtypes and paves the way for precision medicine solutions to prevent and treat AD.
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Aakhte M, Müller HAJ. Multiview tiling light sheet microscopy for 3D high-resolution live imaging. Development 2021; 148:272173. [PMID: 34409448 DOI: 10.1242/dev.199725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 08/13/2021] [Indexed: 11/20/2022]
Abstract
Light-sheet or selective plane illumination microscopy (SPIM) is ideally suited for in toto imaging of living specimens at high temporal-spatial resolution. In SPIM, the light scattering that occurs during imaging of opaque specimens brings about limitations in terms of resolution and the imaging field of view. To ameliorate this shortcoming, the illumination beam can be engineered into a highly confined light sheet over a large field of view and multi-view imaging can be performed by applying multiple lenses combined with mechanical rotation of the sample. Here, we present a Multiview tiling SPIM (MT-SPIM) that combines the Multi-view SPIM (M-SPIM) with a confined, multi-tiled light sheet. The MT-SPIM provides high-resolution, robust and rotation-free imaging of living specimens. We applied the MT-SPIM to image nuclei and Myosin II from the cellular to subcellular spatial scale in early Drosophila embryogenesis. We show that the MT-SPIM improves the axial-resolution relative to the conventional M-SPIM by a factor of two. We further demonstrate that this axial resolution enhancement improves the automated segmentation of Myosin II distribution and of nuclear volumes and shapes.
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Affiliation(s)
- Mostafa Aakhte
- Developmental Genetics Group, Institute of Biology, University of Kassel, Heinrich-Plett Strasse 40, 34132 Kassel, Germany
| | - Hans-Arno J Müller
- Developmental Genetics Group, Institute of Biology, University of Kassel, Heinrich-Plett Strasse 40, 34132 Kassel, Germany
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Kapsokalyvas D, Rosas R, Janssen RWA, Vanoevelen JM, Nabben M, Strauch M, Merhof D, van Zandvoort MAMJ. Multiview deconvolution approximation multiphoton microscopy of tissues and zebrafish larvae. Sci Rep 2021; 11:10160. [PMID: 33980963 PMCID: PMC8115086 DOI: 10.1038/s41598-021-89566-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/30/2021] [Indexed: 02/03/2023] Open
Abstract
Imaging in three dimensions is necessary for thick tissues and small organisms. This is possible with tomographic optical microscopy techniques such as confocal, multiphoton and light sheet microscopy. All these techniques suffer from anisotropic resolution and limited penetration depth. In the past, Multiview microscopy-imaging the sample from different angles followed by 3D image reconstruction-was developed to address this issue for light sheet microscopy based on fluorescence signal. In this study we applied this methodology to accomplish Multiview imaging with multiphoton microscopy based on fluorescence and additionally second harmonic signal from myosin and collagen. It was shown that isotropic resolution was achieved, the entirety of the sample was visualized, and interference artifacts were suppressed allowing clear visualization of collagen fibrils and myofibrils. This method can be applied to any scanning microscopy technique without microscope modifications. It can be used for imaging tissue and whole mount small organisms such as heart tissue, and zebrafish larva in 3D, label-free or stained, with at least threefold axial resolution improvement which can be significant for the accurate quantification of small 3D structures.
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Affiliation(s)
- Dimitrios Kapsokalyvas
- grid.5012.60000 0001 0481 6099Department of Genetics and Cell Biology, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, the Netherlands ,grid.412301.50000 0000 8653 1507Institute for Molecular Cardiovascular Research (IMCAR), University Hospital RWTH Aachen University, Aachen, Germany
| | - Rodrigo Rosas
- grid.5012.60000 0001 0481 6099Department of Genetics and Cell Biology, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, the Netherlands
| | - Rob W. A. Janssen
- grid.5012.60000 0001 0481 6099Department of Genetics and Cell Biology, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, the Netherlands
| | - Jo M. Vanoevelen
- grid.5012.60000 0001 0481 6099Department of Genetics and Cell Biology, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, the Netherlands
| | - Miranda Nabben
- grid.5012.60000 0001 0481 6099Department of Genetics and Cell Biology, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, the Netherlands
| | - Martin Strauch
- grid.1957.a0000 0001 0728 696XInstitute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
| | - Dorit Merhof
- grid.1957.a0000 0001 0728 696XInstitute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
| | - Marc A. M. J. van Zandvoort
- grid.5012.60000 0001 0481 6099Department of Genetics and Cell Biology, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, the Netherlands ,grid.412301.50000 0000 8653 1507Institute for Molecular Cardiovascular Research (IMCAR), University Hospital RWTH Aachen University, Aachen, Germany
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Preusser F, dos Santos N, Contzen J, Stachelscheid H, Costa ÉT, Mergenthaler P, Preibisch S. FRC-QE: a robust and comparable 3D microscopy image quality metric for cleared organoids. Bioinformatics 2021; 37:3088-3090. [PMID: 33693580 PMCID: PMC8479654 DOI: 10.1093/bioinformatics/btab160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/04/2021] [Accepted: 03/04/2021] [Indexed: 02/02/2023] Open
Abstract
SUMMARY Here, we propose Fourier ring correlation-based quality estimation (FRC-QE) as a new metric for automated image quality estimation in 3D fluorescence microscopy acquisitions of cleared organoids that yields comparable measurements across experimental replicates, clearing protocols and works for different microscopy modalities. AVAILABILITY AND IMPLEMENTATION FRC-QE is written in ImgLib2/Java and provided as an easy-to-use and macro-scriptable plugin for Fiji. Code, documentation, sample images and further information can be found under https://github.com/PreibischLab/FRC-QE. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Friedrich Preusser
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin 10115, Germany
| | - Natália dos Santos
- Molecular Oncology Center, Hospital Sirio-Libanese, São Paulo, SP 01308-050, Brazil
| | - Jörg Contzen
- Department of Experimental Neurology, Center for Stroke Research Berlin, Charité – Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Harald Stachelscheid
- Stem Cell Core Facility, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin 13353, Germany
| | - Érico Tosoni Costa
- Molecular Oncology Center, Hospital Sirio-Libanese, São Paulo, SP 01308-050, Brazil
| | - Philipp Mergenthaler
- Department of Experimental Neurology, Center for Stroke Research Berlin, Charité – Universitätsmedizin Berlin, Berlin 10117, Germany,Department of Neurology, Charité – Universitätsmedizin Berlin, Berlin 10117, Germany,BIH Academy, Berlin Institute of Health at Charité –Universitätsmedizin Berlin, Berlin 10117, Germany,To whom correspondence should be addressed. or
| | - Stephan Preibisch
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin 10115, Germany,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA,To whom correspondence should be addressed. or
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Liu Y, Zhang Y, Li S, Cui J. Gene expression pattern of trophoblast-specific transcription factors in trophectoderm by analysis of single-cell RNA-seq data of human blastocyst. Funct Integr Genomics 2021; 21:205-214. [PMID: 33543402 DOI: 10.1007/s10142-021-00770-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/23/2021] [Accepted: 01/28/2021] [Indexed: 12/15/2022]
Abstract
The dysfunction of placenta development is correlated to the defects of pregnancy and fetal growth. The detailed molecular mechanism of placenta development is not identified in humans due to the lack of material in vivo. Trophoblast (TB) lineage derived from human embryonic stem cells (hESCs) induced by bone morphogenetic protein 4 (BMP4) has been applied as a model for studying TB lineage specification in vitro. With the development of single-cell sequencing technology, it became possible to detect the transcriptome of the post-implantation embryo at unprecedented precision. In this study, we reanalyzed single-cell RNA-seq of post-implantation embryos derived from two separate groups and identified different subtypes of trophoblast cells and their marker, respectively. At the same time, we focused on the gene expression patterns of trophoblast-specific transcription factors in different models. Our analysis sheds new light on the transcription regulation mechanism of trophoblast differentiation at the early stage of pregnancy establishment in human.
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Affiliation(s)
- Yajun Liu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Henan No. 2, Jingba Road, Zhengzhou, 450001, China. .,Academy of Medical Sciences of Zhengzhou University Translational Medicine Platform, Zhengzhou University, No.100 Science Avenue, Zhengzhou, 450001, China.
| | - Yi Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Henan No. 2, Jingba Road, Zhengzhou, 450001, China.,Academy of Medical Sciences of Zhengzhou University Translational Medicine Platform, Zhengzhou University, No.100 Science Avenue, Zhengzhou, 450001, China
| | - Shiwen Li
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Henan No. 2, Jingba Road, Zhengzhou, 450001, China
| | - Jinquan Cui
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Henan No. 2, Jingba Road, Zhengzhou, 450001, China. .,Academy of Medical Sciences of Zhengzhou University Translational Medicine Platform, Zhengzhou University, No.100 Science Avenue, Zhengzhou, 450001, China.
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Eisenstein M. Smart solutions for automated imaging. Nat Methods 2020. [PMID: 33077968 DOI: 10.15932/j.0253-9713.2020.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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