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Moos F, Suppinger S, de Medeiros G, Oost KC, Boni A, Rémy C, Weevers SL, Tsiairis C, Strnad P, Liberali P. Open-top multisample dual-view light-sheet microscope for live imaging of large multicellular systems. Nat Methods 2024; 21:798-803. [PMID: 38509326 PMCID: PMC11093739 DOI: 10.1038/s41592-024-02213-w] [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: 08/18/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
Multicellular systems grow over the course of weeks from single cells to tissues or even full organisms, making live imaging challenging. To bridge spatiotemporal scales, we present an open-top dual-view and dual-illumination light-sheet microscope dedicated to live imaging of large specimens at single-cell resolution. The configuration of objectives together with a customizable multiwell mounting system combines dual view with high-throughput multiposition imaging. We use this microscope to image a wide variety of samples and highlight its capabilities to gain quantitative single-cell information in large specimens such as mature intestinal organoids and gastruloids.
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Affiliation(s)
- Franziska Moos
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Simon Suppinger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Gustavo de Medeiros
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Viventis Microscopy Sàrl, Lausanne, Switzerland
| | | | - Andrea Boni
- Viventis Microscopy Sàrl, Lausanne, Switzerland
| | | | - Sera Lotte Weevers
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Charisios Tsiairis
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Petr Strnad
- Viventis Microscopy Sàrl, Lausanne, Switzerland.
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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2
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Dibaji H, Nasaban Shotorban AK, Grattan RM, Lucero S, Schodt DJ, Lidke KA, Petruccelli J, Lidke DS, Liu S, Chakraborty T. Axial de-scanning using remote focusing in the detection arm of light-sheet microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.07.556729. [PMID: 38659774 PMCID: PMC11042218 DOI: 10.1101/2023.09.07.556729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The ability to image at high speeds is necessary for biological imaging to capture fast-moving or transient events or to efficiently image large samples. However, due to the lack of rigidity of biological specimens, carrying out fast, high-resolution volumetric imaging without moving and agitating the sample has been a challenging problem. Pupil-matched remote focusing has been promising for high NA imaging systems with their low aberrations and wavelength independence, making it suitable for multicolor imaging. However, owing to the incoherent and unpolarized nature of the fluorescence signal, manipulating this emission light through remote focusing is challenging. Therefore, remote focusing has been primarily limited to the illumination arm, using polarized laser light to facilitate coupling in and out of the remote focusing optics. Here, we introduce a novel optical design that can de-scan the axial focus movement in the detection arm of a microscope. Our method splits the fluorescence signal into S and P-polarized light, lets them pass through the remote focusing module separately, and combines them with the camera. This allows us to use only one focusing element to perform aberration-free, multi-color, volumetric imaging without (a) compromising the fluorescent signal and (b) needing to perform sample/detection-objective translation. We demonstrate the capabilities of this scheme by acquiring fast dual-color 4D (3D space + time) image stacks with an axial range of 70 μm and camera-limited acquisition speed. Owing to its general nature, we believe this technique will find its application in many other microscopy techniques that currently use an adjustable Z-stage to carry out volumetric imaging, such as confocal, 2-photon, and light sheet variants.
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3
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Sirinakis G, Allgeyer ES, Nashchekin D, St Johnston D. User-friendly oblique plane microscopy on a fully functional commercially available microscope base. BIOMEDICAL OPTICS EXPRESS 2024; 15:2358-2376. [PMID: 38633100 PMCID: PMC11019673 DOI: 10.1364/boe.518856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 04/19/2024]
Abstract
In this work we present an oblique plane microscope designed to work seamlessly with a commercially available microscope base. To support all the functionality offered by the microscope base, where the position of the objective lens is not fixed, we adopted a two-mirror scanning geometry that can compensate for changes to the position of the objective lens during routine microscope operation. We showed that within a ± 1 mm displacement range of the 100X, 1.35 NA objective lens away from its designed position, the PSF size increased by <3% and <11% in the lateral and axial dimensions, respectively, while the error in magnification was <0.5% within volumes extending ± 10 µm about the focal plane. Compared to the more traditional scan-lens/galvo-mirror combination, the two-mirror scanning geometry offers higher light efficiency and a more compact footprint, which could be beneficial to all OPM designs regardless of the use of a commercial base or not.
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Affiliation(s)
- George Sirinakis
- The Gurdon Institute and the Department of Genetics University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom
| | - Edward S Allgeyer
- The Gurdon Institute and the Department of Genetics University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom
| | - Dmitry Nashchekin
- The Gurdon Institute and the Department of Genetics University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom
| | - Daniel St Johnston
- The Gurdon Institute and the Department of Genetics University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom
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4
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Sommernes JR, Millett-Sikking A, Ströhl F. S-polarized light-sheets improve resolution and light-efficiency in oblique plane microscopy. Sci Rep 2024; 14:3540. [PMID: 38347049 PMCID: PMC10861444 DOI: 10.1038/s41598-024-53900-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/06/2024] [Indexed: 02/15/2024] Open
Abstract
Oblique plane microscopy (OPM) offers 3D optically sectioned imaging with high spatial- and temporal-resolution while enabling conventional sample mounting. The technique uses a concatenation of three microscopes, two for remote focusing and a tilted tertiary microscope, often including an immersion objective, to image an oblique sample plane. This design induces Fresnel reflections and a reduced effective aperture, thus impacting the resolution and light efficiency of the system. Using vectorial diffraction simulations, the system performance was characterized based on illumination angle and polarization, signal to noise ratio, and refractive index of the tertiary objective immersion. We show that for samples with high fluorescent anisotropy, s-polarized light-sheets yield higher average resolution for all system configurations, as well as higher light-efficiency. We also provide a tool for performance characterization of arbitrary light-sheet imaging systems.
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Affiliation(s)
- Jon-Richard Sommernes
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Florian Ströhl
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway.
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5
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Nemr CR, Sklavounos AA, Wheeler AR, Kelley SO. WITHDRAWN: Digital microfluidics as an emerging tool for bacterial protocols. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 29:133. [PMID: 38101571 DOI: 10.1016/j.slasd.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/30/2022] [Accepted: 10/25/2022] [Indexed: 12/17/2023]
Affiliation(s)
- Carine R Nemr
- Department of Chemistry, Harvey Mudd College, 301 Platt Boulevard, Claremont, CA, 91711, USA; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
| | - Alexandros A Sklavounos
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3G9, Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3G9, Canada; Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, M5S 3G9, Canada
| | - Shana O Kelley
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada; Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, M5S 3G9, Canada; Department of Pharmaceutical Science, University of Toronto, 144 College Street, Toronto, Ontario, M5S 3E5, Canada; Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA; Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
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6
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Park S, Na M, Chang S, Kim KH. High-resolution open-top axially swept light sheet microscopy. BMC Biol 2023; 21:248. [PMID: 37940973 PMCID: PMC10634022 DOI: 10.1186/s12915-023-01747-3] [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: 04/19/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Open-top light-sheet microscopy (OT-LSM) is a specialized microscopic technique for the high-throughput cellular imaging of optically cleared, large-sized specimens, such as the brain. Despite the development of various OT-LSM techniques, achieving submicron resolution in all dimensions remains. RESULTS We developed a high-resolution open-top axially swept LSM (HR-OTAS-LSM) for high-throughput and high-resolution imaging in all dimensions. High axial and lateral resolutions were achieved by using an aberration-corrected axially swept excitation light sheet in the illumination arm and a high numerical aperture (NA) immersion objective lens in the imaging arm, respectively. The high-resolution, high-throughput visualization of neuronal networks in mouse brain and retina specimens validated the performance of HR-OTAS-LSM. CONCLUSIONS The proposed HR-OTAS-LSM method represents a significant advancement in the high-resolution mapping of cellular networks in biological systems such as the brain and retina.
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Affiliation(s)
- Soohyun Park
- Department of Mechanical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Myeongsu Na
- Department of Research and Development Center, Crayon Technologies, 19 Sanmaru-ro, Guri, Gyeonggi-do, 11901, Republic of Korea
| | - Sunghoe Chang
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Ki Hean Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea.
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7
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DIBAJI HASSAN, SHOTORBAN ALIKAZEMINASABAN, HABIBI MAHSA, GRATTAN RACHELM, LUCERO SHAYNA, SCHODT DAVIDJ, LIDKE KEITHA, PETRUCCELLI JONATHAN, LIDKE DIANES, LIU SHENG, CHAKRABORTY TONMOY. Axial de-scanning using remote focusing in the detection arm of light-sheet microscopy. RESEARCH SQUARE 2023:rs.3.rs-3338831. [PMID: 37886461 PMCID: PMC10602066 DOI: 10.21203/rs.3.rs-3338831/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The ability to image at high speeds is necessary in biological imaging to capture fast-moving or transient events or to efficiently image large samples. However, due to the lack of rigidity of biological specimens, carrying out fast, high-resolution volumetric imaging without moving and agitating the sample has been a challenging problem. Pupil-matched remote focusing has been promising for high NA imaging systems with their low aberrations and wavelength independence, making it suitable for multicolor imaging. However, owing to the incoherent and unpolarized nature of the fluorescence signal, manipulating this emission light through remote focusing is challenging. Therefore, remote focusing has been primarily limited to the illumination arm, using polarized laser light for facilitating coupling in and out of the remote focusing optics. Here we introduce a novel optical design that can de-scan the axial focus movement in the detection arm of a microscope. Our method splits the fluorescence signal into S and P-polarized light and lets them pass through the remote focusing module separately and combines them with the camera. This allows us to use only one focusing element to perform aberration-free, multi-color, volumetric imaging without (a) compromising the fluorescent signal and (b) needing to perform sample/detection-objective translation. We demonstrate the capabilities of this scheme by acquiring fast dual-color 4D (3D space + time) image stacks, with an axial range of 70 μm and camera limited acquisition speed. Owing to its general nature, we believe this technique will find its application to many other microscopy techniques that currently use an adjustable Z-stage to carry out volumetric imaging such as confocal, 2-photon, and light sheet variants.
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Affiliation(s)
- HASSAN DIBAJI
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | | | - MAHSA HABIBI
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - RACHEL M GRATTAN
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, 87131, USA
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - SHAYNA LUCERO
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, 87131, USA
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - DAVID J. SCHODT
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - KEITH A. LIDKE
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, 87131, USA
| | - JONATHAN PETRUCCELLI
- Department of Physics, University at Albany–State University of NewYork,1400 Washington Avenue, Albany, NY 12222, USA
| | - DIANE S. LIDKE
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, 87131, USA
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - SHENG LIU
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - TONMOY CHAKRABORTY
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, 87131, USA
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8
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Hong W, Sparks H, Dunsby C. Alignment and characterization of remote-refocusing systems. APPLIED OPTICS 2023; 62:7431-7440. [PMID: 37855511 PMCID: PMC10575606 DOI: 10.1364/ao.500281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 10/20/2023]
Abstract
The technique of remote refocusing is used in optical microscopy to provide rapid axial scanning without mechanically perturbing the sample and in techniques such as oblique plane microscopy that build on remote refocusing to image a tilted plane within the sample. The magnification between the pupils of the primary (O1) and secondary (O2) microscope objectives of the remote-refocusing system has been shown previously by Mohanan and Corbett [J. Microsc.288, 95 (2022)JMICAR0022-272010.1111/jmi.12991] to be crucial in obtaining the broadest possible remote-refocusing range. In this work, we performed an initial alignment of a remote-refocusing system and then studied the effect of axial misalignments of O1 and O2, axial misalignment of the primary tube lens (TL1) relative to the secondary tube lens (TL2), lateral misalignments of TL2, and changes in the focal length of TL2. For each instance of the setup, we measured the mean point spread function F W H M xy of 100 nm fluorescent beads and the normalized bead integrated fluorescence signal, and we calculated the axial and lateral distortion of the system; all of these quantities were mapped over the remote-refocusing range and as a function of lateral image position. This allowed us to estimate the volume over which diffraction-limited performance is achieved and how this changes with the alignment of the system.
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Affiliation(s)
- Wenzhi Hong
- Photonics Group, Physics Department, Imperial College London, London, UK
| | - Hugh Sparks
- Photonics Group, Physics Department, Imperial College London, London, UK
| | - Chris Dunsby
- Photonics Group, Physics Department, Imperial College London, London, UK
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9
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Way GP, Sailem H, Shave S, Kasprowicz R, Carragher NO. Evolution and impact of high content imaging. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:292-305. [PMID: 37666456 DOI: 10.1016/j.slasd.2023.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/09/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023]
Abstract
The field of high content imaging has steadily evolved and expanded substantially across many industry and academic research institutions since it was first described in the early 1990's. High content imaging refers to the automated acquisition and analysis of microscopic images from a variety of biological sample types. Integration of high content imaging microscopes with multiwell plate handling robotics enables high content imaging to be performed at scale and support medium- to high-throughput screening of pharmacological, genetic and diverse environmental perturbations upon complex biological systems ranging from 2D cell cultures to 3D tissue organoids to small model organisms. In this perspective article the authors provide a collective view on the following key discussion points relevant to the evolution of high content imaging: • Evolution and impact of high content imaging: An academic perspective • Evolution and impact of high content imaging: An industry perspective • Evolution of high content image analysis • Evolution of high content data analysis pipelines towards multiparametric and phenotypic profiling applications • The role of data integration and multiomics • The role and evolution of image data repositories and sharing standards • Future perspective of high content imaging hardware and software.
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Affiliation(s)
- Gregory P Way
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Heba Sailem
- School of Cancer and Pharmaceutical Sciences, King's College London, UK
| | - Steven Shave
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Rd, Stevenage SG1 2NY, UK; Edinburgh Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, UK
| | - Richard Kasprowicz
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Rd, Stevenage SG1 2NY, UK
| | - Neil O Carragher
- Edinburgh Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, UK.
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10
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Saliba N, Gagliano G, Gustavsson AK. Whole-cell multi-target single-molecule super-resolution imaging in 3D with microfluidics and a single-objective tilted light sheet. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559876. [PMID: 37808751 PMCID: PMC10557638 DOI: 10.1101/2023.09.27.559876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Multi-target single-molecule super-resolution fluorescence microscopy offers a powerful means of understanding the distributions and interplay between multiple subcellular structures at the nanoscale. However, single-molecule super-resolution imaging of whole mammalian cells is often hampered by high fluorescence background and slow acquisition speeds, especially when imaging multiple targets in 3D. In this work, we have mitigated these issues by developing a steerable, dithered, single-objective tilted light sheet for optical sectioning to reduce fluorescence background and a pipeline for 3D nanoprinting microfluidic systems for reflection of the light sheet into the sample and for efficient and automated solution exchange. By combining these innovations with PSF engineering for nanoscale localization of individual molecules in 3D, deep learning for analysis of overlapping emitters, active 3D stabilization for drift correction and long-term imaging, and Exchange-PAINT for sequential multi-target imaging without chromatic offsets, we demonstrate whole-cell multi-target 3D single-molecule super-resolution imaging with improved precision and imaging speed.
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Affiliation(s)
- Nahima Saliba
- Department of Chemistry, Rice University, Houston, TX, 77005
| | - Gabriella Gagliano
- Department of Chemistry, Rice University, Houston, TX, 77005
- Smalley-Curl Institute, Rice University, Houston, TX, 77005
- Applied Physics Program, Rice University, Houston, TX, 77005
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, 77005
- Smalley-Curl Institute, Rice University, Houston, TX, 77005
- Department of BioSciences, Rice University, Houston, TX, 77005
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, 77005
- Institute of Biosciences and Bioengineering, Rice University, Houston, TX, 77005
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030
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11
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Smith MB, Sparks H, Almagro J, Chaigne A, Behrens A, Dunsby C, Salbreux G. Active mesh and neural network pipeline for cell aggregate segmentation. Biophys J 2023; 122:1586-1599. [PMID: 37002604 PMCID: PMC10183373 DOI: 10.1016/j.bpj.2023.03.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/16/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
Segmenting cells within cellular aggregates in 3D is a growing challenge in cell biology due to improvements in capacity and accuracy of microscopy techniques. Here, we describe a pipeline to segment images of cell aggregates in 3D. The pipeline combines neural network segmentations with active meshes. We apply our segmentation method to cultured mouse mammary gland organoids imaged over 24 h with oblique plane microscopy, a high-throughput light-sheet fluorescence microscopy technique. We show that our method can also be applied to images of mouse embryonic stem cells imaged with a spinning disc microscope. We segment individual cells based on nuclei and cell membrane fluorescent markers, and track cells over time. We describe metrics to quantify the quality of the automated segmentation. Our segmentation pipeline involves a Fiji plugin that implements active mesh deformation and allows a user to create training data, automatically obtain segmentation meshes from original image data or neural network prediction, and manually curate segmentation data to identify and correct mistakes. Our active meshes-based approach facilitates segmentation postprocessing, correction, and integration with neural network prediction.
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Affiliation(s)
| | - Hugh Sparks
- Photonics Group, Department of Physics, Imperial College London, London, United Kingdom
| | | | - Agathe Chaigne
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Axel Behrens
- Cancer Stem Cell Team, The Institute of Cancer Research, London, United Kingdom
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, London, United Kingdom
| | - Guillaume Salbreux
- The Francis Crick Institute, London, United Kingdom; Department of Genetics and Evolution, Geneva, Switzerland.
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12
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Zhu T, Nie J, Yu T, Zhu D, Huang Y, Chen Z, Gu Z, Tang J, Li D, Fei P. Large-scale high-throughput 3D culture, imaging, and analysis of cell spheroids using microchip-enhanced light-sheet microscopy. BIOMEDICAL OPTICS EXPRESS 2023; 14:1659-1669. [PMID: 37078040 PMCID: PMC10110308 DOI: 10.1364/boe.485217] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/24/2023] [Accepted: 03/06/2023] [Indexed: 05/03/2023]
Abstract
Light sheet microscopy combined with a microchip is an emerging tool in biomedical research that notably improves efficiency. However, microchip-enhanced light-sheet microscopy is limited by noticeable aberrations induced by the complex refractive indices in the chip. Herein, we report a droplet microchip that is specifically engineered to be capable of large-scale culture of 3D spheroids (over 600 samples per chip) and has a polymer index matched to water (difference <1%). When combined with a lab-built open-top light-sheet microscope, this microchip-enhanced microscopy technique allows 3D time-lapse imaging of the cultivated spheroids with ∼2.5-µm single-cell resolution and a high throughput of ∼120 spheroids per minute. This technique was validated by a comparative study on the proliferation and apoptosis rates of hundreds of spheroids with or without treatment with the apoptosis-inducing drug Staurosporine.
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Affiliation(s)
- Tingting Zhu
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jun Nie
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Tingting Yu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yanyi Huang
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
- College of Chemistry, Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Zaozao Chen
- State Key Laboratory of Bioelectronics School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhongze Gu
- State Key Laboratory of Bioelectronics School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jiang Tang
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Dongyu Li
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Peng Fei
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, China
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13
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Culley J, Nagle PW, Dawson JC, Carragher NO. Patient derived glioma stem cell spheroid reporter assays for live cell high content analysis. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:13-19. [PMID: 36116760 DOI: 10.1016/j.slasd.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/03/2022] [Accepted: 09/13/2022] [Indexed: 12/01/2022]
Abstract
Three dimensional models of cell culture enables researchers to recreate aspects of tumour biology not replicated by traditional two dimensional techniques. Here we describe a protocol to enable automated high throughput phenotypic profiling across panels of patient derived glioma stem cell spheroid models. We demonstrate the use of both live/dead cell end-points and monitor the dynamic changes in the cell cycle using cell lines expressing the FUCCI cell cycle reporter. Together, these assays provide additional insight into the mechanism of action of compound treatments over traditional cell viability assay endpoints.
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Affiliation(s)
- Jayne Culley
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Peter W Nagle
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK; MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, Scotland, EH16 4TJ, UK
| | - John C Dawson
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK.
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14
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Singh R, Subramanian K, Power RM, Paix A, Gil A, Ikmi A, Prevedel R. Oblique plane microscope for mesoscopic imaging of freely moving organisms with cellular resolution. OPTICS EXPRESS 2023; 31:2292-2301. [PMID: 36785246 DOI: 10.1364/oe.471845] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/25/2022] [Indexed: 05/25/2023]
Abstract
Several important questions in biology require non-invasive and three-dimensional imaging techniques with an appropriate spatiotemporal resolution that permits live organisms to move in an unconstrained fashion over an extended field-of-view. While selective-plane illumination microscopy (SPIM) has emerged as a powerful method to observe live biological specimens at high spatio-temporal resolution, typical implementations often necessitate constraining sample mounting or lack the required volumetric speed. Here, we report on an open-top, dual-objective oblique plane microscope (OPM) capable of observing millimeter-sized, freely moving animals at cellular resolution. We demonstrate the capabilities of our mesoscopic OPM (MesOPM) by imaging the behavioral dynamics of the sea anemone Nematostella vectensis over 1.56 × 1.56 × 0.25 mm at 1.5 × 2.8 × 5.3 µm resolution and 0.5 Hz volume rate.
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15
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Shao W, Chang M, Emmerich K, Kanold PO, Mumm JS, Yi J. Mesoscopic oblique plane microscopy with a diffractive light-sheet for large-scale 4D cellular resolution imaging. OPTICA 2022; 9:1374-1385. [PMID: 38384442 PMCID: PMC10881189 DOI: 10.1364/optica.471101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/31/2022] [Indexed: 02/23/2024]
Abstract
Fundamental understanding of large-scale dynamic connectivity within a living organism requires volumetric imaging over a large field of view (FOV) at biologically relevant speed and resolution. However, most microscopy methods make trade-offs between FOV and axial resolution, making it challenging to observe highly dynamic processes at cellular resolution in 3D across mesoscopic scales (e.g., whole zebrafish larva). To overcome this limitation, we have developed mesoscopic oblique plane microscopy (Meso-OPM) with a diffractive light sheet. By augmenting the illumination angle of the light sheet with a transmission grating, we improved the axial resolution approximately sixfold over existing methods and approximately twofold beyond the diffraction limitation of the primary objective lens. We demonstrated a FOV up to 5.4 mm × 3.3 mm with resolution of 2.5 μm × 3 μm × 6 μm, allowing volumetric imaging of 3D cellular structures with a single scan. Applying Meso-OPM for in vivo imaging of zebrafish larvae, we report here in toto whole-body volumetric recordings of neuronal activity at 2 Hz volume rate and whole-body volumetric recordings of blood flow dynamics at 5 Hz with 3D cellular resolution.
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Affiliation(s)
- Wenjun Shao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21231, USA
- Department of Ophthalmology, Johns Hopkins University, Baltimore, Maryland 21231, USA
| | - Minzi Chang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21231, USA
| | - Kevin Emmerich
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21231, USA
| | - Patrick O. Kanold
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21231, USA
| | - Jeff S. Mumm
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21231, USA
| | - Ji Yi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21231, USA
- Department of Ophthalmology, Johns Hopkins University, Baltimore, Maryland 21231, USA
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16
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Dilliway C, Dyer O, Mandrou E, Mitchell D, Menon G, Sparks H, Kapitany V, Payne-Dwyer A. Working at the interface of physics and biology: An early career researcher perspective. iScience 2022; 25:105615. [DOI: 10.1016/j.isci.2022.105615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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17
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Hung ST, Cnossen J, Fan D, Siemons M, Jurriens D, Grußmayer K, Soloviev O, Kapitein LC, Smith CS. SOLEIL: single-objective lens inclined light sheet localization microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:3275-3294. [PMID: 35781973 PMCID: PMC9208595 DOI: 10.1364/boe.451634] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
High-NA light sheet illumination can improve the resolution of single-molecule localization microscopy (SMLM) by reducing the background fluorescence. These approaches currently require custom-made sample holders or additional specialized objectives, which makes the sample mounting or the optical system complex and therefore reduces the usability of these approaches. Here, we developed a single-objective lens-inclined light sheet microscope (SOLEIL) that is capable of 2D and 3D SMLM in thick samples. SOLEIL combines oblique illumination with point spread function PSF engineering to enable dSTORM imaging in a wide variety of samples. SOLEIL is compatible with standard sample holders and off-the-shelve optics and standard high NA objectives. To accomplish optimal optical sectioning we show that there is an ideal oblique angle and sheet thickness. Furthermore, to show what optical sectioning delivers for SMLM we benchmark SOLEIL against widefield and HILO microscopy with several biological samples. SOLEIL delivers in 15 μm thick Caco2-BBE cells a 374% higher intensity to background ratio and a 54% improvement in the estimated CRLB compared to widefield illumination, and a 184% higher intensity to background ratio and a 20% improvement in the estimated CRLB compared to HILO illumination.
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Affiliation(s)
- Shih-Te Hung
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Jelmer Cnossen
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Daniel Fan
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Marijn Siemons
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Daphne Jurriens
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Kristin Grußmayer
- Department of Bionanoscience and Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Oleg Soloviev
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
- Flexible Optical B.V., Polakweg 10-11, 2288 GG Rijswijk, Netherlands
| | - Lukas C. Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Carlas S. Smith
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
- Department of Imaging Physics, Delft University of Technology, Delft, Netherlands
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18
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A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues. Nat Methods 2022; 19:613-619. [PMID: 35545715 DOI: 10.1038/s41592-022-01468-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/24/2022] [Indexed: 12/15/2022]
Abstract
Light-sheet microscopy has emerged as the preferred means for high-throughput volumetric imaging of cleared tissues. However, there is a need for a flexible system that can address imaging applications with varied requirements in terms of resolution, sample size, tissue-clearing protocol, and transparent sample-holder material. Here, we present a 'hybrid' system that combines a unique non-orthogonal dual-objective and conventional (orthogonal) open-top light-sheet (OTLS) architecture for versatile multi-scale volumetric imaging. We demonstrate efficient screening and targeted sub-micrometer imaging of sparse axons within an intact, cleared mouse brain. The same system enables high-throughput automated imaging of multiple specimens, as spotlighted by a quantitative multi-scale analysis of brain metastases. Compared with existing academic and commercial light-sheet microscopy systems, our hybrid OTLS system provides a unique combination of versatility and performance necessary to satisfy the diverse requirements of a growing number of cleared-tissue imaging applications.
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19
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Yang B, Lange M, Millett-Sikking A, Zhao X, Bragantini J, VijayKumar S, Kamb M, Gómez-Sjöberg R, Solak AC, Wang W, Kobayashi H, McCarroll MN, Whitehead LW, Fiolka RP, Kornberg TB, York AG, Royer LA. DaXi-high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy. Nat Methods 2022; 19:461-469. [PMID: 35314838 PMCID: PMC9007742 DOI: 10.1038/s41592-022-01417-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 02/08/2022] [Indexed: 11/19/2022]
Abstract
The promise of single-objective light-sheet microscopy is to combine the convenience of standard single-objective microscopes with the speed, coverage, resolution and gentleness of light-sheet microscopes. We present DaXi, a single-objective light-sheet microscope design based on oblique plane illumination that achieves: (1) a wider field of view and high-resolution imaging via a custom remote focusing objective; (2) fast volumetric imaging over larger volumes without compromising image quality or necessitating tiled acquisition; (3) fuller image coverage for large samples via multi-view imaging and (4) higher throughput multi-well imaging via remote coverslip placement. Our instrument achieves a resolution of 450 nm laterally and 2 μm axially over an imaging volume of 3,000 × 800 × 300 μm. We demonstrate the speed, field of view, resolution and versatility of our instrument by imaging various systems, including Drosophila egg chamber development, zebrafish whole-brain activity and zebrafish embryonic development – up to nine embryos at a time. The DaXi single-objective light-sheet microscope achieves fast, high-quality imaging of large volumes. DaXi’s design allows increased scanning range without sacrificing imaging speed or quality, multiview imaging and versatile sample mounting.
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Affiliation(s)
- Bin Yang
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | | | | | - Xiang Zhao
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | - Mason Kamb
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | - Wanpeng Wang
- Cardiovascular Research Institute, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | | | - Matthew N McCarroll
- Department of Pharmaceutical Chemistry, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Lachlan W Whitehead
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Reto P Fiolka
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Thomas B Kornberg
- Cardiovascular Research Institute, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Andrew G York
- Calico Life Sciences LLC, South San Francisco, CA, USA
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20
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Munck S, Swoger J, Coll-Lladó M, Gritti N, Vande Velde G. Maximizing content across scales: Moving multimodal microscopy and mesoscopy toward molecular imaging. Curr Opin Chem Biol 2021; 63:188-199. [PMID: 34198170 DOI: 10.1016/j.cbpa.2021.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/06/2021] [Accepted: 05/16/2021] [Indexed: 10/21/2022]
Abstract
Molecular imaging aims to depict the molecules in living patients. However, because this aim is still far beyond reach, patchworks of different solutions need to be used to tackle this overarching goal. From the vast toolbox of imaging techniques, we focus on those recent advances in optical microscopy that image molecules and cells at the submicron to centimeter scale. Mesoscopic imaging covers the "imaging gap" between techniques such as confocal microscopy and magnetic resonance imagingthat image entire live samples but with limited resolution. Microscopy focuses on the cellular level; mesoscopy visualizes the organization of molecules and cells into tissues and organs. The correlation between these techniques allows us to combine disciplines ranging from whole body imaging to basic research of model systems. We review current developments focused on improving microscopic and mesoscopic imaging technologies and on hardware and software that push the current sensitivity and resolution boundaries.
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Affiliation(s)
- Sebastian Munck
- VIB-KU Leuven Center for Brain & Disease Research, Light Microscopy Expertise Unit & VIB BioImaging Core, O&N4 Herestraat 49 box 602, Leuven, 3000, Belgium; KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N4 Herestraat 49 box 602, Leuven, 3000, Belgium
| | - Jim Swoger
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, 08003, Spain
| | | | - Nicola Gritti
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, 08003, Spain
| | - Greetje Vande Velde
- Department of Imaging and Pathology, Faculty of Medicine, KU Leuven, Leuven, Belgium.
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