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Luu P, Fraser SE, Schneider F. More than double the fun with two-photon excitation microscopy. Commun Biol 2024; 7:364. [PMID: 38531976 DOI: 10.1038/s42003-024-06057-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
For generations researchers have been observing the dynamic processes of life through the lens of a microscope. This has offered tremendous insights into biological phenomena that span multiple orders of time- and length-scales ranging from the pure magic of molecular reorganization at the membrane of immune cells, to cell migration and differentiation during development or wound healing. Standard fluorescence microscopy techniques offer glimpses at such processes in vitro, however, when applied in intact systems, they are challenged by reduced signal strengths and signal-to-noise ratios that result from deeper imaging. As a remedy, two-photon excitation (TPE) microscopy takes a special place, because it allows us to investigate processes in vivo, in their natural environment, even in a living animal. Here, we review the fundamental principles underlying TPE aimed at basic and advanced microscopy users interested in adopting TPE for intravital imaging. We focus on applications in neurobiology, present current trends towards faster, wider and deeper imaging, discuss the combination with photon counting technologies for metabolic imaging and spectroscopy, as well as highlight outstanding issues and drawbacks in development and application of these methodologies.
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Affiliation(s)
- Peter Luu
- Translational Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biological Sciences, Division of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Scott E Fraser
- Translational Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biological Sciences, Division of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
- Alfred Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Falk Schneider
- Translational Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA.
- Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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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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Pollak DJ, Chawla G, Andreev A, Prober DA. First steps into the cloud: Using Amazon data storage and computing with Python notebooks. PLoS One 2023; 18:e0278316. [PMID: 36757918 PMCID: PMC9910747 DOI: 10.1371/journal.pone.0278316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 11/15/2022] [Indexed: 02/10/2023] Open
Abstract
With the oncoming age of big data, biologists are encountering more use cases for cloud-based computing to streamline data processing and storage. Unfortunately, cloud platforms are difficult to learn, and there are few resources for biologists to demystify them. We have developed a guide for experimental biologists to set up cloud processing on Amazon Web Services to cheaply outsource data processing and storage. Here we provide a guide for setting up a computing environment in the cloud and showcase examples of using Python and Julia programming languages. We present example calcium imaging data in the zebrafish brain and corresponding analysis using suite2p software. Tools for budget and user management are further discussed in the attached protocol. Using this guide, researchers with limited coding experience can get started with cloud-based computing or move existing coding infrastructure into the cloud environment.
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Affiliation(s)
- Daniel J. Pollak
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Tianqiao and Chrissy Chen Institute for Neuroscience, California Institute of Technology, Pasadena, California, United States of America
| | - Gautam Chawla
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Tianqiao and Chrissy Chen Institute for Neuroscience, California Institute of Technology, Pasadena, California, United States of America
| | - Andrey Andreev
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Tianqiao and Chrissy Chen Institute for Neuroscience, California Institute of Technology, Pasadena, California, United States of America
- * E-mail:
| | - David A. Prober
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Tianqiao and Chrissy Chen Institute for Neuroscience, California Institute of Technology, Pasadena, California, United States of America
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Keomanee-Dizon K, Jones M, Luu P, Fraser SE, Truong TV. Extended depth-of-field light-sheet microscopy improves imaging of large volumes at high numerical aperture. APPLIED PHYSICS LETTERS 2022; 121:163701. [PMID: 36276589 PMCID: PMC9586705 DOI: 10.1063/5.0101426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Light-sheet microscopes must compromise among field of view, optical sectioning, resolution, and detection efficiency. High-numerical-aperture (NA) detection objective lenses provide higher resolution, but their narrow depth of field inefficiently captures the fluorescence signal generated throughout the thickness of the illumination light sheet when imaging large volumes. Here, we present ExD-SPIM (extended depth-of-field selective-plane illumination microscopy), an improved light-sheet microscopy strategy that solves this limitation by extending the depth of field (DOF) of high-NA detection objectives to match the thickness of the illumination light sheet. This extension of the DOF uses a phase mask to axially stretch the point-spread function of the objective lens while largely preserving lateral resolution. This matching of the detection DOF to the illumination-sheet thickness increases the total fluorescence collection, reduces the background, and improves the overall signal-to-noise ratio (SNR), as shown by numerical simulations, imaging of bead phantoms, and imaging living animals. In comparison to conventional light sheet imaging with low-NA detection that yields equivalent DOF, the results show that ExD-SPIM increases the SNR by more than threefold and dramatically reduces the rate of photobleaching. Compared to conventional high-NA detection, ExD-SPIM improves the signal sensitivity and volumetric coverage of whole-brain activity imaging, increasing the number of detected neurons by over a third.
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Affiliation(s)
- Kevin Keomanee-Dizon
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, USA
| | - Matt Jones
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, USA
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Messina A, Potrich D, Perrino M, Sheardown E, Miletto Petrazzini ME, Luu P, Nadtochiy A, Truong TV, Sovrano VA, Fraser SE, Brennan CH, Vallortigara G. Quantity as a Fish Views It: Behavior and Neurobiology. Front Neuroanat 2022; 16:943504. [PMID: 35911657 PMCID: PMC9334151 DOI: 10.3389/fnana.2022.943504] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
An ability to estimate quantities, such as the number of conspecifics or the size of a predator, has been reported in vertebrates. Fish, in particular zebrafish, may be instrumental in advancing the understanding of magnitude cognition. We review here the behavioral studies that have described the ecological relevance of quantity estimation in fish and the current status of the research aimed at investigating the neurobiological bases of these abilities. By combining behavioral methods with molecular genetics and calcium imaging, the involvement of the retina and the optic tectum has been documented for the estimation of continuous quantities in the larval and adult zebrafish brain, and the contributions of the thalamus and the dorsal-central pallium for discrete magnitude estimation in the adult zebrafish brain. Evidence for basic circuitry can now be complemented and extended to research that make use of transgenic lines to deepen our understanding of quantity cognition at genetic and molecular levels.
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Affiliation(s)
- Andrea Messina
- Centre for Mind/Brain Sciences, University of Trento, Rovereto, Italy
| | - Davide Potrich
- Centre for Mind/Brain Sciences, University of Trento, Rovereto, Italy
| | - Matilde Perrino
- Centre for Mind/Brain Sciences, University of Trento, Rovereto, Italy
| | - Eva Sheardown
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, New Hunt’s House, Kings College London, London, United Kingdom
| | | | - Peter Luu
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, United States
| | - Anna Nadtochiy
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, United States
| | - Thai V. Truong
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, United States
| | - Valeria Anna Sovrano
- Centre for Mind/Brain Sciences, University of Trento, Rovereto, Italy
- Department of Psychology and Cognitive Science, University of Trento, Rovereto, Italy
| | - Scott E. Fraser
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, United States
| | - Caroline H. Brennan
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, United Kingdom
| | - Giorgio Vallortigara
- Centre for Mind/Brain Sciences, University of Trento, Rovereto, Italy
- *Correspondence: Giorgio Vallortigara,
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Dyer L, Parker A, Paphiti K, Sanderson J. Lightsheet Microscopy. Curr Protoc 2022; 2:e448. [PMID: 35838628 DOI: 10.1002/cpz1.448] [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: 11/09/2022]
Abstract
In this paper, we review lightsheet (selective plane illumination) microscopy for mouse developmental biologists. There are different means of forming the illumination sheet, and we discuss these. We explain how we introduced the lightsheet microscope economically into our core facility and present our results on fixed and living samples. We also describe methods of clearing fixed samples for three-dimensional imaging and discuss the various means of preparing samples with particular reference to mouse cilia, adipose spheroids, and cochleae. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Laura Dyer
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Andrew Parker
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Keanu Paphiti
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
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de Vito G, Turrini L, Müllenbroich C, Ricci P, Sancataldo G, Mazzamuto G, Tiso N, Sacconi L, Fanelli D, Silvestri L, Vanzi F, Pavone FS. Fast whole-brain imaging of seizures in zebrafish larvae by two-photon light-sheet microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:1516-1536. [PMID: 35414999 PMCID: PMC8973167 DOI: 10.1364/boe.434146] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 05/27/2023]
Abstract
Light-sheet fluorescence microscopy (LSFM) enables real-time whole-brain functional imaging in zebrafish larvae. Conventional one-photon LSFM can however induce undesirable visual stimulation due to the use of visible excitation light. The use of two-photon (2P) excitation, employing near-infrared invisible light, provides unbiased investigation of neuronal circuit dynamics. However, due to the low efficiency of the 2P absorption process, the imaging speed of this technique is typically limited by the signal-to-noise-ratio. Here, we describe a 2P LSFM setup designed for non-invasive imaging that enables quintuplicating state-of-the-art volumetric acquisition rate of the larval zebrafish brain (5 Hz) while keeping low the laser intensity on the specimen. We applied our system to the study of pharmacologically-induced acute seizures, characterizing the spatial-temporal dynamics of pathological activity and describing for the first time the appearance of caudo-rostral ictal waves (CRIWs).
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Affiliation(s)
- Giuseppe de Vito
- University of Florence, Department of Neuroscience, Psychology, Drug Research and Child Health, Viale Pieraccini 6, Florence, Italy, 50139, Italy
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- Co-first authors with equal contribution
| | - Lapo Turrini
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- University of Florence, Department of Physics and Astronomy, Via Sansone 1, Sesto Fiorentino 50019, Italy
- Co-first authors with equal contribution
| | - Caroline Müllenbroich
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- School of Physics and Astronomy, Kelvin Building, University of Glasgow, G12 8QQ, Glasgow, UK
- National Institute of Optics, National Research Council, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
| | - Pietro Ricci
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
| | - Giuseppe Sancataldo
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- University of Florence, Department of Physics and Astronomy, Via Sansone 1, Sesto Fiorentino 50019, Italy
| | - Giacomo Mazzamuto
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- National Institute of Optics, National Research Council, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
| | - Natascia Tiso
- University of Padova, Department of Biology, Via U. Bassi 58/B, Padova 35131, Italy
| | - Leonardo Sacconi
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- National Institute of Optics, National Research Council, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
| | - Duccio Fanelli
- University of Florence, Department of Physics and Astronomy, Via Sansone 1, Sesto Fiorentino 50019, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- University of Florence, Department of Physics and Astronomy, Via Sansone 1, Sesto Fiorentino 50019, Italy
- National Institute of Optics, National Research Council, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
| | - Francesco Vanzi
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino 50019, Italy
| | - Francesco Saverio Pavone
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- University of Florence, Department of Physics and Astronomy, Via Sansone 1, Sesto Fiorentino 50019, Italy
- National Institute of Optics, National Research Council, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
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