1
|
Tan Q, Wu H, Liu Y, Chen Q, Zuo C. Advances in Axial Resolution Strategies for Super-Resolution Imaging Systems. SMALL METHODS 2025:e2401926. [PMID: 39981781 DOI: 10.1002/smtd.202401926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Revised: 12/25/2024] [Indexed: 02/22/2025]
Abstract
3D fluorescence super-resolution imaging technology can reconstruct the 3D structure of biological cells in space, which is crucial for observing the intricate internal structures of cells and studying the organization and function of tissues and organs. However, even with super-resolution imaging techniques that surpass the diffraction limit, the axial resolution typically only reaches one-third to one-half of the lateral resolution. Achieving true axial or 3D super-resolution imaging of samples remains a significant challenge. In light of this, this review summarizes the research progress in axial super-resolution imaging techniques, with a focus on the principles, developments, and characteristics of these techniques, and provides an outlook on their future development directions. This paper aims to provide valuable reference material for researchers in the field.
Collapse
Affiliation(s)
- Qiwen Tan
- Smart Computational Imaging Laboratory (SCILab), School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu Province, 210094, China
- Jiangsu Key Laboratory of Spectral Imaging & Intelligent Sense, Nanjing University of Science and Technology, Nanjing, Jiangsu Province, 210094, China
- Smart Computational Imaging Research Institute (SCIRI) of Nanjing University of Science and Technology, Nanjing, Jiangsu Province, 210094, China
| | - Hongjun Wu
- Smart Computational Imaging Laboratory (SCILab), School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu Province, 210094, China
- Jiangsu Key Laboratory of Spectral Imaging & Intelligent Sense, Nanjing University of Science and Technology, Nanjing, Jiangsu Province, 210094, China
- Smart Computational Imaging Research Institute (SCIRI) of Nanjing University of Science and Technology, Nanjing, Jiangsu Province, 210094, China
| | - Yongtao Liu
- Smart Computational Imaging Laboratory (SCILab), School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu Province, 210094, China
- Jiangsu Key Laboratory of Spectral Imaging & Intelligent Sense, Nanjing University of Science and Technology, Nanjing, Jiangsu Province, 210094, China
- Smart Computational Imaging Research Institute (SCIRI) of Nanjing University of Science and Technology, Nanjing, Jiangsu Province, 210094, China
| | - Qian Chen
- Jiangsu Key Laboratory of Spectral Imaging & Intelligent Sense, Nanjing University of Science and Technology, Nanjing, Jiangsu Province, 210094, China
| | - Chao Zuo
- Smart Computational Imaging Laboratory (SCILab), School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu Province, 210094, China
- Jiangsu Key Laboratory of Spectral Imaging & Intelligent Sense, Nanjing University of Science and Technology, Nanjing, Jiangsu Province, 210094, China
- Smart Computational Imaging Research Institute (SCIRI) of Nanjing University of Science and Technology, Nanjing, Jiangsu Province, 210094, China
| |
Collapse
|
2
|
Ruan X, Mueller M, Liu G, Görlitz F, Fu TM, Milkie DE, Lillvis JL, Kuhn A, Gan Chong J, Hong JL, Herr CYA, Hercule W, Nienhaus M, Killilea AN, Betzig E, Upadhyayula S. Image processing tools for petabyte-scale light sheet microscopy data. Nat Methods 2024; 21:2342-2352. [PMID: 39420143 PMCID: PMC11621031 DOI: 10.1038/s41592-024-02475-4] [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: 02/15/2024] [Accepted: 09/16/2024] [Indexed: 10/19/2024]
Abstract
Light sheet microscopy is a powerful technique for high-speed three-dimensional imaging of subcellular dynamics and large biological specimens. However, it often generates datasets ranging from hundreds of gigabytes to petabytes in size for a single experiment. Conventional computational tools process such images far slower than the time to acquire them and often fail outright due to memory limitations. To address these challenges, we present PetaKit5D, a scalable software solution for efficient petabyte-scale light sheet image processing. This software incorporates a suite of commonly used processing tools that are optimized for memory and performance. Notable advancements include rapid image readers and writers, fast and memory-efficient geometric transformations, high-performance Richardson-Lucy deconvolution and scalable Zarr-based stitching. These features outperform state-of-the-art methods by over one order of magnitude, enabling the processing of petabyte-scale image data at the full teravoxel rates of modern imaging cameras. The software opens new avenues for biological discoveries through large-scale imaging experiments.
Collapse
Affiliation(s)
- Xiongtao Ruan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, US.
| | - Matthew Mueller
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, US
- Howard Hughes Medical Institute, Berkeley, CA, US
| | - Gaoxiang Liu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, US
| | - Frederik Görlitz
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, US
- Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Tian-Ming Fu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, US
- Department of Electrical and Computer Engineering, Princeton University, Princeton, NJ, US
| | - Daniel E Milkie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, US
| | - Joshua L Lillvis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, US
| | | | - Johnny Gan Chong
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, US
| | - Jason Li Hong
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, US
| | - Chu Yi Aaron Herr
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, US
| | - Wilmene Hercule
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, US
| | | | - Alison N Killilea
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, US
| | - Eric Betzig
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, US.
- Howard Hughes Medical Institute, Berkeley, CA, US.
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, US.
- Department of Physics, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, US.
| | - Srigokul Upadhyayula
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, US.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, US.
- Chan Zuckerberg Biohub, San Francisco, CA, US.
| |
Collapse
|
3
|
Neyhart E, Zhou N, Munn BR, Law RG, Smith C, Mridha ZH, Blanco FA, Li G, Li Y, Hu M, McGinley MJ, Shine JM, Reimer J. Cortical acetylcholine dynamics are predicted by cholinergic axon activity and behavior state. Cell Rep 2024; 43:114808. [PMID: 39383037 PMCID: PMC11755675 DOI: 10.1016/j.celrep.2024.114808] [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: 01/29/2024] [Revised: 07/18/2024] [Accepted: 09/13/2024] [Indexed: 10/11/2024] Open
Abstract
Acetylcholine (ACh) is thought to play a role in driving the rapid, spontaneous brain-state transitions that occur during wakefulness; however, the spatiotemporal properties of cortical ACh activity during these state changes are still unclear. We perform simultaneous imaging of GRAB-ACh sensors, GCaMP-expressing basal forebrain axons, and behavior to address this question. We observed a high correlation between axon and GRAB-ACh activity around periods of locomotion and pupil dilation. GRAB-ACh fluorescence could be accurately predicted from axonal activity alone, and local ACh activity decreased at farther distances from an axon. Deconvolution of GRAB-ACh traces allowed us to account for sensor kinetics and emphasized rapid clearance of small ACh transients. We trained a model to predict ACh from pupil size and running speed, which generalized well to unseen data. These results contribute to a growing understanding of the precise timing and spatial characteristics of cortical ACh during fast brain-state transitions.
Collapse
Affiliation(s)
- Erin Neyhart
- Neuroscience Department, Baylor College of Medicine, Houston, TX 77030, USA
| | - Na Zhou
- Neuroscience Department, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brandon R Munn
- Brain and Mind Centre, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; Complex Systems Group, School of Physics, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Robert G Law
- Neuroscience Department, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cameron Smith
- Neuroscience Department, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zakir H Mridha
- Neuroscience Department, Baylor College of Medicine, Houston, TX 77030, USA
| | - Francisco A Blanco
- Neuroscience Department, Baylor College of Medicine, Houston, TX 77030, USA
| | - Guochuan Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Ming Hu
- Neuroscience Department, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew J McGinley
- Neuroscience Department, Baylor College of Medicine, Houston, TX 77030, USA
| | - James M Shine
- Brain and Mind Centre, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; Complex Systems Group, School of Physics, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jacob Reimer
- Neuroscience Department, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
4
|
Kumar P, Mondal PP. Multicolor iLIFE (m-iLIFE) volume cytometry for high-throughput imaging of multiple organelles. Sci Rep 2024; 14:23798. [PMID: 39394224 PMCID: PMC11470118 DOI: 10.1038/s41598-024-73667-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 09/19/2024] [Indexed: 10/13/2024] Open
Abstract
To be able to resolve multiple organelles at high throughput is an incredible achievement. This will have immediate implications in a range of fields ranging from fundamental cell biology to translational medicine. To realize such a high-throughput multicolor interrogation modality, we have developed a light-sheet based flow imaging system that is capable of visualizing multiple sub-cellular components with organelle-level resolution. This is possible due to the unique optical design that combines an illumination system comprising two collinear light sheets illuminating the flowing cells and a dedicated dual-color 4f-detection, enabling simultaneous recording of multiple organelles. The system PSF sections up to 4 parallel microfluidic channels through which cells are flowing, and multicolor images of cell cross-sections are recorded. The data is then computationally processed (filtered using ML algorithm, shift-corrected, and merged) and combined to reconstruct the 3D multicolor volume. System testing is conducted using multicolor fluorescent nano-beads (size ∼ 175 nm) and flow-based imaging parameters (PSF size, motion-blur, flow rate, frame rate, and number of cell-sections) are determined for quality imaging. Drug treatment studies were carried out for healthy and cancerous HeLa cells to check the performance of the proposed system. The cells were treated with a drug (Vincristine, which is known to promote mitochondrial fission in cells), and the same is compared with untreated control cells. The proposed multicolor iLIFE system could screen ∼ 800 cells/min (at a flow speed of 2490 μ m/s), and the drug treatment studies were carried out up to 24 h. Studies showed the disintegration of mitochondrial network and dysfunctional lysosomes and their accumulation at the cell membrane, which is a clear indication of cell apoptosis. Compared to control cells (untreated), the mortality is highest at a concentration of 500 nM post 12 h of drug treatment. With the capability of multiorganelle interrogation and organelle-level resolution, the multicolor iLIFE cytometry system is suitably placed to assist optical imaging and biomedical research.
Collapse
Affiliation(s)
- Prashant Kumar
- Mondal Lab, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Partha Pratim Mondal
- Mondal Lab, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India.
- Centre for Cryogenic Technology, Indian Institute of Science, Bangalore, 560012, India.
| |
Collapse
|
5
|
Zhu E, Li YR, Margolis S, Wang J, Wang K, Zhang Y, Wang S, Park J, Zheng C, Yang L, Chu A, Zhang Y, Gao L, Hsiai TK. Frontiers in artificial intelligence-directed light-sheet microscopy for uncovering biological phenomena and multi-organ imaging. VIEW 2024; 5:20230087. [PMID: 39478956 PMCID: PMC11521201 DOI: 10.1002/viw.20230087] [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: 04/02/2024] [Accepted: 07/18/2024] [Indexed: 11/02/2024] Open
Abstract
Light-sheet fluorescence microscopy (LSFM) introduces fast scanning of biological phenomena with deep photon penetration and minimal phototoxicity. This advancement represents a significant shift in 3-D imaging of large-scale biological tissues and 4-D (space + time) imaging of small live animals. The large data associated with LSFM requires efficient imaging acquisition and analysis with the use of artificial intelligence (AI)/machine learning (ML) algorithms. To this end, AI/ML-directed LSFM is an emerging area for multi-organ imaging and tumor diagnostics. This review will present the development of LSFM and highlight various LSFM configurations and designs for multi-scale imaging. Optical clearance techniques will be compared for effective reduction in light scattering and optimal deep-tissue imaging. This review will further depict a diverse range of research and translational applications, from small live organisms to multi-organ imaging to tumor diagnosis. In addition, this review will address AI/ML-directed imaging reconstruction, including the application of convolutional neural networks (CNNs) and generative adversarial networks (GANs). In summary, the advancements of LSFM have enabled effective and efficient post-imaging reconstruction and data analyses, underscoring LSFM's contribution to advancing fundamental and translational research.
Collapse
Affiliation(s)
- Enbo Zhu
- Department of Bioengineering, UCLA, California, 90095, USA
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, UCLA, California, 90095, USA
- Department of Medicine, Greater Los Angeles VA Healthcare System, California, 90073, USA
- Department of Microbiology, Immunology & Molecular Genetics, UCLA, California, 90095, USA
| | - Yan-Ruide Li
- Department of Microbiology, Immunology & Molecular Genetics, UCLA, California, 90095, USA
| | - Samuel Margolis
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, UCLA, California, 90095, USA
| | - Jing Wang
- Department of Bioengineering, UCLA, California, 90095, USA
| | - Kaidong Wang
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, UCLA, California, 90095, USA
- Department of Medicine, Greater Los Angeles VA Healthcare System, California, 90073, USA
| | - Yaran Zhang
- Department of Bioengineering, UCLA, California, 90095, USA
| | - Shaolei Wang
- Department of Bioengineering, UCLA, California, 90095, USA
| | - Jongchan Park
- Department of Bioengineering, UCLA, California, 90095, USA
| | - Charlie Zheng
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, UCLA, California, 90095, USA
| | - Lili Yang
- Department of Microbiology, Immunology & Molecular Genetics, UCLA, California, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, California, 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, UCLA, California, 90095, USA
- Molecular Biology Institute, UCLA, California, 90095, USA
| | - Alison Chu
- Division of Neonatology and Developmental Biology, Department of Pediatrics, David Geffen School of Medicine, UCLA, California, 90095, USA
| | - Yuhua Zhang
- Doheny Eye Institute, Department of Ophthalmology, UCLA, California, 90095, USA
| | - Liang Gao
- Department of Bioengineering, UCLA, California, 90095, USA
| | - Tzung K. Hsiai
- Department of Bioengineering, UCLA, California, 90095, USA
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, UCLA, California, 90095, USA
- Department of Medicine, Greater Los Angeles VA Healthcare System, California, 90073, USA
| |
Collapse
|
6
|
Neyhart E, Zhou N, Munn BR, Law RG, Smith C, Mridha ZH, Blanco FA, Li G, Li Y, McGinley MJ, Shine JM, Reimer J. Cortical acetylcholine dynamics are predicted by cholinergic axon activity and behavior state. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.14.567116. [PMID: 38352527 PMCID: PMC10862699 DOI: 10.1101/2023.11.14.567116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Even under spontaneous conditions and in the absence of changing environmental demands, awake animals alternate between increased or decreased periods of alertness. These changes in brain state can occur rapidly, on a timescale of seconds, and neuromodulators such as acetylcholine (ACh) are thought to play an important role in driving these spontaneous state transitions. Here, we perform the first simultaneous imaging of ACh sensors and GCaMP-expressing axons in vivo, to examine the spatiotemporal properties of cortical ACh activity and release during spontaneous changes in behavioral state. We observed a high correlation between simultaneously recorded basal forebrain axon activity and neuromodulator sensor fluorescence around periods of locomotion and pupil dilation. Consistent with volume transmission of ACh, increases in axon activity were accompanied by increases in local ACh levels that fell off with the distance from the nearest axon. GRAB-ACh fluorescence could be accurately predicted from axonal activity alone, providing the first validation that neuromodulator axon activity is a reliable proxy for nearby neuromodulator levels. Deconvolution of fluorescence traces allowed us to account for the kinetics of the GRAB-ACh sensor and emphasized the rapid clearance of ACh for smaller transients outside of running periods. Finally, we trained a predictive model of ACh fluctuations from the combination of pupil size and running speed; this model performed better than using either variable alone, and generalized well to unseen data. Overall, these results contribute to a growing understanding of the precise timing and spatial characteristics of cortical ACh during fast brain state transitions.
Collapse
Affiliation(s)
- Erin Neyhart
- Neuroscience Department, Baylor College of Medicine, Houston, Texas, USA
| | - Na Zhou
- Neuroscience Department, Baylor College of Medicine, Houston, Texas, USA
| | - Brandon R Munn
- Brain and Mind Centre, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Australia
- Complex Systems Group, School of Physics, Faculty of Science, The University of Sydney, Australia
| | - Robert G Law
- Neuroscience Department, Baylor College of Medicine, Houston, Texas, USA
| | - Cameron Smith
- Neuroscience Department, Baylor College of Medicine, Houston, Texas, USA
| | - Zakir H Mridha
- Neuroscience Department, Baylor College of Medicine, Houston, Texas, USA
| | - Francisco A Blanco
- Neuroscience Department, Baylor College of Medicine, Houston, Texas, USA
| | - Guochuan Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Matthew J McGinley
- Neuroscience Department, Baylor College of Medicine, Houston, Texas, USA
| | - James M Shine
- Brain and Mind Centre, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Australia
- Complex Systems Group, School of Physics, Faculty of Science, The University of Sydney, Australia
| | - Jacob Reimer
- Neuroscience Department, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|
7
|
Lee SH, Son HJ. Second Wave, Late-Stage Neuroinflammation in Cleared Brains of Aged 5xFAD Alzheimer's Mice Detected by Macrolaser Light Sheet Microscopy Imaging. Int J Mol Sci 2023; 24:17058. [PMID: 38069392 PMCID: PMC10707588 DOI: 10.3390/ijms242317058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
This study leverages the innovative imaging capabilities of macrolaser light-sheet microscopy to elucidate the 3D spatial visualization of AD-associated neuropathologic networks in the transparent brains of 44-week-old 5xFAD mice. Brain samples from ten AD and seven control mice were prepared through a hydrophilic tissue-clearing pipeline and immunostained with thioflavin S (β-amyloid), anti-CD11b antibody (microglia), and anti-ACSA-2 antibody (astrocytes). The 5xFAD group exhibited significantly higher average total surface volumes of β-amyloid accumulation than the control group (AD, 898,634,368 µm3 [383,355,488-1,324,986,752]; control, 33,320,178 µm3 [11,156,785-65,390,988], p = 0.0006). Within the AD group, there was significant interindividual and interindividual variability concerning the number and surface volume of individual amyloid particles throughout the entire brain. In the context of neuroinflammation, the 5xFAD group showed significantly higher average total surface volumes of anti-ACSA-2-labeled astrocytes (AD, 59,064,360 µm3 [27,815,500-222,619,280]; control, 20,272,722 µm3 [9,317,288-27,223,352], p = 0.0047) and anti-CD11b labeled microglia (AD, 51,210,100 µm3 [15,309,118-135,532,144]; control, 23,461,593 µm3 [14,499,170-27,924,110], p = 0.0162) than the control group. Contrary to the long-standing finding that early-stage neuroinflammation precedes the subsequent later-stage of neurodegeneration, our data reveal that the second wave, late-stage active neuroinflammation persists in the aged AD brains, even as they continue to show signs of ongoing neurodegeneration and significant amyloid accumulation.
Collapse
Affiliation(s)
- Suk Hyun Lee
- Department of Radiology, Hallym University Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07441, Republic of Korea
| | - Hye Joo Son
- Department of Nuclear Medicine, Dankook University Medical Center, Dankook University College of Medicine, Cheonan 31116, Republic of Korea
| |
Collapse
|
8
|
Liang X, Holy TE, Taghert PH. Polyphasic circadian neural circuits drive differential activities in multiple downstream rhythmic centers. Curr Biol 2023; 33:351-363.e3. [PMID: 36610393 PMCID: PMC9877191 DOI: 10.1016/j.cub.2022.12.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 01/08/2023]
Abstract
Circadian clocks align various behaviors such as locomotor activity, sleep/wake, feeding, and mating to times of day that are most adaptive. How rhythmic information in pacemaker circuits is translated to neuronal outputs is not well understood. Here, we used brain-wide, 24-h in vivo calcium imaging in the Drosophila brain and searched for circadian rhythmic activity among identified clusters of dopaminergic (DA) and peptidergic neurosecretory (NS) neurons. Such rhythms were widespread and imposed by the PERIOD-dependent clock activity within the ∼150-cell circadian pacemaker network. The rhythms displayed either a morning (M), evening (E), or mid-day (MD) phase. Different subgroups of circadian pacemakers imposed neural activity rhythms onto different downstream non-clock neurons. Outputs from the canonical M and E pacemakers converged to regulate DA-PPM3 and DA-PAL neurons. E pacemakers regulate the evening-active DA-PPL1 neurons. In addition to these canonical M and E oscillators, we present evidence for a third dedicated phase occurring at mid-day: the l-LNv pacemakers present the MD activity peak, and they regulate the MD-active DA-PPM1/2 neurons and three distinct NS cell types. Thus, the Drosophila circadian pacemaker network is a polyphasic rhythm generator. It presents dedicated M, E, and MD phases that are functionally transduced as neuronal outputs to organize diverse daily activity patterns in downstream circuits.
Collapse
Affiliation(s)
- Xitong Liang
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Timothy E Holy
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Paul H Taghert
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO 63110, USA.
| |
Collapse
|
9
|
Wang J, Karbasi P, Wang L, Meeks JP. A Layered, Hybrid Machine Learning Analytic Workflow for Mouse Risk Assessment Behavior. eNeuro 2023; 10:ENEURO.0335-22.2022. [PMID: 36564214 PMCID: PMC9833056 DOI: 10.1523/eneuro.0335-22.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/06/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022] Open
Abstract
Accurate and efficient quantification of animal behavior facilitates the understanding of the brain. An emerging approach within machine learning (ML) field is to combine multiple ML-based algorithms to quantify animal behavior. These so-called hybrid models have emerged because of limitations associated with supervised [e.g., random forest (RF)] and unsupervised [e.g., hidden Markov model (HMM)] ML models. For example, RF models lack temporal information across video frames, and HMM latent states are often difficult to interpret. We sought to develop a hybrid model, and did so in the context of a study of mouse risk assessment behavior. We used DeepLabCut to estimate the positions of mouse body parts. Positional features were calculated using DeepLabCut outputs and were used to train RF and HMM models with equal number of states, separately. The per-frame predictions from RF and HMM models were then passed to a second HMM model layer ("reHMM"). The outputs of the reHMM layer showed improved interpretability over the initial HMM output. Finally, we combined predictions from RF and HMM models with selected positional features to train a third HMM model ("reHMM+"). This reHMM+ layered hybrid model unveiled distinctive temporal and human-interpretable behavioral patterns. We applied this workflow to investigate risk assessment to trimethylthiazoline and snake feces odor, finding unique behavioral patterns to each that were separable from attractive and neutral stimuli. We conclude that this layered, hybrid ML workflow represents a balanced approach for improving the depth and reliability of ML classifiers in chemosensory and other behavioral contexts.
Collapse
Affiliation(s)
- Jinxin Wang
- Department of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642
| | - Paniz Karbasi
- Lyda Hill Department of Bioinformatics and BioHPC, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Liqiang Wang
- Lyda Hill Department of Bioinformatics and BioHPC, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Julian P Meeks
- Department of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642
| |
Collapse
|
10
|
Lightsheet optical tweezer (LOT) for optical manipulation of microscopic particles and live cells. Sci Rep 2022; 12:10229. [PMID: 35715431 PMCID: PMC9205896 DOI: 10.1038/s41598-022-13095-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/20/2022] [Indexed: 11/09/2022] Open
Abstract
Optical trapping and patterning cells or microscopic particles is fascinating. We developed a light sheet-based optical tweezer to trap dielectric particles and live HeLa cells. The technique requires the generation of a tightly focussed diffraction-limited light-sheet realized by a combination of cylindrical lens and high NA objective lens. The resultant field is a focussed line (along x-axis) perpendicular to the beam propagation direction (z-axis). This is unlike traditional optical tweezers that are fundamentally point-traps and can trap one particle at a time. Several spherical beads undergoing Brownian motion in the solution are trapped by the lightsheet gradient potential, and the time (to reach trap-centre) is estimated from the video captured at 230 frames/s. High-speed imaging of beads with increasing laser power shows a steady increase in trap stiffness with a maximum of 0.00118 pN/nm at 52.5 mW. This is order less than the traditional point-traps, and hence may be suitable for applications requiring delicate optical forces. On the brighter side, light sheet tweezer (LOT) can simultaneously trap multiple objects with the distinct ability to manipulate them in the transverse (xy) plane via translation and rotation. However, the trapped beads displayed free movement along the light-sheet axis (x-axis), exhibiting a single degree of freedom. Furthermore, the tweezer is used to trap and pattern live HeLa cells in various shapes and structures. Subsequently, the cells were cultured for a prolonged period of time (> 18 h), and cell viability was ascertained. We anticipate that LOT can be used to study constrained dynamics of microscopic particles and help understand the patterned cell growth that has implications in optical imaging, microscopy, and cell biology.
Collapse
|
11
|
Liang X, Holy TE, Taghert PH. Circadian pacemaker neurons display cophasic rhythms in basal calcium level and in fast calcium fluctuations. Proc Natl Acad Sci U S A 2022; 119:e2109969119. [PMID: 35446620 PMCID: PMC9173584 DOI: 10.1073/pnas.2109969119] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 03/17/2022] [Indexed: 12/02/2022] Open
Abstract
Circadian pacemaker neurons in the Drosophila brain display daily rhythms in the levels of intracellular calcium. These calcium rhythms are driven by molecular clocks and are required for normal circadian behavior. To study their biological basis, we employed genetic manipulations in conjunction with improved methods of in vivo light-sheet microscopy to measure calcium dynamics in individual pacemaker neurons over complete 24-h durations at sampling frequencies as high as 5 Hz. This technological advance unexpectedly revealed cophasic daily rhythms in basal calcium levels and in high-frequency calcium fluctuations. Further, we found that the rhythms of basal calcium levels and of fast calcium fluctuations reflect the activities of two proteins that mediate distinct forms of calcium fluxes. One is the inositol trisphosphate receptor (ITPR), a channel that mediates calcium fluxes from internal endoplasmic reticulum calcium stores, and the other is a T-type voltage-gated calcium channel, which mediates extracellular calcium influx. These results suggest that Drosophila molecular clocks regulate ITPR and T-type channels to generate two distinct but coupled rhythms in basal calcium and in fast calcium fluctuations. We propose that both internal and external calcium fluxes are essential for circadian pacemaker neurons to provide rhythmic outputs and thereby, regulate the activities of downstream brain centers.
Collapse
Affiliation(s)
- Xitong Liang
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO 63110
| | - Timothy E. Holy
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO 63110
| | - Paul H. Taghert
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO 63110
| |
Collapse
|
12
|
Engelbrecht L, Ollewagen T, de Swardt D. Advances in fluorescence microscopy can reveal important new aspects of tissue regeneration. Biochimie 2022; 196:194-202. [DOI: 10.1016/j.biochi.2022.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/19/2022] [Accepted: 02/02/2022] [Indexed: 12/12/2022]
|
13
|
Gagliano G, Nelson T, Saliba N, Vargas-Hernández S, Gustavsson AK. Light Sheet Illumination for 3D Single-Molecule Super-Resolution Imaging of Neuronal Synapses. Front Synaptic Neurosci 2021; 13:761530. [PMID: 34899261 PMCID: PMC8651567 DOI: 10.3389/fnsyn.2021.761530] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/27/2021] [Indexed: 01/02/2023] Open
Abstract
The function of the neuronal synapse depends on the dynamics and interactions of individual molecules at the nanoscale. With the development of single-molecule super-resolution microscopy over the last decades, researchers now have a powerful and versatile imaging tool for mapping the molecular mechanisms behind the biological function. However, imaging of thicker samples, such as mammalian cells and tissue, in all three dimensions is still challenging due to increased fluorescence background and imaging volumes. The combination of single-molecule imaging with light sheet illumination is an emerging approach that allows for imaging of biological samples with reduced fluorescence background, photobleaching, and photodamage. In this review, we first present a brief overview of light sheet illumination and previous super-resolution techniques used for imaging of neurons and synapses. We then provide an in-depth technical review of the fundamental concepts and the current state of the art in the fields of three-dimensional single-molecule tracking and super-resolution imaging with light sheet illumination. We review how light sheet illumination can improve single-molecule tracking and super-resolution imaging in individual neurons and synapses, and we discuss emerging perspectives and new innovations that have the potential to enable and improve single-molecule imaging in brain tissue.
Collapse
Affiliation(s)
- Gabriella Gagliano
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Tyler Nelson
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Nahima Saliba
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Sofía Vargas-Hernández
- Department of Chemistry, Rice University, Houston, TX, United States
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
- Department of Biosciences, Rice University, Houston, TX, United States
- Laboratory for Nanophotonics, Rice University, Houston, TX, United States
| |
Collapse
|
14
|
Fluorescence based rapid optical volume screening system (OVSS) for interrogating multicellular organisms. Sci Rep 2021; 11:7616. [PMID: 33828140 PMCID: PMC8027194 DOI: 10.1038/s41598-021-86951-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 03/22/2021] [Indexed: 11/08/2022] Open
Abstract
Continuous monitoring of large specimens for long durations requires fast volume imaging. This is essential for understanding the processes occurring during the developmental stages of multicellular organisms. One of the key obstacles of fluorescence based prolonged monitoring and data collection is photobleaching. To capture the biological processes and simultaneously overcome the effect of bleaching, we developed single- and multi-color lightsheet based OVSS imaging technique that enables rapid screening of multiple tissues in an organism. Our approach based on OVSS imaging employs quantized step rotation of the specimen to record 2D angular data that reduces data acquisition time when compared to the existing light sheet imaging system (SPIM). A co-planar multicolor light sheet PSF is introduced to illuminate the tissues labelled with spectrally-separated fluorescent probes. The detection is carried out using a dual-channel sub-system that can simultaneously record spectrally separate volume stacks of the target organ. Arduino-based control systems were employed to automatize and control the volume data acquisition process. To illustrate the advantages of our approach, we have noninvasively imaged the Drosophila larvae and Zebrafish embryo. Dynamic studies of multiple organs (muscle and yolk-sac) in Zebrafish for a prolonged duration (5 days) were carried out to understand muscle structuring (Dystrophin, microfibers), primitive Macrophages (in yolk-sac) and inter-dependent lipid and protein-based metabolism. The volume-based study, intensity line-plots and inter-dependence ratio analysis allowed us to understand the transition from lipid-based metabolism to protein-based metabolism during early development (Pharyngula period with a critical transition time, [Formula: see text] h post-fertilization) in Zebrafish. The advantage of multicolor lightsheet illumination, fast volume scanning, simultaneous visualization of multiple organs and an order-less photobleaching makes OVSS imaging the system of choice for rapid monitoring and real-time assessment of macroscopic biological organisms with microscopic resolution.
Collapse
|
15
|
Wang F, Ma Z, Zhong Y, Salazar F, Xu C, Ren F, Qu L, Wu AM, Dai H. In vivo NIR-II structured-illumination light-sheet microscopy. Proc Natl Acad Sci U S A 2021; 118:e2023888118. [PMID: 33526701 PMCID: PMC8017937 DOI: 10.1073/pnas.2023888118] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Noninvasive optical imaging with deep tissue penetration depth and high spatiotemporal resolution is important to longitudinally studying the biology at the single-cell level in live mammals, but has been challenging due to light scattering. Here, we developed near-infrared II (NIR-II) (1,000 to 1,700 nm) structured-illumination light-sheet microscopy (NIR-II SIM) with ultralong excitation and emission wavelengths up to ∼1,540 and ∼1,700 nm, respectively, suppressing light scattering to afford large volumetric three-dimensional (3D) imaging of tissues with deep-axial penetration depths. Integrating structured illumination into NIR-II light-sheet microscopy further diminished background and improved spatial resolution by approximately twofold. In vivo oblique NIR-II SIM was performed noninvasively for 3D volumetric multiplexed molecular imaging of the CT26 tumor microenvironment in mice, longitudinally mapping out CD4, CD8, and OX40 at the single-cell level in response to immunotherapy by cytosine-phosphate-guanine (CpG), a Toll-like receptor 9 (TLR-9) agonist combined with OX40 antibody treatment. NIR-II SIM affords an additional tool for noninvasive volumetric molecular imaging of immune cells in live mammals.
Collapse
Affiliation(s)
- Feifei Wang
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Bio-X, Stanford University, Stanford, CA 94305
| | - Zhuoran Ma
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Bio-X, Stanford University, Stanford, CA 94305
| | - Yeteng Zhong
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Bio-X, Stanford University, Stanford, CA 94305
| | - Felix Salazar
- Molecular Imaging and Therapy, Beckman Research Institute, City of Hope, Duarte, CA 91010
| | - Chun Xu
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Bio-X, Stanford University, Stanford, CA 94305
| | - Fuqiang Ren
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Bio-X, Stanford University, Stanford, CA 94305
| | - Liangqiong Qu
- School of Medicine, Stanford University, Stanford, CA 94303
| | - Anna M Wu
- Molecular Imaging and Therapy, Beckman Research Institute, City of Hope, Duarte, CA 91010
| | - Hongjie Dai
- Department of Chemistry, Stanford University, Stanford, CA 94305;
- Bio-X, Stanford University, Stanford, CA 94305
| |
Collapse
|
16
|
Daria VR, Castañares ML, Bachor HA. Spatio-temporal parameters for optical probing of neuronal activity. Biophys Rev 2021; 13:13-33. [PMID: 33747244 PMCID: PMC7930150 DOI: 10.1007/s12551-021-00780-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 01/01/2021] [Indexed: 12/28/2022] Open
Abstract
The challenge to understand the complex neuronal circuit functions in the mammalian brain has brought about a revolution in light-based neurotechnologies and optogenetic tools. However, while recent seminal works have shown excellent insights on the processing of basic functions such as sensory perception, memory, and navigation, understanding more complex brain functions is still unattainable with current technologies. We are just scratching the surface, both literally and figuratively. Yet, the path towards fully understanding the brain is not totally uncertain. Recent rapid technological advancements have allowed us to analyze the processing of signals within dendritic arborizations of single neurons and within neuronal circuits. Understanding the circuit dynamics in the brain requires a good appreciation of the spatial and temporal properties of neuronal activity. Here, we assess the spatio-temporal parameters of neuronal responses and match them with suitable light-based neurotechnologies as well as photochemical and optogenetic tools. We focus on the spatial range that includes dendrites and certain brain regions (e.g., cortex and hippocampus) that constitute neuronal circuits. We also review some temporal characteristics of some proteins and ion channels responsible for certain neuronal functions. With the aid of the photochemical and optogenetic markers, we can use light to visualize the circuit dynamics of a functioning brain. The challenge to understand how the brain works continue to excite scientists as research questions begin to link macroscopic and microscopic units of brain circuits.
Collapse
Affiliation(s)
- Vincent R. Daria
- Research School of Physics, The Australian National University, Canberra, Australia
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | | | - Hans-A. Bachor
- Research School of Physics, The Australian National University, Canberra, Australia
| |
Collapse
|
17
|
Zhang Z, Cong L, Bai L, Wang K. Light-field microscopy for fast volumetric brain imaging. J Neurosci Methods 2021; 352:109083. [PMID: 33484746 DOI: 10.1016/j.jneumeth.2021.109083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/23/2020] [Accepted: 01/14/2021] [Indexed: 01/06/2023]
Abstract
Recording neural activities over large populations is critical for a better understanding of the functional mechanisms of animal brains. Traditional optical imaging technologies for in vivo neural activity recording are usually limited in throughput and cannot cover a large imaging volume at high speed. Light-field microscopy features a highly parallelized imaging collection mechanism and can simultaneously record optical signals from different depths. Therefore, it can potentially increase the imaging throughput substantially. Furthermore, its unique instantaneous volumetric imaging capability enables the capture of highly dynamic processes, such as recording whole-animal neural activities in freely moving Caenorhabditis elegans and whole-brain neural activity in freely swimming larval zebrafish during prey capture. Here, we summarize the principles of and considerations in the practical implementation of light-field microscopy as currently applied in biological imaging experiments. We also discuss the strategies that light-field microscopy can employ when imaging thick tissues in the presence of scattering and background interference. Finally, we present a few examples of applying light-field microscopy in neuroscientific studies in several important animal models.
Collapse
Affiliation(s)
- Zhenkun Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin Cong
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Lu Bai
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
| |
Collapse
|
18
|
Zhao F, Zhu L, Fang C, Yu T, Zhu D, Fei P. Deep-learning super-resolution light-sheet add-on microscopy (Deep-SLAM) for easy isotropic volumetric imaging of large biological specimens. BIOMEDICAL OPTICS EXPRESS 2020; 11:7273-7285. [PMID: 33408995 PMCID: PMC7747920 DOI: 10.1364/boe.409732] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/06/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
Isotropic 3D histological imaging of large biological specimens is highly desired but remains highly challenging to current fluorescence microscopy technique. Here we present a new method, termed deep-learning super-resolution light-sheet add-on microscopy (Deep-SLAM), to enable fast, isotropic light-sheet fluorescence imaging on a conventional wide-field microscope. After integrating a minimized add-on device that transforms an inverted microscope into a 3D light-sheet microscope, we further integrate a deep neural network (DNN) procedure to quickly restore the ambiguous z-reconstructed planes that suffer from still insufficient axial resolution of light-sheet illumination, thereby achieving isotropic 3D imaging of thick biological specimens at single-cell resolution. We apply this easy and cost-effective Deep-SLAM approach to the anatomical imaging of single neurons in a meso-scale mouse brain, demonstrating its potential for readily converting commonly-used commercialized 2D microscopes to high-throughput 3D imaging, which is previously exclusive for high-end microscopy implementations.
Collapse
Affiliation(s)
- Fang Zhao
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
- These authors contribute equally to this work
| | - Lanxin Zhu
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
- These authors contribute equally to this work
| | - Chunyu Fang
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Tingting Yu
- Britton Chance center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Dan Zhu
- Britton Chance center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Peng Fei
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| |
Collapse
|
19
|
Tang Q, Tsytsarev V, Yan F, Wang C, Erzurumlu RS, Chen Y. In vivo voltage-sensitive dye imaging of mouse cortical activity with mesoscopic optical tomography. NEUROPHOTONICS 2020; 7:041402. [PMID: 33274250 PMCID: PMC7708784 DOI: 10.1117/1.nph.7.4.041402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 11/11/2020] [Indexed: 05/11/2023]
Abstract
Significance: Cellular layering is a hallmark of the mammalian neocortex with layer and cell type-specific connections within the cortical mantle and subcortical connections. A key challenge in studying circuit function within the neocortex is to understand the spatial and temporal patterns of information flow between different columns and layers. Aim: We aimed to investigate the three-dimensional (3D) layer- and area-specific interactions in mouse cortex in vivo. Approach: We applied a new promising neuroimaging method-fluorescence laminar optical tomography in combination with voltage-sensitive dye imaging (VSDi). VSDi is a powerful technique for interrogating membrane potential dynamics in assemblies of cortical neurons, but it is traditionally used for two-dimensional (2D) imaging. Our mesoscopic technique allows visualization of neuronal activity in a 3D manner with high temporal resolution. Results: We first demonstrated the depth-resolved capability of 3D mesoscopic imaging technology in Thy1-ChR2-YFP transgenic mice. Next, we recorded the long-range functional projections between sensory cortex (S1) and motor cortex (M1) in mice, in vivo, following single whisker deflection. Conclusions: The results show that mesoscopic imaging technique has the potential to investigate the layer-specific neural connectivity in the mouse cortex in vivo. Combination of mesoscopic imaging technique with optogenetic control strategy is a promising platform for determining depth-resolved interactions between cortical circuit elements.
Collapse
Affiliation(s)
- Qinggong Tang
- University of Oklahoma, Stephenson School of Biomedical Engineering, Norman, Oklahoma, United States
- University of Maryland, Fischell Department of Bioengineering, College Park, Maryland, United States
- Address all correspondence to Qinggong Tang, ; Reha S. Erzurumlu, ; Yu Chen,
| | - Vassiliy Tsytsarev
- University of Maryland School of Medicine, Department of Anatomy and Neurobiology, Baltimore, Maryland, United States
| | - Feng Yan
- University of Oklahoma, Stephenson School of Biomedical Engineering, Norman, Oklahoma, United States
| | - Chen Wang
- University of Oklahoma, Stephenson School of Biomedical Engineering, Norman, Oklahoma, United States
| | - Reha S. Erzurumlu
- University of Maryland School of Medicine, Department of Anatomy and Neurobiology, Baltimore, Maryland, United States
- Address all correspondence to Qinggong Tang, ; Reha S. Erzurumlu, ; Yu Chen,
| | - Yu Chen
- University of Maryland, Fischell Department of Bioengineering, College Park, Maryland, United States
- University of Massachusetts, Department of Biomedical Engineering, Amherst, Massachusetts, United States
- Address all correspondence to Qinggong Tang, ; Reha S. Erzurumlu, ; Yu Chen,
| |
Collapse
|
20
|
Imaging volumetric dynamics at high speed in mouse and zebrafish brain with confocal light field microscopy. Nat Biotechnol 2020; 39:74-83. [PMID: 32778840 DOI: 10.1038/s41587-020-0628-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 07/08/2020] [Indexed: 12/12/2022]
Abstract
A detailed understanding of the function of neural networks and how they are supported by a dynamic vascular system requires fast three-dimensional imaging in thick tissues. Here we present confocal light field microscopy, a method that enables fast volumetric imaging in the brain at depths of hundreds of micrometers. It uses a generalized confocal detection scheme that selectively collects fluorescent signals from the in-focus volume and provides optical sectioning capability to improve imaging resolution and sensitivity in thick tissues. We demonstrate recording of whole-brain calcium transients in freely swimming zebrafish larvae and observe behaviorally correlated activities in single neurons during prey capture. Furthermore, in the mouse brain, we detect neural activities at depths of up to 370 μm and track blood cells at 70 Hz over a volume of diameter 800 μm × thickness 150 μm and depth of up to 600 μm.
Collapse
|
21
|
Tubiana J, Wolf S, Panier T, Debregeas G. Blind deconvolution for spike inference from fluorescence recordings. J Neurosci Methods 2020; 342:108763. [PMID: 32479972 DOI: 10.1016/j.jneumeth.2020.108763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 10/24/2022]
Abstract
The parallel developments of genetically-encoded calcium indicators and fast fluorescence imaging techniques allows one to simultaneously record neural activity of extended neuronal populations in vivo. To fully harness the potential of functional imaging, one needs to infer the sequence of action potentials from fluorescence traces. Here we build on recently proposed computational approaches to develop a blind sparse deconvolution (BSD) algorithm based on a generative model for inferring spike trains from fluorescence traces. BSD features, (1) automatic (fully unsupervised) estimation of the hyperparameters, such as spike amplitude, noise level and rise and decay time constants, (2) a novel analytical estimate of the sparsity prior, which yields enhanced robustness and computational speed with respect to existing methods, (3) automatic thresholding for binarizing spikes that maximizes the precision-recall performance, (4) super-resolution capabilities increasing the temporal resolution beyond the fluorescence signal acquisition rate. BSD also uniquely provides theoretically-grounded estimates of the expected performance of the spike reconstruction in terms of precision-recall and temporal accuracy for each recording. The performance of the algorithm is established using synthetic data and through the SpikeFinder challenge, a community-based initiative for spike-rate inference benchmarking based on a collection of joint electrophysiological and fluorescence recordings. Our method outperforms classical sparse deconvolution algorithms in terms of robustness, speed and/or accuracy and performs competitively in the SpikeFinder challenge. This algorithm is modular, easy-to-use and made freely available. Its novel features can thus be incorporated in a straightforward way into existing calcium imaging packages.
Collapse
Affiliation(s)
- Jérôme Tubiana
- Blavatnik School of Computer Science, Tel Aviv University, Israel
| | - Sébastien Wolf
- Laboratoire de Physique de l'Ecole Normale Supérieure, CNRS UMR 8023 & PSL Research, France; Institut de Biologie de l'Ecole Normale Supérieure, CNRS, INSERM, UMR 8197 & PSL Research, France
| | - Thomas Panier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), France
| | - Georges Debregeas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), France.
| |
Collapse
|
22
|
Sparks H, Dvinskikh L, Firth JM, Francis AJ, Harding SE, Paterson C, MacLeod KT, Dunsby C. Development a flexible light-sheet fluorescence microscope for high-speed 3D imaging of calcium dynamics and 3D imaging of cellular microstructure. JOURNAL OF BIOPHOTONICS 2020; 13:e201960239. [PMID: 32101366 DOI: 10.1002/jbio.201960239] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/07/2020] [Accepted: 02/22/2020] [Indexed: 06/10/2023]
Abstract
We report a flexible light-sheet fluorescence microscope (LSFM) designed for studying dynamic events in cardiac tissue at high speed in 3D and the correlation of these events to cell microstructure. The system employs two illumination-detection modes: the first uses angle-dithering of a Gaussian light sheet combined with remote refocusing of the detection plane for video-rate volumetric imaging; the second combines digitally-scanned light-sheet illumination with an axially-swept light-sheet waist and stage-scanned acquisition for improved axial resolution compared to the first mode. We present a characterisation of the spatial resolution of the system in both modes. The first illumination-detection mode achieves dual spectral-channel imaging at 25 volumes per second with 1024 × 200 × 50 voxel volumes and is demonstrated by time-lapse imaging of calcium dynamics in a live cardiomyocyte. The second illumination-detection mode is demonstrated through the acquisition of a higher spatial resolution structural map of the t-tubule network in a fixed cardiomyocyte cell.
Collapse
Affiliation(s)
- Hugh Sparks
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Liuba Dvinskikh
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, London, UK
- Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Jahn M Firth
- Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Alice J Francis
- Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Sian E Harding
- Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Carl Paterson
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Ken T MacLeod
- Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Centre for Pathology, Faculty of Medicine, Imperial College London, London, UK
| |
Collapse
|
23
|
Zhao F, Yang Y, Li Y, Jiang H, Xie X, Yu T, Wang X, Liu Q, Zhang H, Jia H, Liu S, Zhen M, Zhu D, Gao S, Fei P. Efficient and cost-effective 3D cellular imaging by sub-voxel-resolving light-sheet add-on microscopy. JOURNAL OF BIOPHOTONICS 2020; 13:e201960243. [PMID: 32077244 DOI: 10.1002/jbio.201960243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/01/2020] [Accepted: 02/11/2020] [Indexed: 06/10/2023]
Abstract
Light-sheet fluorescence microscopy (LSFM) allows volumetric live imaging at high-speed and with low photo-toxicity. Various LSFM modalities are commercially available, but their size and cost limit their access by the research community. A new method, termed sub-voxel-resolving (SVR) light-sheet add-on microscopy (SLAM), is presented to enable fast, resolution-enhanced light-sheet fluorescence imaging from a conventional wide-field microscope. This method contains two components: a miniature add-on device to regular wide-field microscopes, which contains a horizontal laser light-sheet illumination path to confine fluorophore excitation at the vicinity of the focal plane for optical sectioning; an off-axis scanning strategy and a SVR algorithm that utilizes sub-voxel spatial shifts to reconstruct the image volume that results in a twofold increase in resolution. SLAM method has been applied to observe the muscle activity change of crawling C. elegans, the heartbeat of developing zebrafish embryo, and the neural anatomy of cleared mouse brains, at high spatiotemporal resolution. It provides an efficient and cost-effective solution to convert the vast number of in-service microscopes for fast 3D live imaging with voxel-super-resolved capability.
Collapse
Affiliation(s)
- Fang Zhao
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Yicong Yang
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Li
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Jiang
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Xinlin Xie
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Tingting Yu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Xuechun Wang
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Qing Liu
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Zhang
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Haibo Jia
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng Liu
- School of Power and Mechanical Engineering, Wuhan University, Wuhan, China
| | - Mei Zhen
- Department of Molecular Genetics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Shangbang Gao
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Fei
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
24
|
Kumar M, Kozorovitskiy Y. Tilt (in)variant lateral scan in oblique plane microscopy: a geometrical optics approach. BIOMEDICAL OPTICS EXPRESS 2020; 11:3346-3359. [PMID: 32637259 PMCID: PMC7316005 DOI: 10.1364/boe.389654] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Oblique plane microscopy (OPM) is a single objective light-sheet microscopy that performs three dimensional (3D) imaging by axial scan of the generated light-sheet. Recently, multiple techniques for lateral scanning of the generated light-sheet in OPM have emerged. However, their suitability for geometrically distortion free 3D imaging, which essentially requires a constant tilt light-sheet scan, has not been evaluated. In this work, we use a geometrical optics approach and derive analytical relationship for the amount of tilt variance in planar mirror based scanned oblique plane illumination (SOPi) arrangement. We experimentally validate the derived relationship and use it to arrive at an optimized scanner geometry and to understand its associated limitations. We discuss the effects of scanning on optical aberrations and 3D field of view in optimized, tilt invariant, lateral scanning OPM systems. We also provide experimental strategies enabling precise scanner alignment for tilt invariance, as well as an open source platform for rapid design of new oblique light-sheet microscopes.
Collapse
|
25
|
Ueda HR, Dodt HU, Osten P, Economo MN, Chandrashekar J, Keller PJ. Whole-Brain Profiling of Cells and Circuits in Mammals by Tissue Clearing and Light-Sheet Microscopy. Neuron 2020; 106:369-387. [PMID: 32380050 PMCID: PMC7213014 DOI: 10.1016/j.neuron.2020.03.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/11/2020] [Accepted: 03/04/2020] [Indexed: 01/12/2023]
Abstract
Tissue clearing and light-sheet microscopy have a 100-year-plus history, yet these fields have been combined only recently to facilitate novel experiments and measurements in neuroscience. Since tissue-clearing methods were first combined with modernized light-sheet microscopy a decade ago, the performance of both technologies has rapidly improved, broadening their applications. Here, we review the state of the art of tissue-clearing methods and light-sheet microscopy and discuss applications of these techniques in profiling cells and circuits in mice. We examine outstanding challenges and future opportunities for expanding these techniques to achieve brain-wide profiling of cells and circuits in primates and humans. Such integration will help provide a systems-level understanding of the physiology and pathology of our central nervous system.
Collapse
Affiliation(s)
- Hiroki R Ueda
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan; Laboratory for Synthetic Biology, RIKEN BDR, Suita, Osaka 565-0871, Japan.
| | - Hans-Ulrich Dodt
- Department of Bioelectronics, FKE, Vienna University of Technology-TU Wien, Vienna, Austria; Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Pavel Osten
- Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724, USA
| | - Michael N Economo
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | | | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| |
Collapse
|
26
|
Wong WM, Cao J, Zhang X, Doyle WI, Mercado LL, Gautron L, Meeks JP. Physiology-forward identification of bile acid-sensitive vomeronasal receptors. SCIENCE ADVANCES 2020; 6:eaaz6868. [PMID: 32523992 PMCID: PMC7259934 DOI: 10.1126/sciadv.aaz6868] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
The mouse accessory olfactory system (AOS) supports social and reproductive behavior through the sensation of environmental chemosignals. A growing number of excreted steroids have been shown to be potent AOS cues, including bile acids (BAs) found in feces. As is still the case with most AOS ligands, the specific receptors used by vomeronasal sensory neurons (VSNs) to detect BAs remain unknown. To identify VSN BA receptors, we first performed a deep analysis of VSN BA tuning using volumetric GCaMP6f/s Ca2+ imaging. These experiments revealed multiple populations of BA-receptive VSNs with submicromolar sensitivities. We then developed a new physiology-forward approach for identifying AOS ligand-receptor interactions, which we call Fluorescence Live Imaging for Cell Capture and RNA sequencing, or FLICCR-seq. FLICCR-seq analysis revealed five specific V1R family receptors enriched in BA-sensitive VSNs. These studies introduce a powerful new approach for ligand-receptor matching and reveal biological mechanisms underlying mammalian BA chemosensation.
Collapse
Affiliation(s)
- Wen Mai Wong
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA
| | - Jie Cao
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA
| | - Xingjian Zhang
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA
| | - Wayne I. Doyle
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA
| | - Luis L. Mercado
- Division of Hypothalamic Research and Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA
| | - Laurent Gautron
- Division of Hypothalamic Research and Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA
| | - Julian P. Meeks
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA
| |
Collapse
|
27
|
Ryan TM, Hinojosa AJ, Vroman R, Papasavvas C, Lagnado L. Correction of z-motion artefacts to allow population imaging of synaptic activity in behaving mice. J Physiol 2020; 598:1809-1827. [PMID: 32020615 PMCID: PMC7318612 DOI: 10.1113/jp278957] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/24/2020] [Indexed: 11/08/2022] Open
Abstract
KEY POINTS Motion artefacts associated with motor behaviour are an inevitable problem of multiphoton imaging in awake behaving animals, particularly when imaging synapses. Correction of axial motion artefacts usually requires volumetric imaging resulting in slower rates of acquisition. We describe a method to correct z-motion artefacts that is easy to implement and allows population imaging of synaptic activity while scanning a single plane in a standard multiphoton microscope. The method uses a reference volume acquired in two colour channels - an activity reporter and an anatomical marker of blood vessels. The procedure estimates the z-displacement in every frame and applies an intensity correction in which the z intensity profile for each synapse is modelled as a Moffat function. We demonstrate that the method allows synaptic calcium signals to be collected from populations of synaptic boutons in mouse primary visual cortex during locomotion. ABSTRACT Functional imaging of head-fixed, behaving mice using two-photon imaging of fluorescent activity reporters has become a powerful tool for studying the function of the brain. Motion artefacts are an inevitable problem during such experiments and are routinely corrected for in x and y dimensions. However, axial (z) shifts of several microns can also occur, leading to intensity fluctuations in structures such as synapses that are small compared to the axial point-spread function of the microscope. Here we present a simple strategy to correct z-motion artefacts arising over the course of a time-series experiment in a single optical plane. Displacement in z was calculated using dye-filled blood vessels as an anatomical marker, providing high contrast images and accuracy to within ∼0.1 µm. The axial profiles of ROIs corresponding to synapses were described using a Moffat function and this 'ROI-spread function' used to correct activity traces on an ROI-by-ROI basis. We demonstrate the accuracy and utility of the procedures in simulation experiments using fluorescent beads and then apply them to correcting measurements of synaptic activity in populations of vasoactive-intestinal peptide (VIP) interneurons expressing the synaptic reporter SyGCaMP6f. Correction of z-motion artefacts had a substantial impact on the apparent correlation between synaptic activity and running speed, demonstrating the importance of correcting these when performing imaging experiments in awake mice.
Collapse
Affiliation(s)
- Thomas Michael Ryan
- Sussex NeuroscienceSchool of Life SciencesUniversity of SussexBrightonBN1 9QGUK
| | | | - Rozan Vroman
- Sussex NeuroscienceSchool of Life SciencesUniversity of SussexBrightonBN1 9QGUK
| | | | - Leon Lagnado
- Sussex NeuroscienceSchool of Life SciencesUniversity of SussexBrightonBN1 9QGUK
| |
Collapse
|
28
|
Turaga D, Matthys OB, Hookway TA, Joy DA, Calvert M, McDevitt TC. Single-Cell Determination of Cardiac Microtissue Structure and Function Using Light Sheet Microscopy. Tissue Eng Part C Methods 2020; 26:207-215. [PMID: 32111148 DOI: 10.1089/ten.tec.2020.0020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Native cardiac tissue is composed of heterogeneous cell populations that work cooperatively for proper tissue function; thus, engineered tissue models have moved toward incorporating multiple cardiac cell types in an effort to recapitulate native multicellular composition and organization. Cardiac tissue models composed of stem cell-derived cardiomyocytes (CMs) require inclusion of non-myocytes to promote stable tissue formation, yet the specific contributions of the supporting non-myocyte population on the parenchymal CMs and cardiac microtissues have to be fully dissected. This gap can be partly attributed to limitations in technologies able to accurately study the individual cellular structure and function that comprise intact three-dimensional (3D) tissues. The ability to interrogate the cell-cell interactions in 3D tissue constructs has been restricted by conventional optical imaging techniques that fail to adequately penetrate multicellular microtissues with sufficient spatial resolution. Light sheet fluorescence microscopy (LSFM) overcomes these constraints to enable single-cell resolution structural and functional imaging of intact cardiac microtissues. Multicellular spatial distribution analysis of heterotypic cardiac cell populations revealed that CMs and cardiac fibroblasts were randomly distributed throughout 3D microtissues. Furthermore, calcium imaging of live cardiac microtissues enabled single-cell detection of CM calcium activity, which showed that functional heterogeneity correlated with spatial location within the tissues. This study demonstrates that LSFM can be utilized to determine single-cell spatial and functional interactions of multiple cell types within intact 3D engineered microtissues, thereby facilitating the determination of structure-function relationships at both tissue-level and single-cell resolution. Impact statement The ability to achieve single-cell resolution by advanced three-dimensional light imaging techniques enables exquisite new investigation of multicellular analyses in native and engineered tissues. In this study, light sheet fluorescence microscopy was used to define structure-function relationships of distinct cell types in engineered cardiac microtissues by determining heterotypic cell distributions and interactions throughout the tissues as well as by assessing regional differences in calcium handing functional properties at the individual cardiomyocyte level.
Collapse
Affiliation(s)
| | - Oriane B Matthys
- Gladstone Institutes, San Francisco, California
- UC Berkeley-UCSF Graduate Program in Bioengineering, San Francisco, California
| | | | - David A Joy
- Gladstone Institutes, San Francisco, California
- UC Berkeley-UCSF Graduate Program in Bioengineering, San Francisco, California
| | | | - Todd C McDevitt
- Gladstone Institutes, San Francisco, California
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California
| |
Collapse
|
29
|
Farouj Y, Karahanoglu FI, Van De Ville D. Deconvolution of Sustained Neural Activity From Large-Scale Calcium Imaging Data. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:1094-1103. [PMID: 31545714 DOI: 10.1109/tmi.2019.2942765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recent technological advances in light-sheet microscopy make it possible to perform whole-brain functional imaging at the cellular level with the use of Ca2+ indicators. The outstanding spatial extent and resolution of this type of data open unique opportunities for understanding the complex organization of neuronal circuits across the brain. However, the analysis of this data remains challenging because the observed variations in fluorescence are, in fact, noisy indirect measures of the neuronal activity. Moreover, measuring over large field-of-view negatively impact temporal resolution and signal-to-noise ratio, which further impedes conventional spike inference. Here we argue that meaningful information can be extracted from large-scale functional imaging data by deconvolving with the calcium response and by modeling moments of sustained neuronal activity instead of individual spikes. Specifically, we characterize the calcium response by a linear system of which the inverse is a differential operator. This operator is then included in a regularization term promoting sparsity of activity transients through generalized total variation. Our results illustrate the numerical performance of the algorithm on simulated signals; i.e., we show the firing rate phase transition at which our model outperforms spike inference. Finally, we apply the proposed algorithm to experimental data from zebrafish larvæ. In particular, we show that, when applied to a specific group of neurons, the algorithm retrieves neural activation that matches the locomotor behavior unknown to the method.
Collapse
|
30
|
Cheng Z, Sun S, Gan W, Cui M. Contrast gain through simple illumination control for wide-field fluorescence imaging of scattering samples. OPTICS EXPRESS 2020; 28:2326-2336. [PMID: 32121925 PMCID: PMC7053499 DOI: 10.1364/oe.385319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/05/2020] [Accepted: 01/05/2020] [Indexed: 06/10/2023]
Abstract
Wide field fluorescence microscopy is the most commonly employed fluorescence imaging modality. However, a major drawback of wide field imaging is the very limited imaging depth in scattering samples. By experimentally varying the control of illumination, we found that the optimized illumination profile can lead to large contrast improvement for imaging at a depth beyond four scattering path lengths. At such imaging depth, we found that the achieved image signal-to-noise ratio can rival that of confocal measurement. As the employed illumination control is very simple, the method can be broadly applied to a wide variety of wide field fluorescence imaging systems.
Collapse
Affiliation(s)
- Zongyue Cheng
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang 330031, China
- Skirball Institute, Department of Neuroscience and Physiology, Department of Anesthesiology, New York University School of Medicine, New York, NY 10016, USA
| | - Shiyi Sun
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
- State Key Laboratory of Modern Optical Instrumentation, Department of Optical Engineering, Zhejiang University, Hangzhou 310027, China
| | - Wenbiao Gan
- Skirball Institute, Department of Neuroscience and Physiology, Department of Anesthesiology, New York University School of Medicine, New York, NY 10016, USA
| | - Meng Cui
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA
- Department of Biology, Purdue University, West Lafayette, IN 47907, USA
| |
Collapse
|
31
|
Lee D, Kume M, Holy TE. Sensory coding mechanisms revealed by optical tagging of physiologically defined neuronal types. Science 2019; 366:1384-1389. [PMID: 31831669 PMCID: PMC7591936 DOI: 10.1126/science.aax8055] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 10/25/2019] [Indexed: 01/27/2023]
Abstract
Neural circuit analysis relies on having molecular markers for specific cell types. However, for a cell type identified only by its circuit function, the process of identifying markers remains laborious. We developed physiological optical tagging sequencing (PhOTseq), a technique for tagging and expression profiling of cells on the basis of their functional properties. PhOTseq was capable of selecting rare cell types and enriching them by nearly 100-fold. We applied PhOTseq to the challenge of mapping receptor-ligand pairings among pheromone-sensing neurons in mice. Together with in vivo ectopic expression of vomeronasal chemoreceptors, PhOTseq identified the complete combinatorial receptor code for a specific set of ligands.
Collapse
Affiliation(s)
- Donghoon Lee
- Department of Neuroscience, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Maiko Kume
- Department of Neuroscience, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Timothy E Holy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, St. Louis, MO 63110, USA.,Correspondence to
| |
Collapse
|
32
|
Kozlov A, Nagoshi E. Decoding Drosophila circadian pacemaker circuit. CURRENT OPINION IN INSECT SCIENCE 2019; 36:33-38. [PMID: 31376574 DOI: 10.1016/j.cois.2019.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/22/2019] [Accepted: 06/24/2019] [Indexed: 06/10/2023]
Abstract
Drosophila circadian circuit is one of the best described neural circuits but is complex enough to obscure our understanding of how it actually works. Animals' rhythmic behavior, the seemingly simple outcome of their internal clocks, relies on the interaction of heterogeneous clock neurons that are spread across the brain. Direct observations of their coordinated network interactions can bring us forward in understanding the circuit. The current challenge is to observe activity of each of these neurons over a long span of time - hours to days - in live animals. Here we review the progress in circadian circuit interrogation powered by in vivo calcium imaging.
Collapse
Affiliation(s)
- Anatoly Kozlov
- Department of Genetics and Evolution, University of Geneva, Sciences III, 30 Quai Ernest-Ansermet, CH-1211, Geneva-4, Switzerland
| | - Emi Nagoshi
- Department of Genetics and Evolution, University of Geneva, Sciences III, 30 Quai Ernest-Ansermet, CH-1211, Geneva-4, Switzerland.
| |
Collapse
|
33
|
Zhang T, Hernandez O, Chrapkiewicz R, Shai A, Wagner MJ, Zhang Y, Wu CH, Li JZ, Inoue M, Gong Y, Ahanonu B, Zeng H, Bito H, Schnitzer MJ. Kilohertz two-photon brain imaging in awake mice. Nat Methods 2019; 16:1119-1122. [PMID: 31659327 PMCID: PMC9438750 DOI: 10.1038/s41592-019-0597-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 07/25/2019] [Accepted: 09/11/2019] [Indexed: 02/03/2023]
Abstract
Two-photon microscopy is a mainstay technique for imaging in scattering media and normally provides frame-acquisition rates of ~10–30 Hz. To track high-speed phenomena, we created a two-photon microscope with 400 illumination beams that collectively sample 95,000–211,000 μm2 areas at rates up to 1 kHz. Using this microscope, we visualized microcirculatory flow, fast venous constrictions, and neuronal Ca2+ spiking with millisecond-scale timing resolution in the brains of awake mice.
Collapse
|
34
|
Abstract
Among optical imaging techniques light sheet fluorescence microscopy is one of the most attractive for capturing high-speed biological dynamics unfolding in three dimensions. The technique is potentially millions of times faster than point-scanning techniques such as two-photon microscopy. However light sheet microscopes are limited by volume scanning rate and/or camera speed. We present speed-optimized Objective Coupled Planar Illumination (OCPI) microscopy, a fast light sheet technique that avoids compromising image quality or photon efficiency. Our fast scan system supports 40 Hz imaging of 700 μm-thick volumes if camera speed is sufficient. We also address the camera speed limitation by introducing Distributed Planar Imaging (DPI), a scaleable technique that parallelizes image acquisition across cameras. Finally, we demonstrate fast calcium imaging of the larval zebrafish brain and find a heartbeat-induced artifact, removable when the imaging rate exceeds 15 Hz. These advances extend the reach of fluorescence microscopy for monitoring fast processes in large volumes. Light sheet microscopy holds potential for imaging dynamics in 3D biological specimens, but is limited by scan speed and camera acquisition rate. Here the authors address both issues by developing speed-optimized Objective Coupled Planar Illumination and parallelizing image acquisition across cameras to achieve 40 Hz imaging over thick samples.
Collapse
|
35
|
Rakotoson I, Delhomme B, Djian P, Deeg A, Brunstein M, Seebacher C, Uhl R, Ricard C, Oheim M. Fast 3-D Imaging of Brain Organoids With a New Single-Objective Planar-Illumination Two-Photon Microscope. Front Neuroanat 2019; 13:77. [PMID: 31481880 PMCID: PMC6710410 DOI: 10.3389/fnana.2019.00077] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 07/16/2019] [Indexed: 12/28/2022] Open
Abstract
Human inducible pluripotent stem cells (hiPSCs) hold a large potential for disease modeling. hiPSC-derived human astrocyte and neuronal cultures permit investigations of neural signaling pathways with subcellular resolution. Combinatorial cultures, and three-dimensional (3-D) embryonic bodies (EBs) enlarge the scope of investigations to multi-cellular phenomena. The highest level of complexity, brain organoids that-in many aspects-recapitulate anatomical and functional features of the developing brain permit the study of developmental and morphological aspects of human disease. An ideal microscope for 3-D tissue imaging at these different scales would combine features from both confocal laser-scanning and light-sheet microscopes: a micrometric optical sectioning capacity and sub-micrometric spatial resolution, a large field of view and high frame rate, and a low degree of invasiveness, i.e., ideally, a better photon efficiency than that of a confocal microscope. In the present work, we describe such an instrument that uses planar two-photon (2P) excitation. Its particularity is that-unlike two- or three-lens light-sheet microscopes-it uses a single, low-magnification, high-numerical aperture objective for the generation and scanning of a virtual light sheet. The microscope builds on a modified Nipkow-Petráň spinning-disk scheme for achieving wide-field excitation. However, unlike the Yokogawa design that uses a tandem disk, our concept combines micro lenses, dichroic mirrors and detection pinholes on a single disk. This new design, advantageous for 2P excitation, circumvents problems arising with the tandem disk from the large wavelength difference between the infrared excitation light and visible fluorescence. 2P fluorescence excited by the light sheet is collected with the same objective and imaged onto a fast sCMOS camera. We demonstrate 3-D imaging of TO-PRO3-stained EBs and of brain organoids, uncleared and after rapid partial transparisation with triethanolamine formamide (RTF) and we compare the performance of our instrument to that of a confocal laser-scanning microscope (CLSM) having a similar numerical aperture. Our large-field 2P-spinning disk microscope permits one order of magnitude faster imaging, affords less photobleaching and permits better depth penetration than a confocal microscope with similar spatial resolution.
Collapse
Affiliation(s)
- Irina Rakotoson
- Centre National de la Recherche Scientifique (CNRS) UMR 8118, Brain Physiology Laboratory, Paris, France
- Fédération de Recherche en Neurosciences CNRS FR 3636, Paris, France
- Faculté de Sciences Fondamentales et Biomédicales, Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France
- Master Program: MASTER Mention Biologie Cellulaire, Physiologie, Pathologies (BCPP), Spécialité Neurosciences, Université Paris Descartes - Paris 5, Paris, France
| | - Brigitte Delhomme
- Centre National de la Recherche Scientifique (CNRS) UMR 8118, Brain Physiology Laboratory, Paris, France
- Fédération de Recherche en Neurosciences CNRS FR 3636, Paris, France
- Faculté de Sciences Fondamentales et Biomédicales, Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France
| | - Philippe Djian
- Centre National de la Recherche Scientifique (CNRS) UMR 8118, Brain Physiology Laboratory, Paris, France
- Fédération de Recherche en Neurosciences CNRS FR 3636, Paris, France
- Faculté de Sciences Fondamentales et Biomédicales, Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France
| | | | - Maia Brunstein
- Centre National de la Recherche Scientifique (CNRS) UMR 8118, Brain Physiology Laboratory, Paris, France
- Fédération de Recherche en Neurosciences CNRS FR 3636, Paris, France
- Faculté de Sciences Fondamentales et Biomédicales, Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France
| | | | | | - Clément Ricard
- Centre National de la Recherche Scientifique (CNRS) UMR 8118, Brain Physiology Laboratory, Paris, France
- Fédération de Recherche en Neurosciences CNRS FR 3636, Paris, France
- Faculté de Sciences Fondamentales et Biomédicales, Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France
| | - Martin Oheim
- Centre National de la Recherche Scientifique (CNRS) UMR 8118, Brain Physiology Laboratory, Paris, France
- Fédération de Recherche en Neurosciences CNRS FR 3636, Paris, France
- Faculté de Sciences Fondamentales et Biomédicales, Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France
| |
Collapse
|
36
|
Abstract
Light-sheet microscopy is an imaging approach that offers unique advantages for a diverse range of neuroscience applications. Unlike point-scanning techniques such as confocal and two-photon microscopy, light-sheet microscopes illuminate an entire plane of tissue, while imaging this plane onto a camera. Although early implementations of light sheet were optimized for longitudinal imaging of embryonic development in small specimens, emerging implementations are capable of capturing light-sheet images in freely moving, unconstrained specimens and even the intact in vivo mammalian brain. Meanwhile, the unique photobleaching and signal-to-noise benefits afforded by light-sheet microscopy's parallelized detection deliver the ability to perform volumetric imaging at much higher speeds than can be achieved using point scanning. This review describes the basic principles and evolution of light-sheet microscopy, followed by perspectives on emerging applications and opportunities for both imaging large, cleared, and expanded neural tissues and high-speed, functional imaging in vivo.
Collapse
Affiliation(s)
- Elizabeth M C Hillman
- Departments of Biomedical Engineering and Radiology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA;
| | - Venkatakaushik Voleti
- Departments of Biomedical Engineering and Radiology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA;
| | - Wenze Li
- Departments of Biomedical Engineering and Radiology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA;
| | - Hang Yu
- Departments of Biomedical Engineering and Radiology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA;
| |
Collapse
|
37
|
Madrid-Wolff J, Forero-Shelton M. Protocol for the Design and Assembly of a Light Sheet Light Field Microscope. Methods Protoc 2019; 2:mps2030056. [PMID: 31277384 PMCID: PMC6789549 DOI: 10.3390/mps2030056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/29/2019] [Accepted: 07/01/2019] [Indexed: 11/23/2022] Open
Abstract
Light field microscopy is a recent development that makes it possible to obtain images of volumes with a single camera exposure, enabling studies of fast processes such as neural activity in zebrafish brains at high temporal resolution, at the expense of spatial resolution. Light sheet microscopy is also a recent method that reduces illumination intensity while increasing the signal-to-noise ratio with respect to confocal microscopes. While faster and gentler to samples than confocals for a similar resolution, light sheet microscopy is still slower than light field microscopy since it must collect volume slices sequentially. Nonetheless, the combination of the two methods, i.e., light field microscopes that have light sheet illumination, can help to improve the signal-to-noise ratio of light field microscopes and potentially improve their resolution. Building these microscopes requires much expertise, and the resources for doing so are limited. Here, we present a protocol to build a light field microscope with light sheet illumination. This protocol is also useful to build a light sheet microscope.
Collapse
Affiliation(s)
- Jorge Madrid-Wolff
- Biomedical Computer Vision Group, Universidad de los Andes, Bogota 111711, Colombia
| | | |
Collapse
|
38
|
Oh J, Lee C, Kaang BK. Imaging and analysis of genetically encoded calcium indicators linking neural circuits and behaviors. THE KOREAN JOURNAL OF PHYSIOLOGY & PHARMACOLOGY : OFFICIAL JOURNAL OF THE KOREAN PHYSIOLOGICAL SOCIETY AND THE KOREAN SOCIETY OF PHARMACOLOGY 2019; 23:237-249. [PMID: 31297008 PMCID: PMC6609268 DOI: 10.4196/kjpp.2019.23.4.237] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 12/21/2022]
Abstract
Confirming the direct link between neural circuit activity and animal behavior has been a principal aim of neuroscience. The genetically encoded calcium indicator (GECI), which binds to calcium ions and emits fluorescence visualizing intracellular calcium concentration, enables detection of in vivo neuronal firing activity. Various GECIs have been developed and can be chosen for diverse purposes. These GECI-based signals can be acquired by several tools including two-photon microscopy and microendoscopy for precise or wide imaging at cellular to synaptic levels. In addition, the images from GECI signals can be analyzed with open source codes including constrained non-negative matrix factorization for endoscopy data (CNMF_E) and miniscope 1-photon-based calcium imaging signal extraction pipeline (MIN1PIPE), and considering parameters of the imaged brain regions (e.g., diameter or shape of soma or the resolution of recorded images), the real-time activity of each cell can be acquired and linked with animal behaviors. As a result, GECI signal analysis can be a powerful tool for revealing the functions of neuronal circuits related to specific behaviors.
Collapse
Affiliation(s)
- Jihae Oh
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Chiwoo Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Bong-Kiun Kaang
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| |
Collapse
|
39
|
Yang B, Chen X, Wang Y, Feng S, Pessino V, Stuurman N, Cho NH, Cheng KW, Lord SJ, Xu L, Xie D, Mullins RD, Leonetti MD, Huang B. Epi-illumination SPIM for volumetric imaging with high spatial-temporal resolution. Nat Methods 2019; 16:501-504. [PMID: 31061492 PMCID: PMC6557432 DOI: 10.1038/s41592-019-0401-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/29/2019] [Indexed: 11/16/2022]
Abstract
We designed an epi-illumination SPIM system that uses a single objective and has a sample interface identical to that of an inverted fluorescence microscope with no additional reflection elements. It achieves subcellular resolution and single-molecule sensitivity, and is compatible with common biological sample holders, including multi-well plates. We demonstrated multicolor fast volumetric imaging, single-molecule localization microscopy, parallel imaging of 16 cell lines and parallel recording of cellular responses to perturbations.
Collapse
Affiliation(s)
- Bin Yang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Xingye Chen
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Department of Automation, Tsinghua University, Beijing, China
| | - Yina Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Siyu Feng
- The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA
| | - Veronica Pessino
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Nico Stuurman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | | | - Karen W Cheng
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Samuel J Lord
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Linfeng Xu
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Dan Xie
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - R Dyche Mullins
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | | | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
40
|
Liang X, Ho MCW, Zhang Y, Li Y, Wu MN, Holy TE, Taghert PH. Morning and Evening Circadian Pacemakers Independently Drive Premotor Centers via a Specific Dopamine Relay. Neuron 2019; 102:843-857.e4. [PMID: 30981533 PMCID: PMC6533154 DOI: 10.1016/j.neuron.2019.03.028] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/06/2019] [Accepted: 03/19/2019] [Indexed: 12/23/2022]
Abstract
Many animals exhibit morning and evening peaks of locomotor behavior. In Drosophila, two corresponding circadian neural oscillators-M (morning) cells and E (evening) cells-exhibit a corresponding morning or evening neural activity peak. Yet we know little of the neural circuitry by which distinct circadian oscillators produce specific outputs to precisely control behavioral episodes. Here, we show that ring neurons of the ellipsoid body (EB-RNs) display spontaneous morning and evening neural activity peaks in vivo: these peaks coincide with the bouts of locomotor activity and result from independent activation by M and E pacemakers. Further, M and E cells regulate EB-RNs via identified PPM3 dopaminergic neurons, which project to the EB and are normally co-active with EB-RNs. These in vivo findings establish the fundamental elements of a circadian neuronal output pathway: distinct circadian oscillators independently drive a common pre-motor center through the agency of specific dopaminergic interneurons.
Collapse
Affiliation(s)
- Xitong Liang
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Margaret C W Ho
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yajun Zhang
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China; Chinese Institute for Brain Research, Beijing 100871, China
| | - Mark N Wu
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Timothy E Holy
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Paul H Taghert
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO 63110, USA.
| |
Collapse
|
41
|
Corsetti S, Gunn-Moore F, Dholakia K. Light sheet fluorescence microscopy for neuroscience. J Neurosci Methods 2019; 319:16-27. [DOI: 10.1016/j.jneumeth.2018.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/03/2018] [Accepted: 07/16/2018] [Indexed: 12/29/2022]
|
42
|
Reder NP, Glaser AK, McCarty EF, Chen Y, True LD, Liu JTC. Open-Top Light-Sheet Microscopy Image Atlas of Prostate Core Needle Biopsies. Arch Pathol Lab Med 2019; 143:1069-1075. [PMID: 30892067 DOI: 10.5858/arpa.2018-0466-oa] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
CONTEXT.— Ex vivo microscopy encompasses a range of techniques to examine fresh or fixed tissue with microscopic resolution, eliminating the need to embed the tissue in paraffin or produce a glass slide. One such technique is light-sheet microscopy, which enables rapid 3D imaging. Our pathology-engineering collaboration has resulted in an open-top light-sheet (OTLS) microscope that is specifically tailored to the needs of pathology practice. OBJECTIVE.— To present an image atlas of OTLS images of prostate core needle biopsies. DESIGN.— Core needle biopsies (N = 9) were obtained from fresh radical prostatectomy specimens. Each biopsy was fixed in formalin, dehydrated in ethanol, stained with TO-PRO3 and eosin, optically cleared, and imaged using OTLS microscopy. The biopsies were then processed, paraffin embedded, and sectioned. Hematoxylin-eosin and immunohistochemical staining for cytokeratin 5 and cytokeratin 8 was performed. RESULTS.— Benign and neoplastic histologic structures showed high fidelity between OTLS and traditional light microscopy. OTLS microscopy had no discernible effect on hematoxylin-eosin or immunohistochemical staining in this pilot study. The 3D histology information obtained using OTLS microscopy enabled new structural insights, including the observation of cribriform and well-formed gland morphologies within the same contiguous glandular structures, as well as the continuity of poorly formed glands with well-formed glands. CONCLUSIONS.— Three-dimensional OTLS microscopy images have a similar appearance to traditional hematoxylin-eosin histology images, with the added benefit of useful 3D structural information. Further studies are needed to continue to document the OTLS appearance of a wide range of tissues and to better understand 3D histologic structures.
Collapse
Affiliation(s)
- Nicholas P Reder
- From the Departments of Pathology (Drs Reder, True, and Liu and Ms McCarty) and Mechanical Engineering (Drs Glaser and Liu and Mr Chen), University of Washington, Seattle
| | - Adam K Glaser
- From the Departments of Pathology (Drs Reder, True, and Liu and Ms McCarty) and Mechanical Engineering (Drs Glaser and Liu and Mr Chen), University of Washington, Seattle
| | - Erin F McCarty
- From the Departments of Pathology (Drs Reder, True, and Liu and Ms McCarty) and Mechanical Engineering (Drs Glaser and Liu and Mr Chen), University of Washington, Seattle
| | - Ye Chen
- From the Departments of Pathology (Drs Reder, True, and Liu and Ms McCarty) and Mechanical Engineering (Drs Glaser and Liu and Mr Chen), University of Washington, Seattle
| | - Lawrence D True
- From the Departments of Pathology (Drs Reder, True, and Liu and Ms McCarty) and Mechanical Engineering (Drs Glaser and Liu and Mr Chen), University of Washington, Seattle
| | - Jonathan T C Liu
- From the Departments of Pathology (Drs Reder, True, and Liu and Ms McCarty) and Mechanical Engineering (Drs Glaser and Liu and Mr Chen), University of Washington, Seattle
| |
Collapse
|
43
|
Jewell SW, Hocking TD, Fearnhead P, Witten DM. Fast nonconvex deconvolution of calcium imaging data. Biostatistics 2019; 21:709-726. [PMID: 30753436 DOI: 10.1093/biostatistics/kxy083] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 12/03/2018] [Accepted: 12/10/2018] [Indexed: 11/14/2022] Open
Abstract
Calcium imaging data promises to transform the field of neuroscience by making it possible to record from large populations of neurons simultaneously. However, determining the exact moment in time at which a neuron spikes, from a calcium imaging data set, amounts to a non-trivial deconvolution problem which is of critical importance for downstream analyses. While a number of formulations have been proposed for this task in the recent literature, in this article, we focus on a formulation recently proposed in Jewell and Witten (2018. Exact spike train inference via $\ell_{0} $ optimization. The Annals of Applied Statistics12(4), 2457-2482) that can accurately estimate not just the spike rate, but also the specific times at which the neuron spikes. We develop a much faster algorithm that can be used to deconvolve a fluorescence trace of 100 000 timesteps in less than a second. Furthermore, we present a modification to this algorithm that precludes the possibility of a "negative spike". We demonstrate the performance of this algorithm for spike deconvolution on calcium imaging datasets that were recently released as part of the $\texttt{spikefinder}$ challenge (http://spikefinder.codeneuro.org/). The algorithm presented in this article was used in the Allen Institute for Brain Science's "platform paper" to decode neural activity from the Allen Brain Observatory; this is the main scientific paper in which their data resource is presented. Our $\texttt{C++}$ implementation, along with $\texttt{R}$ and $\texttt{python}$ wrappers, is publicly available. $\texttt{R}$ code is available on $\texttt{CRAN}$ and $\texttt{Github}$, and $\texttt{python}$ wrappers are available on $\texttt{Github}$; see https://github.com/jewellsean/FastLZeroSpikeInference.
Collapse
Affiliation(s)
- Sean W Jewell
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - Toby Dylan Hocking
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 83011, USA
| | - Paul Fearnhead
- Department of Mathematics and Statistics, Lancaster University, Lancaster LA1 4YF, UK
| | - Daniela M Witten
- Department of Statistics, University of Washington, Seattle, WA 98195, USA and Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
44
|
Albert-Smet I, Marcos-Vidal A, Vaquero JJ, Desco M, Muñoz-Barrutia A, Ripoll J. Applications of Light-Sheet Microscopy in Microdevices. Front Neuroanat 2019; 13:1. [PMID: 30760983 PMCID: PMC6362405 DOI: 10.3389/fnana.2019.00001] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/09/2019] [Indexed: 11/23/2022] Open
Abstract
Light-sheet fluorescence microscopy (LSFM) has been present in cell biology laboratories for quite some time, mainly as custom-made systems, with imaging applications ranging from single cells (in the micrometer scale) to small organisms (in the millimeter scale). Such microscopes distinguish themselves for having very low phototoxicity levels and high spatial and temporal resolution, properties that make them ideal for a large range of applications. These include the study of cellular dynamics, in particular cellular motion which is essential to processes such as tumor metastasis and tissue development. Experimental setups make extensive use of microdevices (bioMEMS) that provide better control over the substrate environment than traditional cell culture experiments. For example, to mimic in vivo conditions, experiment biochemical dynamics, and trap, move or count cells. Microdevices provide a higher degree of empirical complexity but, so far, most have been designed to be imaged through wide-field or confocal microscopes. Nonetheless, the properties of LSFM render it ideal for 3D characterization of active cells. When working with microdevices, confocal microscopy is more widespread than LSFM even though it suffers from higher phototoxicity and slower acquisition speeds. It is sometimes possible to illuminate with a light-sheet microdevices designed for confocal microscopes. However, these bioMEMS must be redesigned to exploit the full potential of LSFM and image more frequently on a wider scale phenomena such as motion, traction, differentiation, and diffusion of molecules. The use of microdevices for LSFM has extended beyond cell tracking studies into experiments regarding cytometry, spheroid cultures and lab-on-a-chip automation. Due to light-sheet microscopy being in its early stages, a setup of these characteristics demands some degree of optical expertise; and designing three-dimensional microdevices requires facilities, ingenuity, and experience in microfabrication. In this paper, we explore different approaches where light-sheet microscopy can achieve single-cell and subcellular resolution within microdevices, and provide a few pointers on how these experiments may be improved.
Collapse
Affiliation(s)
- Ignacio Albert-Smet
- Department of Bioengineering and Aerospace Engineering, Universidad Carlos III de Madrid, Madrid, Spain
| | - Asier Marcos-Vidal
- Department of Bioengineering and Aerospace Engineering, Universidad Carlos III de Madrid, Madrid, Spain
| | - Juan José Vaquero
- Department of Bioengineering and Aerospace Engineering, Universidad Carlos III de Madrid, Madrid, Spain
- Experimental Medicine and Surgery Unit, Instituto de Investigación Sanitaria del Hospital Gregorio Marañón, Madrid, Spain
| | - Manuel Desco
- Department of Bioengineering and Aerospace Engineering, Universidad Carlos III de Madrid, Madrid, Spain
- Experimental Medicine and Surgery Unit, Instituto de Investigación Sanitaria del Hospital Gregorio Marañón, Madrid, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Arrate Muñoz-Barrutia
- Department of Bioengineering and Aerospace Engineering, Universidad Carlos III de Madrid, Madrid, Spain
- Experimental Medicine and Surgery Unit, Instituto de Investigación Sanitaria del Hospital Gregorio Marañón, Madrid, Spain
| | - Jorge Ripoll
- Department of Bioengineering and Aerospace Engineering, Universidad Carlos III de Madrid, Madrid, Spain
- Experimental Medicine and Surgery Unit, Instituto de Investigación Sanitaria del Hospital Gregorio Marañón, Madrid, Spain
| |
Collapse
|
45
|
Abstract
In recent years new technologies in neuroscience have made it possible to measure the activities of large numbers of neurons simultaneously in behaving animals. For each neuron a fluorescence trace is measured; this can be seen as a first-order approximation of the neuron's activity over time. Determining the exact time at which a neuron spikes on the basis of its fluorescence trace is an important open problem in the field of computational neuroscience. Recently, a convex optimization problem involving an ℓ1 penalty was proposed for this task. In this paper we slightly modify that recent proposal by replacing the ℓ1 penalty with an ℓ0 penalty. In stark contrast to the conventional wisdom that ℓ0 optimization problems are computationally intractable, we show that the resulting optimization problem can be efficiently solved for the global optimum using an extremely simple and efficient dynamic programming algorithm. Our R-language implementation of the proposed algorithm runs in a few minutes on fluorescence traces of 100,000 timesteps. Furthermore, our proposal leads to substantial improvements over the previous ℓ1 proposal, in simulations as well as on two calcium imaging datasets. R-language software for our proposal is available on CRAN in the package LZeroSpikeInference. Instructions for running this software in python can be found at https://github.com/jewellsean/LZeroSpikeInference.
Collapse
Affiliation(s)
- Sean Jewell
- Department of Statistics, University of Washington, Seattle, Washington 98195, USA,
| | - Daniela Witten
- Departments of Statistics and Biostatistics, University of Washington, Seattle, Washington 98195, USA,
| |
Collapse
|
46
|
Ding Y, Ma J, Langenbacher AD, Baek KI, Lee J, Chang CC, Hsu JJ, Kulkarni RP, Belperio J, Shi W, Ranjbarvaziri S, Ardehali R, Tintut Y, Demer LL, Chen JN, Fei P, Packard RRS, Hsiai TK. Multiscale light-sheet for rapid imaging of cardiopulmonary system. JCI Insight 2018; 3:e121396. [PMID: 30135307 PMCID: PMC6141183 DOI: 10.1172/jci.insight.121396] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The ability to image tissue morphogenesis in real-time and in 3-dimensions (3-D) remains an optical challenge. The advent of light-sheet fluorescence microscopy (LSFM) has advanced developmental biology and tissue regeneration research. In this review, we introduce a LSFM system in which the illumination lens reshapes a thin light-sheet to rapidly scan across a sample of interest while the detection lens orthogonally collects the imaging data. This multiscale strategy provides deep-tissue penetration, high-spatiotemporal resolution, and minimal photobleaching and phototoxicity, allowing in vivo visualization of a variety of tissues and processes, ranging from developing hearts in live zebrafish embryos to ex vivo interrogation of the microarchitecture of optically cleared neonatal hearts. Here, we highlight multiple applications of LSFM and discuss several studies that have allowed better characterization of developmental and pathological processes in multiple models and tissues. These findings demonstrate the capacity of multiscale light-sheet imaging to uncover cardiovascular developmental and regenerative phenomena.
Collapse
Affiliation(s)
- Yichen Ding
- Department of Medicine, David Geffen School of Medicine at UCLA, and
- Department of Bioengineering, UCLA, Los Angeles, California, USA
| | - Jianguo Ma
- Department of Medicine, David Geffen School of Medicine at UCLA, and
- School of Instrumentation Science and Opto-electronics Engineering, Beihang University, Beijing, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beijing, China
| | - Adam D. Langenbacher
- Department of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, California, USA
| | - Kyung In Baek
- Department of Bioengineering, UCLA, Los Angeles, California, USA
| | - Juhyun Lee
- Department of Bioengineering, UCLA, Los Angeles, California, USA
| | | | - Jeffrey J. Hsu
- Department of Medicine, David Geffen School of Medicine at UCLA, and
| | - Rajan P. Kulkarni
- Department of Medicine, David Geffen School of Medicine at UCLA, and
| | - John Belperio
- Department of Medicine, David Geffen School of Medicine at UCLA, and
| | - Wei Shi
- Developmental Biology and Regenerative Medicine Program, Department of Surgery, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | | | - Reza Ardehali
- Department of Medicine, David Geffen School of Medicine at UCLA, and
| | - Yin Tintut
- Department of Medicine, David Geffen School of Medicine at UCLA, and
| | - Linda L. Demer
- Department of Medicine, David Geffen School of Medicine at UCLA, and
| | - Jau-Nian Chen
- Department of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, California, USA
| | - Peng Fei
- Department of Medicine, David Geffen School of Medicine at UCLA, and
- School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, China
| | | | - Tzung K. Hsiai
- Department of Medicine, David Geffen School of Medicine at UCLA, and
- Department of Bioengineering, UCLA, Los Angeles, California, USA
| |
Collapse
|
47
|
Sensory Adaptation to Chemical Cues by Vomeronasal Sensory Neurons. eNeuro 2018; 5:eN-NWR-0223-18. [PMID: 30105301 PMCID: PMC6088365 DOI: 10.1523/eneuro.0223-18.2018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/13/2018] [Accepted: 07/18/2018] [Indexed: 01/03/2023] Open
Abstract
Sensory adaptation is a source of experience-dependent feedback that impacts responses to environmental cues. In the mammalian main olfactory system (MOS), adaptation influences sensory coding at its earliest processing stages. Sensory adaptation in the accessory olfactory system (AOS) remains incompletely explored, leaving many aspects of the phenomenon unclear. We investigated sensory adaptation in vomeronasal sensory neurons (VSNs) using a combination of in situ Ca2+ imaging and electrophysiology. Parallel studies revealed prominent short-term sensory adaptation in VSNs upon repeated stimulation with mouse urine and monomolecular bile acid ligands at interstimulus intervals (ISIs) less than 30 s. In such conditions, Ca2+ signals and spike rates were often reduced by more than 50%, leading to dramatically reduced chemosensory sensitivity. Short-term adaptation was reversible over the course of minutes. Population Ca2+ imaging experiments revealed the presence of a slower form of VSN adaptation that accumulated over dozens of stimulus presentations delivered over tens of minutes. Most VSNs showed strong adaptation, but in a substantial VSN subpopulation adaptation was diminished or absent. Investigation of same- and opposite-sex urine responses in male and female VSNs revealed that adaptation to same-sex cues occurred at ISIs up to 180 s, conditions that did not induce adaptation to opposite-sex cues. This result suggests that VSN sensory adaptation can be modulated by sensory experience. These studies comprehensively establish the presence of VSN sensory adaptation and provide a foundation for future inquiries into the molecular and cellular mechanisms of this phenomenon and its impact on mammalian behavior.
Collapse
|
48
|
Chatterjee K, Pratiwi FW, Wu FCM, Chen P, Chen BC. Recent Progress in Light Sheet Microscopy for Biological Applications. APPLIED SPECTROSCOPY 2018; 72:1137-1169. [PMID: 29926744 DOI: 10.1177/0003702818778851] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The introduction of light sheet fluorescence microscopy (LSFM) has overcome the challenges in conventional optical microscopy. Among the recent breakthroughs in fluorescence microscopy, LSFM had been proven to provide a high three-dimensional spatial resolution, high signal-to-noise ratio, fast imaging acquisition rate, and minuscule levels of phototoxic and photodamage effects. The aforementioned auspicious properties are crucial in the biomedical and clinical research fields, covering a broad range of applications: from the super-resolution imaging of intracellular dynamics in a single cell to the high spatiotemporal resolution imaging of developmental dynamics in an entirely large organism. In this review, we provided a systematic outline of the historical development of LSFM, detailed discussion on the variants and improvements of LSFM, and delineation on the most recent technological advancements of LSFM and its potential applications in single molecule/particle detection, single-molecule super-resolution imaging, imaging intracellular dynamics of a single cell, multicellular imaging: cell-cell and cell-matrix interactions, plant developmental biology, and brain imaging and developmental biology.
Collapse
Affiliation(s)
- Krishnendu Chatterjee
- 1 Nanoscience and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- 3 Department of Engineering and System Science, National Tsing-Hua University, Hsinchu, Taiwan
| | - Feby Wijaya Pratiwi
- 1 Nanoscience and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- 4 Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | | | - Peilin Chen
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Bi-Chang Chen
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
49
|
Weisenburger S, Vaziri A. A Guide to Emerging Technologies for Large-Scale and Whole-Brain Optical Imaging of Neuronal Activity. Annu Rev Neurosci 2018; 41:431-452. [PMID: 29709208 PMCID: PMC6037565 DOI: 10.1146/annurev-neuro-072116-031458] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The mammalian brain is a densely interconnected network that consists of millions to billions of neurons. Decoding how information is represented and processed by this neural circuitry requires the ability to capture and manipulate the dynamics of large populations at high speed and high resolution over a large area of the brain. Although the use of optical approaches by the neuroscience community has rapidly increased over the past two decades, most microscopy approaches are unable to record the activity of all neurons comprising a functional network across the mammalian brain at relevant temporal and spatial resolutions. In this review, we survey the recent development in optical technologies for Ca2+ imaging in this regard and provide an overview of the strengths and limitations of each modality and its potential for scalability. We provide guidance from the perspective of a biological user driven by the typical biological applications and sample conditions. We also discuss the potential for future advances and synergies that could be obtained through hybrid approaches or other modalities.
Collapse
Affiliation(s)
- Siegfried Weisenburger
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, New York 10065, USA
| | - Alipasha Vaziri
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, New York 10065, USA
- Kavli Neural Systems Institute, The Rockefeller University, New York, New York 10065, USA
- Research Institute of Molecular Pathology, 1030 Vienna, Austria;
| |
Collapse
|
50
|
Holy TE. The Accessory Olfactory System: Innately Specialized or Microcosm of Mammalian Circuitry? Annu Rev Neurosci 2018; 41:501-525. [DOI: 10.1146/annurev-neuro-080317-061916] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In mammals, the accessory olfactory system is a distinct circuit that has received attention for its role in detecting and responding to pheromones. While the neuroscientific investigation of this system is comparatively new, recent advances and its compact size have made it an attractive model for developing an end-to-end understanding of such questions as regulation of essential behaviors, plasticity, and individual recognition. Recent discoveries have indicated a need to reevaluate our conception of this system, suggesting that ( a) physical principles—rather than biological necessity—play an underappreciated role in its raison d'être and that ( b) the anatomy of downstream projections is not dominated by unique specializations but instead consists of an abbreviated cortical/basal ganglia motif reminiscent of other sensorimotor systems. These observations suggest that the accessory olfactory system distinguishes itself primarily by the physicochemical properties of its ligands, but its architecture is otherwise a microcosm of mammalian neurocircuitry.
Collapse
Affiliation(s)
- Timothy E. Holy
- Department of Neuroscience, Washington University, St. Louis, Missouri 63132, USA
| |
Collapse
|