1
|
Liu S, Liu F, Lin Z, Yin W, Fang S, Piao Y, Liu L, Shen Y. Identification of cortical arteries and veins in awake mice using two-photon microscopy. J Anat 2024. [PMID: 39034848 DOI: 10.1111/joa.14110] [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: 03/25/2024] [Revised: 06/03/2024] [Accepted: 06/28/2024] [Indexed: 07/23/2024] Open
Abstract
Distinguishing arteries from veins in the cerebral cortex is critical for studying hemodynamics under pathophysiological conditions, which plays an important role in the diagnosis and treatment of various vessel-related diseases. However, due to the complexity of the cerebral vascular network, it is challenging to identify arteries and veins in vivo. Here, we demonstrate an artery-vein separation method that employs a combination of multiple scanning modes of two-photon microscopy and a custom-designed stereoscopic fixation device for mice. In this process, we propose a novel method for determining the line scanning direction, which allows us to determine the blood flow directions. The vasculature branches have been identified using an optimized z-stack scanning mode, followed by the separation of blood vessel types according to the directions of blood flow and branching patterns. Using this strategy, the penetrating arterioles and penetrating venules in awake mice could be accurately identified and the type of cerebral thrombus has been also successfully isolated without any empirical knowledge or algorithms. Our research presents a new, more accurate, and efficient method for cortical artery-vein separation in awake mice, providing a useful strategy for the application of two-photon microscopy in the study of cerebrovascular pathophysiology.
Collapse
Affiliation(s)
- Shuangshuang Liu
- Core Facilities, Zhejiang University School of Medicine, Hangzhou, China
| | - FangYue Liu
- School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhaoxiaonan Lin
- Core Facilities, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Yin
- Core Facilities, Zhejiang University School of Medicine, Hangzhou, China
| | - Sanhua Fang
- Core Facilities, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Piao
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Li Liu
- Core Facilities, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Shen
- School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou, China
- National Health and Disease Human Brain Tissue Resource Center, Hangzhou, China
| |
Collapse
|
2
|
Kaushik V, Dąbrowski M, Gessa L, Kumar N, Fernandes H. Two-photon excitation fluorescence in ophthalmology: safety and improved imaging for functional diagnostics. Front Med (Lausanne) 2024; 10:1293640. [PMID: 38235268 PMCID: PMC10791900 DOI: 10.3389/fmed.2023.1293640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Two-photon excitation fluorescence (TPEF) is emerging as a powerful imaging technique with superior penetration power in scattering media, allowing for functional imaging of biological tissues at a subcellular level. TPEF is commonly used in cancer diagnostics, as it enables the direct observation of metabolism within living cells. The technique is now widely used in various medical fields, including ophthalmology. The eye is a complex and delicate organ with multiple layers of different cell types and tissues. Although this structure is ideal for visual perception, it generates aberrations in TPEF eye imaging. However, adaptive optics can now compensate for these aberrations, allowing for improved imaging of the eyes of animal models for human diseases. The eye is naturally built to filter out harmful wavelengths, but these wavelengths can be mimicked and thereby utilized in diagnostics via two-photon (2Ph) excitation. Recent advances in laser-source manufacturing have made it possible to minimize the exposure of in vivo measurements within safety, while achieving sufficient signals to detect for functional images, making TPEF a viable option for human application. This review explores recent advances in wavefront-distortion correction in animal models and the safety of use of TPEF on human subjects, both of which make TPEF a potentially powerful tool for ophthalmological diagnostics.
Collapse
Affiliation(s)
- Vineeta Kaushik
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Michał Dąbrowski
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
- International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Luca Gessa
- International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Nelam Kumar
- International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Humberto Fernandes
- International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| |
Collapse
|
3
|
Ko T, Jou C, Grau-Perales AB, Reynders M, Fenton AA, Trauner D. Photoactivated Protein Degrader for Optical Control of Synaptic Function. ACS Chem Neurosci 2023; 14:3704-3713. [PMID: 37712589 PMCID: PMC10557063 DOI: 10.1021/acschemneuro.3c00390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/04/2023] [Indexed: 09/16/2023] Open
Abstract
Hundreds of proteins determine the function of synapses, and synapses define the neuronal circuits that subserve myriad brain, cognitive, and behavioral functions. It is thus necessary to precisely manipulate specific proteins at specific sub-cellular locations and times to elucidate the roles of particular proteins and synapses in brain function. We developed PHOtochemically TArgeting Chimeras (PHOTACs) as a strategy to optically degrade specific proteins with high spatial and temporal precision. PHOTACs are small molecules that, upon wavelength-selective illumination, catalyze ubiquitylation and degradation of target proteins through endogenous proteasomes. Here, we describe the design and chemical properties of a PHOTAC that targets Ca2+/calmodulin-dependent protein kinase II alpha (CaMKIIα), which is abundant and crucial for the baseline synaptic function of excitatory neurons. We validate the PHOTAC strategy, showing that the CaMKIIα-PHOTAC is effective in mouse brain tissue. Light activation of CaMKIIα-PHOTAC removed CaMKIIα from regions of the mouse hippocampus only within 25 μm of the illuminated brain surface. The optically controlled degradation decreases synaptic function within minutes of light activation, measured by the light-initiated attenuation of evoked field excitatory postsynaptic potential (fEPSP) responses to physiological stimulation. The PHOTACs methodology should be broadly applicable to other key proteins implicated in synaptic function, especially for evaluating their precise roles in the maintenance of long-term potentiation and memory within subcellular dendritic domains.
Collapse
Affiliation(s)
- Tongil Ko
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Claudia Jou
- Department
of Psychology, Hunter College, New York, New York 10065, United States
| | | | - Martin Reynders
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - André A. Fenton
- Center
for Neural Science, New York University, New York, New York 10003, United States
| | - Dirk Trauner
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
4
|
Zhang K, Chen FR, Wang L, Hu J. Second Near-Infrared (NIR-II) Window for Imaging-Navigated Modulation of Brain Structure and Function. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206044. [PMID: 36670072 DOI: 10.1002/smll.202206044] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/28/2022] [Indexed: 06/17/2023]
Abstract
For a long time, optical imaging of the deep brain with high resolution has been a challenge. Recently, with the advance in second near-infrared (NIR-II) bioimaging techniques and imaging contrast agents, NIR-II window bioimaging has attracted great attention to monitoring deeper biological or pathophysiological processes with high signal-to-noise ratio (SNR) and spatiotemporal resolution. Assisted with NIR-II bioimaging, the modulation of structure and function of brain is promising to be noninvasive and more precise. Herein, in this review, first the advantage of NIR-II light in brain imaging from the interaction between NIR-II and tissue is elaborated. Then, several specific NIR-II bioimaging technologies are introduced, including NIR-II fluorescence imaging, multiphoton fluorescence imaging, and photoacoustic imaging. Furthermore, the corresponding contrast agents are summarized. Next, the application of various NIR-II bioimaging technologies in visualizing the characteristics of cerebrovascular network and monitoring the changes of the pathology signals will be presented. After that, the modulation of brain structure and function based on NIR-II bioimaging will be discussed, including treatment of glioblastoma, guidance of cell transplantation, and neuromodulation. In the end, future perspectives that would help improve the clinical translation of NIR-II light are proposed.
Collapse
Affiliation(s)
- Ke Zhang
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
| | - Fu-Rong Chen
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
| | - Lidai Wang
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
| | - Jinlian Hu
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
| |
Collapse
|
5
|
Ko T, Jou C, Grau-Perales A, Reynders M, Fenton A, Trauner D. A Photoactivated Protein Degrader for Optical Control of Synaptic Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528397. [PMID: 36824807 PMCID: PMC9949324 DOI: 10.1101/2023.02.13.528397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Hundreds of proteins determine the function of synapses, and synapses define the neuronal circuits that subserve myriad brain, cognitive, and behavioral functions. It is thus necessary to precisely manipulate specific proteins at specific sub-cellular locations and times to elucidate the roles of particular proteins and synapses in brain function. We developed PHOtochemically TArgeting Chimeras (PHOTACs) as a strategy to optically degrade specific proteins with high spatial and temporal precision. PHOTACs are small molecules that, upon wavelength-selective illumination, catalyze ubiquitylation and degradation of target proteins through endogenous proteasomes. Here we describe the design and chemical properties of a PHOTAC that targets Ca 2+ /calmodulin-dependent protein kinase II alpha (CaMKIIα), which is abundant and crucial for baseline synaptic function of excitatory neurons. We validate the PHOTAC strategy, showing that the CaMKIIα-PHOTAC is effective in mouse brain tissue. Light activation of CaMKIIα-PHOTAC removed CaMKIIα from regions of the mouse hippocampus only within 25 μm of the illuminated brain surface. The optically-controlled degradation decreases synaptic function within minutes of light activation, measured by the light-initiated attenuation of evoked field excitatory postsynaptic potential (fEPSP) responses to physiological stimulation. The PHOTACs methodology should be broadly applicable to other key proteins implicated in synaptic function, especially for evaluating their precise roles in the maintenance of long-term potentiation and memory within subcellular dendritic domains.
Collapse
Affiliation(s)
- T. Ko
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street Philadelphia, PA 19104-6323, USA
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - C. Jou
- Department of Psychology, Hunter College, 695 Park Avenue, New York, NY, 10065, USA
| | - A.B. Grau-Perales
- Center for Neural Science, New York University, 4 Washington Place, New York, NY 10003, USA
| | - M. Reynders
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - A.A. Fenton
- Center for Neural Science, New York University, 4 Washington Place, New York, NY 10003, USA
| | - D. Trauner
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street Philadelphia, PA 19104-6323, USA
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| |
Collapse
|
6
|
Geng Y, Li Z, Zhu J, Du C, Yuan F, Cai X, Ali A, Yang J, Tang C, Cong Z, Ma C. Advances in Optogenetics Applications for Central Nervous System Injuries. J Neurotrauma 2023. [PMID: 36305381 DOI: 10.1089/neu.2022.0290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Injuries to the central nervous system (CNS) often lead to severe neurological dysfunction and even death. However, there are still no effective measures to improve functional recovery following CNS injuries. Optogenetics, an ideal method to modulate neural activity, has shown various advantages in controlling neural circuits, promoting neural remapping, and improving cell survival. In particular, the emerging technique of optogenetics has exhibited promising therapeutic methods for CNS injuries. In this review, we introduce the light-sensitive proteins and light stimulation system that are important components of optogenetic technology in detail and summarize the development trends. In addition, we construct a comprehensive picture of the current application of optogenetics in CNS injuries and highlight recent advances for the treatment and functional recovery of neurological deficits. Finally, we discuss the therapeutic challenges and prospective uses of optogenetics therapy by photostimulation/photoinhibition modalities that would be suitable for clinical applications.
Collapse
Affiliation(s)
- Yuanming Geng
- Department of Neurosurgery, The Affiliated Jinling Hospital of Nanjing Medical University, Nanjing, China
| | - Zhenxing Li
- Department of Neurosurgery, Jinling Hospital, Nanjing, China.,Department of Neurosurgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Junhao Zhu
- Department of Neurosurgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Chaonan Du
- Department of Neurosurgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Feng Yuan
- Department of Neurosurgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Xiangming Cai
- School of Medicine, Southeast University, Nanjing, China
| | - Alleyar Ali
- Department of Neurosurgery, The Affiliated Jinling Hospital of Nanjing Medical University, Nanjing, China
| | - Jin Yang
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
| | - Chao Tang
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
| | - Zixiang Cong
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
| | - Chiyuan Ma
- Department of Neurosurgery, The Affiliated Jinling Hospital of Nanjing Medical University, Nanjing, China.,Department of Neurosurgery, Jinling Hospital, Nanjing, China.,Department of Neurosurgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.,School of Medicine, Southeast University, Nanjing, China.,Department of Neurosurgery, Jinling Hospital, the First School of Clinical Medicine, Southern Medical University, Nanjing, China
| |
Collapse
|
7
|
Lee M, Kannan S, Muniraj G, Rosa V, Lu WF, Fuh JYH, Sriram G, Cao T. Two-Photon Fluorescence Microscopy and Applications in Angiogenesis and Related Molecular Events. TISSUE ENGINEERING PART B-REVIEWS 2021; 28:926-937. [PMID: 34541887 DOI: 10.1089/ten.teb.2021.0140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The role of angiogenesis in health and disease have gained considerable momentum in recent years. Visualizing angiogenic patterns and associated events of surrounding vascular beds in response to therapeutic and laboratory-grade biomolecules have become a commonplace in regenerative medicine and the biosciences. To aid imaging investigations in angiogenesis, the two-photon excitation fluorescence microscopy (2PEF), or multiphoton fluorescence microscopy is increasingly utilized in scientific investigations. The 2PEF microscope confers several distinct imaging advantages over other fluorescence excitation microscopy techniques - for the observation of in-depth, three-dimensional vascularity in a variety of tissue formats, including fixed tissue specimens and in vivo vasculature in live specimens. Understanding morphological and subcellular changes that occur in cells and tissues during angiogenesis will provide insights to behavioral responses in diseased states, advance the engineering of physiologically-relevant tissue models and provide biochemical clues for the design of therapeutic strategies. We review the applicability and limitations of the 2PEF microscope on the biophysical and molecular-level signatures of angiogenesis in various tissue models. Imaging techniques and strategies for best practices in 2PEF microscopy will be reviewed.
Collapse
Affiliation(s)
- Marcus Lee
- Faculty of Dentistry, National University of Singapore, Singapore, Singapore
| | - Sathya Kannan
- Faculty of Dentistry, National University of Singapore, Singapore, Singapore
| | - Giridharan Muniraj
- Faculty of Dentistry, National University of Singapore, Singapore, Singapore
| | - Vinicius Rosa
- Faculty of Dentistry, National University of Singapore, Singapore, Singapore
| | - Wen Feng Lu
- Department of Mechanical Engineering, National University of Singapore, Singapore, Singapore
| | - Jerry Y H Fuh
- Department of Mechanical Engineering, National University of Singapore, Singapore, Singapore
| | - Gopu Sriram
- Faculty of Dentistry, National University of Singapore, Singapore, Singapore
| | - Tong Cao
- Faculty of Dentistry, National University of Singapore, Singapore, Singapore
| |
Collapse
|
8
|
Chien YF, Lin JY, Yeh PT, Hsu KJ, Tsai YH, Chen SK, Chu SW. Dual GRIN lens two-photon endoscopy for high-speed volumetric and deep brain imaging. BIOMEDICAL OPTICS EXPRESS 2021; 12:162-172. [PMID: 33659072 PMCID: PMC7899523 DOI: 10.1364/boe.405738] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/22/2020] [Accepted: 11/18/2020] [Indexed: 05/30/2023]
Abstract
Studying neural connections and activities in vivo is fundamental to understanding brain functions. Given the cm-size brain and three-dimensional neural circuit dynamics, deep-tissue, high-speed volumetric imaging is highly desirable for brain study. With sub-micrometer spatial resolution, intrinsic optical sectioning, and deep-tissue penetration capability, two-photon microscopy (2PM) has found a niche in neuroscience. However, the current 2PM typically relies on a slow axial scan for volumetric imaging, and the maximal penetration depth is only about 1 mm. Here, we demonstrate that by integrating a gradient-index (GRIN) lens and a tunable acoustic GRIN (TAG) lens into 2PM, both penetration depth and volume-imaging rate can be significantly improved. Specifically, an ∼ 1-cm long GRIN lens allows imaging relay from any target region of a mouse brain, while a TAG lens provides a sub-second volume rate via a 100 kHz ∼ 1 MHz axial scan. This technique enables the study of calcium dynamics in cm-deep brain regions with sub-cellular and sub-second spatiotemporal resolution, paving the way for interrogating deep-brain functional connectome.
Collapse
Affiliation(s)
- Yu-Feng Chien
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Jyun-Yi Lin
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Po-Ting Yeh
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Kuo-Jen Hsu
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yu-Hsuan Tsai
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Shih-Kuo Chen
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Shi-Wei Chu
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
- Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan
| |
Collapse
|
9
|
Zimmermann M, Maia Chagas A, Bartel P, Pop S, Prieto-Godino L, Baden T. LED Zappelin': An open source LED controller for arbitrary spectrum visual stimulation and optogenetics during 2-photon imaging. HARDWAREX 2020; 8:e00127. [PMID: 35498254 PMCID: PMC9041195 DOI: 10.1016/j.ohx.2020.e00127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/16/2020] [Accepted: 07/16/2020] [Indexed: 05/19/2023]
Abstract
Two-photon (2P) microscopy is a cornerstone technique in neuroscience research. However, combining 2P imaging with spectrally arbitrary light stimulation can be challenging due to crosstalk between stimulation light and fluorescence detection. To overcome this limitation, we present a simple and low-cost electronic solution based on an ESP32 microcontroller and a TLC5947 LED driver to rapidly time-interleave stimulation and detection epochs during scans. Implemented for less than $100, our design can independently drive up to 24 arbitrary spectrum LEDs to meet user requirements. We demonstrate the utility of our stimulator for colour vision experiments on the in vivo tetrachromatic zebrafish retina and for optogenetic circuit mapping in Drosophila.
Collapse
Affiliation(s)
- M.J.Y. Zimmermann
- Sussex Neuroscience, School of Life Sciences, University of Sussex, United Kingdom
| | - A. Maia Chagas
- Sussex Neuroscience, School of Life Sciences, University of Sussex, United Kingdom
- TReND in Africa (www.TReNDinAfrica.org), United Kingdom
- GOSH Community (http://openhardware.science/)
- Institute for Ophthalmic Research, University of Tübingen, Germany
| | - P. Bartel
- Sussex Neuroscience, School of Life Sciences, University of Sussex, United Kingdom
| | - S. Pop
- The Francis Crick Institute, London, United Kingdom
| | - L.L. Prieto-Godino
- TReND in Africa (www.TReNDinAfrica.org), United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - T. Baden
- Sussex Neuroscience, School of Life Sciences, University of Sussex, United Kingdom
- TReND in Africa (www.TReNDinAfrica.org), United Kingdom
- Institute for Ophthalmic Research, University of Tübingen, Germany
| |
Collapse
|
10
|
Cantu DA, Wang B, Gongwer MW, He CX, Goel A, Suresh A, Kourdougli N, Arroyo ED, Zeiger W, Portera-Cailliau C. EZcalcium: Open-Source Toolbox for Analysis of Calcium Imaging Data. Front Neural Circuits 2020; 14:25. [PMID: 32499682 PMCID: PMC7244005 DOI: 10.3389/fncir.2020.00025] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/20/2020] [Indexed: 11/13/2022] Open
Abstract
Fluorescence calcium imaging using a range of microscopy approaches, such as two-photon excitation or head-mounted “miniscopes,” is one of the preferred methods to record neuronal activity and glial signals in various experimental settings, including acute brain slices, brain organoids, and behaving animals. Because changes in the fluorescence intensity of genetically encoded or chemical calcium indicators correlate with action potential firing in neurons, data analysis is based on inferring such spiking from changes in pixel intensity values across time within different regions of interest. However, the algorithms necessary to extract biologically relevant information from these fluorescent signals are complex and require significant expertise in programming to develop robust analysis pipelines. For decades, the only way to perform these analyses was for individual laboratories to write their custom code. These routines were typically not well annotated and lacked intuitive graphical user interfaces (GUIs), which made it difficult for scientists in other laboratories to adopt them. Although the panorama is changing with recent tools like CaImAn, Suite2P, and others, there is still a barrier for many laboratories to adopt these packages, especially for potential users without sophisticated programming skills. As two-photon microscopes are becoming increasingly affordable, the bottleneck is no longer the hardware, but the software used to analyze the calcium data optimally and consistently across different groups. We addressed this unmet need by incorporating recent software solutions, namely NoRMCorre and CaImAn, for motion correction, segmentation, signal extraction, and deconvolution of calcium imaging data into an open-source, easy to use, GUI-based, intuitive and automated data analysis software package, which we named EZcalcium.
Collapse
Affiliation(s)
- Daniel A Cantu
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States.,Neuroscience Interdepartmental Program, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Bo Wang
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Michael W Gongwer
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States.,UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Cynthia X He
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States.,UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Anubhuti Goel
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Anand Suresh
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Nazim Kourdougli
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Erica D Arroyo
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States.,Neuroscience Interdepartmental Program, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - William Zeiger
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Carlos Portera-Cailliau
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States.,Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| |
Collapse
|
11
|
Delaney SL, Gendreau JL, D'Souza M, Feng AY, Ho AL. Optogenetic Modulation for the Treatment of Traumatic Brain Injury. Stem Cells Dev 2020; 29:187-197. [DOI: 10.1089/scd.2019.0187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
| | | | | | - Austin Y. Feng
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, Georgia
| | - Allen L. Ho
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, Georgia
| |
Collapse
|
12
|
Advances in adaptive optics-based two-photon fluorescence microscopy for brain imaging. Lasers Med Sci 2019; 35:317-328. [PMID: 31729608 DOI: 10.1007/s10103-019-02908-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/18/2019] [Indexed: 12/20/2022]
Abstract
Deep tissue imaging using two-photon fluorescence (TPF) techniques have revolutionized the optical imaging community by providing in depth molecular information at the single-cell level. These techniques provide structural and functional aspects of mammalian brain at unprecedented depth and resolution. However, wavefront distortions introduced by the optical system as well as the biological sample (tissue) limit the achievable fluorescence signal-to-noise ratio and resolution with penetration depth. In this review, we discuss on the advances in TPF microscopy techniques for in vivo functional imaging and offer guidelines as to which technologies are best suited for different imaging applications with special reference to adaptive optics.
Collapse
|
13
|
Ranawat H, Pal S, Mazumder N. Recent trends in two-photon auto-fluorescence lifetime imaging (2P-FLIM) and its biomedical applications. Biomed Eng Lett 2019; 9:293-310. [PMID: 31456890 PMCID: PMC6694381 DOI: 10.1007/s13534-019-00119-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/30/2019] [Accepted: 06/27/2019] [Indexed: 02/07/2023] Open
Abstract
Two photon fluorescence microscopy and the numerous technical advances to it have served as valuable tools in biomedical research. The fluorophores (exogenous or endogenous) absorb light and emit lower energy photons than the absorption energy and the emission (fluorescence) signal is measured using a fluorescence decay graph. Additionally, high spatial resolution images can be acquired in two photon fluorescence lifetime imaging (2P-FLIM) with improved penetration depth which helps in detection of fluorescence signal in vivo. 2P-FLIM is a non-invasive imaging technique in order to visualize cellular metabolic, by tracking intrinsic fluorophores present in it, such as nicotinamide adenine dinucleotide, flavin adenine dinucleotide and tryptophan etc. 2P-FLIM of these molecules enable the visualization of metabolic alterations, non-invasively. This comprehensive review discusses the numerous applications of 2P-FLIM towards cancer, neuro-degenerative, infectious diseases, and wound healing.
Collapse
Affiliation(s)
- Harsh Ranawat
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Sagnik Pal
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Nirmal Mazumder
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| |
Collapse
|
14
|
Ricard C, Arroyo ED, He CX, Portera-Cailliau C, Lepousez G, Canepari M, Fiole D. Two-photon probes for in vivo multicolor microscopy of the structure and signals of brain cells. Brain Struct Funct 2018; 223:3011-3043. [PMID: 29748872 PMCID: PMC6119111 DOI: 10.1007/s00429-018-1678-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/03/2018] [Indexed: 02/07/2023]
Abstract
Imaging the brain of living laboratory animals at a microscopic scale can be achieved by two-photon microscopy thanks to the high penetrability and low phototoxicity of the excitation wavelengths used. However, knowledge of the two-photon spectral properties of the myriad fluorescent probes is generally scarce and, for many, non-existent. In addition, the use of different measurement units in published reports further hinders the design of a comprehensive imaging experiment. In this review, we compile and homogenize the two-photon spectral properties of 280 fluorescent probes. We provide practical data, including the wavelengths for optimal two-photon excitation, the peak values of two-photon action cross section or molecular brightness, and the emission ranges. Beyond the spectroscopic description of these fluorophores, we discuss their binding to biological targets. This specificity allows in vivo imaging of cells, their processes, and even organelles and other subcellular structures in the brain. In addition to probes that monitor endogenous cell metabolism, studies of healthy and diseased brain benefit from the specific binding of certain probes to pathology-specific features, ranging from amyloid-β plaques to the autofluorescence of certain antibiotics. A special focus is placed on functional in vivo imaging using two-photon probes that sense specific ions or membrane potential, and that may be combined with optogenetic actuators. Being closely linked to their use, we examine the different routes of intravital delivery of these fluorescent probes according to the target. Finally, we discuss different approaches, strategies, and prerequisites for two-photon multicolor experiments in the brains of living laboratory animals.
Collapse
Affiliation(s)
- Clément Ricard
- Brain Physiology Laboratory, CNRS UMR 8118, 75006, Paris, France
- Faculté de Sciences Fondamentales et Biomédicales, Université Paris Descartes, PRES Sorbonne Paris Cité, 75006, Paris, France
- Fédération de Recherche en Neurosciences FR 3636, Paris, 75006, France
| | - Erica D Arroyo
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Cynthia X He
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Carlos Portera-Cailliau
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Gabriel Lepousez
- Unité Perception et Mémoire, Département de Neuroscience, Institut Pasteur, 25 rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Marco Canepari
- Laboratory for Interdisciplinary Physics, UMR 5588 CNRS and Université Grenoble Alpes, 38402, Saint Martin d'Hères, France
- Laboratories of Excellence, Ion Channel Science and Therapeutics, Grenoble, France
- Institut National de la Santé et Recherche Médicale (INSERM), Grenoble, France
| | - Daniel Fiole
- Unité Biothérapies anti-Infectieuses et Immunité, Département des Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, BP 73, 91223, Brétigny-sur-Orge cedex, France.
- Human Histopathology and Animal Models, Infection and Epidemiology Department, Institut Pasteur, 28 rue du docteur Roux, 75725, Paris Cedex 15, France.
- ESRF-The European Synchrotron, 38043, Grenoble cedex, France.
| |
Collapse
|
15
|
Combs CA, Shroff H. Fluorescence Microscopy: A Concise Guide to Current Imaging Methods. ACTA ACUST UNITED AC 2018; 79:2.1.1-2.1.25. [DOI: 10.1002/cpns.29] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Christian A. Combs
- NHLBI Light Microscopy Facility, National Institutes of Health Bethesda Maryland
| | - Hari Shroff
- NIBIB Section on High Resolution Optical Imaging, National Institutes of Health Bethesda Maryland
| |
Collapse
|
16
|
Spangler SM, Bruchas MR. Optogenetic approaches for dissecting neuromodulation and GPCR signaling in neural circuits. Curr Opin Pharmacol 2017; 32:56-70. [PMID: 27875804 PMCID: PMC5395328 DOI: 10.1016/j.coph.2016.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/29/2016] [Accepted: 11/02/2016] [Indexed: 12/19/2022]
Abstract
Optogenetics has revolutionized neuroscience by providing means to control cell signaling with spatiotemporal control in discrete cell types. In this review, we summarize four major classes of optical tools to manipulate neuromodulatory GPCR signaling: opsins (including engineered chimeric receptors); photoactivatable proteins; photopharmacology through caging-photoswitchable molecules; fluorescent protein based reporters and biosensors. Additionally, we highlight technologies to utilize these tools in vitro and in vivo, including Cre dependent viral vector expression and two-photon microscopy. These emerging techniques targeting specific members of the GPCR signaling pathway offer an expansive base for investigating GPCR signaling in behavior and disease states, in addition to paving a path to potential therapeutic developments.
Collapse
Affiliation(s)
- Skylar M Spangler
- Department of Anesthesiology, Basic Research Division, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael R Bruchas
- Department of Anesthesiology, Basic Research Division, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
17
|
Kyrychenko A. Using fluorescence for studies of biological membranes: a review. Methods Appl Fluoresc 2015; 3:042003. [DOI: 10.1088/2050-6120/3/4/042003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|