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Xue T, Stalmashonak A, Chen FD, Ding P, Luo X, Chua H, Lo GQ, Sacher WD, Poon JKS. Implantable photonic neural probes with out-of-plane focusing grating emitters. Sci Rep 2024; 14:13812. [PMID: 38877050 PMCID: PMC11178810 DOI: 10.1038/s41598-024-64037-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
We have designed, fabricated, and characterized implantable silicon neural probes with nanophotonic grating emitters that focus the emitted light at a specified distance above the surface of the probe for spatially precise optogenetic targeting of neurons. Using the holographic principle, we designed gratings for wavelengths of 488 and 594 nm, targeting the excitation spectra of the optogenetic actuators Channelrhodopsin-2 and Chrimson, respectively. The measured optical emission pattern of these emitters in non-scattering medium and tissue matched well with simulations. To our knowledge, this is the first report of focused spots with the size scale of a neuron soma in brain tissue formed from implantable neural probes.
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Affiliation(s)
- Tianyuan Xue
- Department of Nanophotonics, Integration, and Neural Technology, Max Planck Institute of Microstructure Physics, Weinberg 2, Halle, 06120, Germany.
- The Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, M5S 3G4, ON, Canada.
| | - Andrei Stalmashonak
- Department of Nanophotonics, Integration, and Neural Technology, Max Planck Institute of Microstructure Physics, Weinberg 2, Halle, 06120, Germany
| | - Fu-Der Chen
- Department of Nanophotonics, Integration, and Neural Technology, Max Planck Institute of Microstructure Physics, Weinberg 2, Halle, 06120, Germany
- The Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, M5S 3G4, ON, Canada
| | - Peisheng Ding
- Department of Nanophotonics, Integration, and Neural Technology, Max Planck Institute of Microstructure Physics, Weinberg 2, Halle, 06120, Germany
- The Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, M5S 3G4, ON, Canada
| | - Xianshu Luo
- Advanced Micro Foundry Pte. Ltd., 11 Science Park Road, Singapore, 117685, Singapore
| | - Hongyao Chua
- Advanced Micro Foundry Pte. Ltd., 11 Science Park Road, Singapore, 117685, Singapore
| | - Guo-Qiang Lo
- Advanced Micro Foundry Pte. Ltd., 11 Science Park Road, Singapore, 117685, Singapore
| | - Wesley D Sacher
- Department of Nanophotonics, Integration, and Neural Technology, Max Planck Institute of Microstructure Physics, Weinberg 2, Halle, 06120, Germany
| | - Joyce K S Poon
- Department of Nanophotonics, Integration, and Neural Technology, Max Planck Institute of Microstructure Physics, Weinberg 2, Halle, 06120, Germany.
- The Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, M5S 3G4, ON, Canada.
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2
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Vu MAT, Brown EH, Wen MJ, Noggle CA, Zhang Z, Monk KJ, Bouabid S, Mroz L, Graham BM, Zhuo Y, Li Y, Otchy TM, Tian L, Davison IG, Boas DA, Howe MW. Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior. Neuron 2024; 112:909-923.e9. [PMID: 38242115 PMCID: PMC10957316 DOI: 10.1016/j.neuron.2023.12.011] [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: 07/21/2023] [Revised: 11/11/2023] [Accepted: 12/15/2023] [Indexed: 01/21/2024]
Abstract
Neural population dynamics relevant to behavior vary over multiple spatial and temporal scales across three-dimensional volumes. Current optical approaches lack the spatial coverage and resolution necessary to measure and manipulate naturally occurring patterns of large-scale, distributed dynamics within and across deep brain regions such as the striatum. We designed a new micro-fiber array approach capable of chronically measuring and optogenetically manipulating local dynamics across over 100 targeted locations simultaneously in head-fixed and freely moving mice, enabling the investigation of cell-type- and neurotransmitter-specific signals over arbitrary 3D volumes at a spatial resolution and coverage previously inaccessible. We applied this method to resolve rapid dopamine release dynamics across the striatum, revealing distinct, modality-specific spatiotemporal patterns in response to salient sensory stimuli extending over millimeters of tissue. Targeted optogenetics enabled flexible control of neural signaling on multiple spatial scales, better matching endogenous signaling patterns, and the spatial localization of behavioral function across large circuits.
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Affiliation(s)
- Mai-Anh T Vu
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Eleanor H Brown
- Graduate Program for Neuroscience, Boston University, Boston, MA, USA
| | - Michelle J Wen
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA; Howard Hughes Medical Institute, Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Christian A Noggle
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Zicheng Zhang
- Department of Biology, Boston University, Boston, MA, USA
| | - Kevin J Monk
- Department of Biology, Boston University, Boston, MA, USA
| | - Safa Bouabid
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Lydia Mroz
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA; Northeastern University, Boston, MA, USA
| | - Benjamin M Graham
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA
| | - Yizhou Zhuo
- 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, Beijing, China
| | - Yulong Li
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA; 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, Beijing, China
| | | | - Lin Tian
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA; Max Planck Florida Institute of Neuroscience, Jupiter, FL, USA
| | - Ian G Davison
- Department of Biology, Boston University, Boston, MA, USA
| | - David A Boas
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Mark W Howe
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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Albor-Ramírez E, Reyes-Alberto M, Vidal-Flores LM, Gutierrez-Herrera E, Padilla-Castañeda MA. Agarose Gel Characterization for the Fabrication of Brain Tissue Phantoms for Infrared Multispectral Vision Systems. Gels 2023; 9:944. [PMID: 38131930 PMCID: PMC10742522 DOI: 10.3390/gels9120944] [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: 10/28/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
Synthetic phantoms that recreate the characteristics of biological tissues are valuable tools for systematically studying and comprehending physiologies, pathologies, and biological processes related to tissues. The reproduction of mechanical and optical properties allows for the development and evaluation of novel systems and applications in areas such as imaging, optics, ultrasound, or dosimetry, among others. This paper proposes a methodology for manufacturing agarose-based phantoms that mimics the optical properties of healthy brain tissue within the wavelength infrared range of 800 to 820 nm. The fabrication of such phantoms enables the possibility of testing and experimentation in controlled and safe environments toward the design of new near-infrared multispectral imaging systems in neurosurgery. The results of an experimental optical characterization study indicate the validity and reliability of the proposed method for fabricating brain tissue phantoms in a cost-effective and straightforward fashion.
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Affiliation(s)
| | - Miguel Reyes-Alberto
- Applied Sciences and Technology Institute ICAT, National Autonomous University of Mexico UNAM, Ciudad Universitaria, Mexico City 04510, Mexico; (E.A.-R.); (L.M.V.-F.); (E.G.-H.)
| | | | | | - Miguel A. Padilla-Castañeda
- Applied Sciences and Technology Institute ICAT, National Autonomous University of Mexico UNAM, Ciudad Universitaria, Mexico City 04510, Mexico; (E.A.-R.); (L.M.V.-F.); (E.G.-H.)
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4
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Vu MAT, Brown EH, Wen MJ, Noggle CA, Zhang Z, Monk KJ, Bouabid S, Mroz L, Graham BM, Zhuo Y, Li Y, Otchy TM, Tian L, Davison IG, Boas DA, Howe MW. Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.17.567425. [PMID: 38014018 PMCID: PMC10680831 DOI: 10.1101/2023.11.17.567425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Neural population dynamics relevant for behavior vary over multiple spatial and temporal scales across 3-dimensional volumes. Current optical approaches lack the spatial coverage and resolution necessary to measure and manipulate naturally occurring patterns of large-scale, distributed dynamics within and across deep brain regions such as the striatum. We designed a new micro-fiber array and imaging approach capable of chronically measuring and optogenetically manipulating local dynamics across over 100 targeted locations simultaneously in head-fixed and freely moving mice. We developed a semi-automated micro-CT based strategy to precisely localize positions of each optical fiber. This highly-customizable approach enables investigation of multi-scale spatial and temporal patterns of cell-type and neurotransmitter specific signals over arbitrary 3-D volumes at a spatial resolution and coverage previously inaccessible. We applied this method to resolve rapid dopamine release dynamics across the striatum volume which revealed distinct, modality specific spatiotemporal patterns in response to salient sensory stimuli extending over millimeters of tissue. Targeted optogenetics through our fiber arrays enabled flexible control of neural signaling on multiple spatial scales, better matching endogenous signaling patterns, and spatial localization of behavioral function across large circuits.
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Affiliation(s)
- Mai-Anh T. Vu
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Eleanor H. Brown
- Graduate Program for Neuroscience, Boston University, Boston, MA, USA
| | - Michelle J. Wen
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Christian A. Noggle
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Zicheng Zhang
- Department of Biology, Boston University, Boston, MA, USA
| | - Kevin J. Monk
- Department of Biology, Boston University, Boston, MA, USA
| | - Safa Bouabid
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA
| | - Lydia Mroz
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA
- Northeastern University, Boston, MA, USA
| | - Benjamin M. Graham
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA
| | - Yizhou Zhuo
- 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, 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, Beijing, China
| | | | - Lin Tian
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA
| | - Ian G. Davison
- Department of Biology, Boston University, Boston, MA, USA
| | - David A. Boas
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Mark W. Howe
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA
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5
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Kim SJ, Affan RO, Frostig H, Scott BB, Alexander AS. Advances in cellular resolution microscopy for brain imaging in rats. NEUROPHOTONICS 2023; 10:044304. [PMID: 38076724 PMCID: PMC10704261 DOI: 10.1117/1.nph.10.4.044304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/23/2023] [Accepted: 11/07/2023] [Indexed: 02/12/2024]
Abstract
Rats are used in neuroscience research because of their physiological similarities with humans and accessibility as model organisms, trainability, and behavioral repertoire. In particular, rats perform a wide range of sophisticated social, cognitive, motor, and learning behaviors within the contexts of both naturalistic and laboratory environments. Further progress in neuroscience can be facilitated by using advanced imaging methods to measure the complex neural and physiological processes during behavior in rats. However, compared with the mouse, the rat nervous system offers a set of challenges, such as larger brain size, decreased neuron density, and difficulty with head restraint. Here, we review recent advances in in vivo imaging techniques in rats with a special focus on open-source solutions for calcium imaging. Finally, we provide suggestions for both users and developers of in vivo imaging systems for rats.
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Affiliation(s)
- Su Jin Kim
- Johns Hopkins University, Department of Psychological and Brain Sciences, Baltimore, Maryland, United States
| | - Rifqi O. Affan
- Boston University, Center for Systems Neuroscience, Department of Psychological and Brain Sciences, Boston, Massachusetts, United States
- Boston University, Graduate Program in Neuroscience, Boston, Massachusetts, United States
| | - Hadas Frostig
- Boston University, Center for Systems Neuroscience, Department of Psychological and Brain Sciences, Boston, Massachusetts, United States
| | - Benjamin B. Scott
- Boston University, Center for Systems Neuroscience, Department of Psychological and Brain Sciences, Boston, Massachusetts, United States
- Boston University, Neurophotonics Center and Photonics Center, Boston, Massachusetts, United States
| | - Andrew S. Alexander
- University of California Santa Barbara, Department of Psychological and Brain Sciences, Santa Barbara, California, United States
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6
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Chen H, Liu K, Jiang Y, Liu Y, Deng Y. Real-time and accurate estimation ex vivo of four basic optical properties from thin tissue based on a cascade forward neural network. BIOMEDICAL OPTICS EXPRESS 2023; 14:1818-1832. [PMID: 37078046 PMCID: PMC10110315 DOI: 10.1364/boe.489079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Double integrating sphere measurements obtained from thin ex vivo tissues provides more spectral information and hence allows full estimation of all basic optical properties (OPs) theoretically. However, the ill-conditioned nature of the OP determination increases excessively with the reduction in tissue thickness. Therefore, it is crucial to develop a model for thin ex vivo tissues that is robust to noise. Herein, we present a deep learning solution to precisely extract four basic OPs in real-time from thin ex vivo tissues, leveraging a dedicated cascade forward neural network (CFNN) for each OP with an additional introduced input of the refractive index of the cuvette holder. The results show that the CFNN-based model enables accurate and fast evaluation of OPs, as well as robustness to noise. Our proposed method overcomes the highly ill-conditioned restriction of OP evaluation and can distinguish the effects of slight changes in measurable quantities without any a priori knowledge.
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Affiliation(s)
- Haitao Chen
- School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Kaixian Liu
- 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, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yuxuan Jiang
- 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, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yafeng Liu
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yong Deng
- 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, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
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7
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Abdellah M, Cantero JJG, Guerrero NR, Foni A, Coggan JS, Calì C, Agus M, Zisis E, Keller D, Hadwiger M, Magistretti PJ, Markram H, Schürmann F. Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience. Brief Bioinform 2022; 24:6847753. [PMID: 36434788 PMCID: PMC9851302 DOI: 10.1093/bib/bbac491] [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: 08/02/2022] [Revised: 09/27/2022] [Accepted: 10/14/2022] [Indexed: 11/27/2022] Open
Abstract
Ultraliser is a neuroscience-specific software framework capable of creating accurate and biologically realistic 3D models of complex neuroscientific structures at intracellular (e.g. mitochondria and endoplasmic reticula), cellular (e.g. neurons and glia) and even multicellular scales of resolution (e.g. cerebral vasculature and minicolumns). Resulting models are exported as triangulated surface meshes and annotated volumes for multiple applications in in silico neuroscience, allowing scalable supercomputer simulations that can unravel intricate cellular structure-function relationships. Ultraliser implements a high-performance and unconditionally robust voxelization engine adapted to create optimized watertight surface meshes and annotated voxel grids from arbitrary non-watertight triangular soups, digitized morphological skeletons or binary volumetric masks. The framework represents a major leap forward in simulation-based neuroscience, making it possible to employ high-resolution 3D structural models for quantification of surface areas and volumes, which are of the utmost importance for cellular and system simulations. The power of Ultraliser is demonstrated with several use cases in which hundreds of models are created for potential application in diverse types of simulations. Ultraliser is publicly released under the GNU GPL3 license on GitHub (BlueBrain/Ultraliser). SIGNIFICANCE There is crystal clear evidence on the impact of cell shape on its signaling mechanisms. Structural models can therefore be insightful to realize the function; the more realistic the structure can be, the further we get insights into the function. Creating realistic structural models from existing ones is challenging, particularly when needed for detailed subcellular simulations. We present Ultraliser, a neuroscience-dedicated framework capable of building these structural models with realistic and detailed cellular geometries that can be used for simulations.
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Affiliation(s)
- Marwan Abdellah
- Corresponding authors. Marwan Abdellah, Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland. E-mail: ; Felix Schürmann, Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland. E-mail:
| | | | - Nadir Román Guerrero
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Alessandro Foni
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Jay S Coggan
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Corrado Calì
- Biological and Environmental Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal, Saudi Arabia,Neuroscience Institute Cavalieri Ottolenghi (NICO) Orbassano, Italy,Department of Neuroscience, University of Torino Torino, Italy
| | - Marco Agus
- Visual Computing Center King Abdullah University of Science and Technology (KAUST) Thuwal, Saudi Arabia,College of Science and Engineering Hamad Bin Khalifa University Doha, Qatar
| | - Eleftherios Zisis
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Daniel Keller
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Markus Hadwiger
- Visual Computing Center King Abdullah University of Science and Technology (KAUST) Thuwal, Saudi Arabia
| | - Pierre J Magistretti
- Biological and Environmental Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal, Saudi Arabia
| | - Henry Markram
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Felix Schürmann
- Corresponding authors. Marwan Abdellah, Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland. E-mail: ; Felix Schürmann, Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland. E-mail:
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8
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Ji X, Liu W, Xiao H, Xiao Z. The activated synaptic terminals beyond the light illumination range affect the results of optogenetics. Neuroreport 2022; 33:281-290. [PMID: 35594445 DOI: 10.1097/wnr.0000000000001785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Optogenetics is widely applied to study complex brain networks. However, recent studies have found that light alone can produce effects that are unrelated to optogenetics, and it is still unclear whether this can affect the results of optogenetic experiments. METHODS We explored the characteristics of projection of interneurons to excitatory neurons in the auditory cortex with optogenetics, transgenic mice and patch-clamp recording. RESULTS We discovered that postsynaptic responses can be induced when we stimulated a blank area adjacent to the edge of brain slice. Similar results can be observed after blocking the polysynaptic responses by drugs. Together with the results of control experiments, we found that the false response is caused by activating the synaptic terminals beyond the range of the blue light (470 nm). Also, there was a linear relationship between the response and the stimulus distance for all data, which suggested that these false responses may be related to other factors, such as light scattering. CONCLUSIONS The LED-light-evoked response cannot reflect microcircuit of the recorded neuron and the activated neurons within the illumination range accurately. Together, these results confirm that light alone can affect neural activity, but this can be unrelated to the genuine 'optogenetic effect'.
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Affiliation(s)
- Xuying Ji
- Department of Physiology, School of Basic Medical Sciences, Key Laboratory of Psychiatric Disorders of Guangdong Province, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Key Laboratory of Mental Health of the Ministry of Education, Southern Medical University, Guangzhou
| | - Wenhui Liu
- The General Family Medicine Center, The Seventh Affiliated Hospital, Southern Medical University, Foshan, China
| | - Haoran Xiao
- Department of Physiology, School of Basic Medical Sciences, Key Laboratory of Psychiatric Disorders of Guangdong Province, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Key Laboratory of Mental Health of the Ministry of Education, Southern Medical University, Guangzhou
- The General Family Medicine Center, The Seventh Affiliated Hospital, Southern Medical University, Foshan, China
| | - Zhongju Xiao
- Department of Physiology, School of Basic Medical Sciences, Key Laboratory of Psychiatric Disorders of Guangdong Province, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Key Laboratory of Mental Health of the Ministry of Education, Southern Medical University, Guangzhou
- The General Family Medicine Center, The Seventh Affiliated Hospital, Southern Medical University, Foshan, China
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9
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Hamdy O, Mohammed HS. Variations in tissue optical parameters with the incident power of an infrared laser. PLoS One 2022; 17:e0263164. [PMID: 35100314 PMCID: PMC8803203 DOI: 10.1371/journal.pone.0263164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/12/2022] [Indexed: 11/18/2022] Open
Abstract
Infrared (IR) lasers are extensively utilized as an effective tool in many medical practices. Nevertheless, light penetration into the inspected tissue, which is highly affected by tissue optical properties, is a crucial factor for successful optical procedures. Although the optical properties are highly wavelength-dependent, they can be affected by the power of the incident laser. The present study demonstrates a considerable change in the scattering and absorption coefficients as a result of varying the incident laser power probing into biological samples at a constant laser wavelength (808 nm). The optical parameters were investigated using an integrating sphere and Kubelka-Munk model. Additionally, fluence distribution at the sample's surface was modeled using COMSOL-multiphysics software. The experimental results were validated using Receiver Operating Characteristic (ROC) curves and Monte-Carlo simulation. The results showed that tissue scattering coefficient decreases as the incident laser power increases while the absorption coefficient experienced a slight change. Moreover, the penetration depth increases with the optical parameters. The reduction in the scattering coefficients leads to wider and more diffusive fluence rate distribution at the tissue surface. The simulation results showed a good agreement with the experimental data and revealed that tissue anisotropy may be responsible for this scattering reduction. The present findings could be considered in order for the specialists to accurately specify the laser optical dose in various biomedical applications.
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Affiliation(s)
- Omnia Hamdy
- Engineering Applications of Lasers Department, National Institute of Laser Enhanced Sciences, Cairo University, Giza, Egypt
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10
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Lehtinen K, Nokia MS, Takala H. Red Light Optogenetics in Neuroscience. Front Cell Neurosci 2022; 15:778900. [PMID: 35046775 PMCID: PMC8761848 DOI: 10.3389/fncel.2021.778900] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/02/2021] [Indexed: 12/25/2022] Open
Abstract
Optogenetics, a field concentrating on controlling cellular functions by means of light-activated proteins, has shown tremendous potential in neuroscience. It possesses superior spatiotemporal resolution compared to the surgical, electrical, and pharmacological methods traditionally used in studying brain function. A multitude of optogenetic tools for neuroscience have been created that, for example, enable the control of action potential generation via light-activated ion channels. Other optogenetic proteins have been used in the brain, for example, to control long-term potentiation or to ablate specific subtypes of neurons. In in vivo applications, however, the majority of optogenetic tools are operated with blue, green, or yellow light, which all have limited penetration in biological tissues compared to red light and especially infrared light. This difference is significant, especially considering the size of the rodent brain, a major research model in neuroscience. Our review will focus on the utilization of red light-operated optogenetic tools in neuroscience. We first outline the advantages of red light for in vivo studies. Then we provide a brief overview of the red light-activated optogenetic proteins and systems with a focus on new developments in the field. Finally, we will highlight different tools and applications, which further facilitate the use of red light optogenetics in neuroscience.
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Affiliation(s)
- Kimmo Lehtinen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Miriam S. Nokia
- Department of Psychology, University of Jyväskylä, Jyväskylä, Finland
- Centre for Interdisciplinary Brain Research, University of Jyväskylä, Jyväskylä, Finland
| | - Heikki Takala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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11
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Mok AT, Shea J, Wu C, Xia F, Tatarsky R, Yapici N, Xu C. Spatially resolved measurements of ballistic and total transmission in microscale tissue samples from 450 nm to 1624 nm. BIOMEDICAL OPTICS EXPRESS 2022; 13:438-451. [PMID: 35154883 DOI: 10.6084/m9.figshare.16528890] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/05/2021] [Accepted: 12/06/2021] [Indexed: 05/25/2023]
Abstract
We built a simple and versatile setup to measure tissue ballistic and total transmission with customizable wavelength range, spatial resolution, and sample sizes. We performed ballistic transmission and total transmission measurements of overlying structures from biological samples ex vivo. We obtained spatially resolved transmission maps to reveal transmission heterogeneity from five microscale tissue samples: Danionella skin, mouse skull bone, mosquito cuticle, wasp cuticle, and rat dura over a wide spectral range from 450 nm to 1624 nm at a spatial resolution of ∼25 µm for ballistic transmission measurements and ∼50 µm for total transmission measurements. We expect our method can be straightforwardly applied to measuring the transmission of other samples. The measurement results will be valuable for multiphoton microscopy. The total transmission of a sample is important for the collection of multiphoton excited fluorescence and the assessment of laser-induced sample heating. The ballistic transmission determines the excitation power at the focus and hence the fluorescence signal generation. Therefore, knowledge of ballistic transmission, total transmission, and transmission heterogeneity of overlying structures of animals and organs are essential to determine the optimal excitation wavelength and fluorophores for non-invasive multiphoton microscopy.
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Affiliation(s)
- Aaron T Mok
- School of Applied and Engineering Physics, Cornell University, NY 14853-3501, USA
- Meining School of Biomedical Engineering, Cornell University, NY 14853-3501, USA
| | - Jamien Shea
- Department of Neurobiology and Behavior, Cornell University, NY 14853-3501, USA
| | - Chunyan Wu
- School of Applied and Engineering Physics, Cornell University, NY 14853-3501, USA
- College of Veterinary Medicine, Cornell University, NY 14853-3501, USA
| | - Fei Xia
- School of Applied and Engineering Physics, Cornell University, NY 14853-3501, USA
- Meining School of Biomedical Engineering, Cornell University, NY 14853-3501, USA
- Present address: Laboratoire Kastler Brossel, ENS-PSL Research University, CNRS, Sorbonne Université, Collège de France, Paris, France
| | - Rose Tatarsky
- Department of Neurobiology and Behavior, Cornell University, NY 14853-3501, USA
| | - Nilay Yapici
- Department of Neurobiology and Behavior, Cornell University, NY 14853-3501, USA
| | - Chris Xu
- School of Applied and Engineering Physics, Cornell University, NY 14853-3501, USA
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Mok AT, Shea J, Wu C, Xia F, Tatarsky R, Yapici N, Xu C. Spatially resolved measurements of ballistic and total transmission in microscale tissue samples from 450 nm to 1624 nm. BIOMEDICAL OPTICS EXPRESS 2022; 13:438-451. [PMID: 35154883 DOI: 10.6084/m9.figshare.16528887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/05/2021] [Accepted: 12/06/2021] [Indexed: 05/25/2023]
Abstract
We built a simple and versatile setup to measure tissue ballistic and total transmission with customizable wavelength range, spatial resolution, and sample sizes. We performed ballistic transmission and total transmission measurements of overlying structures from biological samples ex vivo. We obtained spatially resolved transmission maps to reveal transmission heterogeneity from five microscale tissue samples: Danionella skin, mouse skull bone, mosquito cuticle, wasp cuticle, and rat dura over a wide spectral range from 450 nm to 1624 nm at a spatial resolution of ∼25 µm for ballistic transmission measurements and ∼50 µm for total transmission measurements. We expect our method can be straightforwardly applied to measuring the transmission of other samples. The measurement results will be valuable for multiphoton microscopy. The total transmission of a sample is important for the collection of multiphoton excited fluorescence and the assessment of laser-induced sample heating. The ballistic transmission determines the excitation power at the focus and hence the fluorescence signal generation. Therefore, knowledge of ballistic transmission, total transmission, and transmission heterogeneity of overlying structures of animals and organs are essential to determine the optimal excitation wavelength and fluorophores for non-invasive multiphoton microscopy.
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Affiliation(s)
- Aaron T Mok
- School of Applied and Engineering Physics, Cornell University, NY 14853-3501, USA
- Meining School of Biomedical Engineering, Cornell University, NY 14853-3501, USA
| | - Jamien Shea
- Department of Neurobiology and Behavior, Cornell University, NY 14853-3501, USA
| | - Chunyan Wu
- School of Applied and Engineering Physics, Cornell University, NY 14853-3501, USA
- College of Veterinary Medicine, Cornell University, NY 14853-3501, USA
| | - Fei Xia
- School of Applied and Engineering Physics, Cornell University, NY 14853-3501, USA
- Meining School of Biomedical Engineering, Cornell University, NY 14853-3501, USA
- Present address: Laboratoire Kastler Brossel, ENS-PSL Research University, CNRS, Sorbonne Université, Collège de France, Paris, France
| | - Rose Tatarsky
- Department of Neurobiology and Behavior, Cornell University, NY 14853-3501, USA
| | - Nilay Yapici
- Department of Neurobiology and Behavior, Cornell University, NY 14853-3501, USA
| | - Chris Xu
- School of Applied and Engineering Physics, Cornell University, NY 14853-3501, USA
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Mok AT, Shea J, Wu C, Xia F, Tatarsky R, Yapici N, Xu C. Spatially resolved measurements of ballistic and total transmission in microscale tissue samples from 450 nm to 1624 nm. BIOMEDICAL OPTICS EXPRESS 2022; 13:438-451. [PMID: 35154883 PMCID: PMC8803029 DOI: 10.1364/boe.441844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/05/2021] [Accepted: 12/06/2021] [Indexed: 05/10/2023]
Abstract
We built a simple and versatile setup to measure tissue ballistic and total transmission with customizable wavelength range, spatial resolution, and sample sizes. We performed ballistic transmission and total transmission measurements of overlying structures from biological samples ex vivo. We obtained spatially resolved transmission maps to reveal transmission heterogeneity from five microscale tissue samples: Danionella skin, mouse skull bone, mosquito cuticle, wasp cuticle, and rat dura over a wide spectral range from 450 nm to 1624 nm at a spatial resolution of ∼25 µm for ballistic transmission measurements and ∼50 µm for total transmission measurements. We expect our method can be straightforwardly applied to measuring the transmission of other samples. The measurement results will be valuable for multiphoton microscopy. The total transmission of a sample is important for the collection of multiphoton excited fluorescence and the assessment of laser-induced sample heating. The ballistic transmission determines the excitation power at the focus and hence the fluorescence signal generation. Therefore, knowledge of ballistic transmission, total transmission, and transmission heterogeneity of overlying structures of animals and organs are essential to determine the optimal excitation wavelength and fluorophores for non-invasive multiphoton microscopy.
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Affiliation(s)
- Aaron T. Mok
- School of Applied and Engineering Physics, Cornell University, NY 14853-3501, USA
- Meining School of Biomedical Engineering, Cornell University, NY 14853-3501, USA
| | - Jamien Shea
- Department of Neurobiology and Behavior, Cornell University, NY 14853-3501, USA
| | - Chunyan Wu
- School of Applied and Engineering Physics, Cornell University, NY 14853-3501, USA
- College of Veterinary Medicine, Cornell University, NY 14853-3501, USA
| | - Fei Xia
- School of Applied and Engineering Physics, Cornell University, NY 14853-3501, USA
- Meining School of Biomedical Engineering, Cornell University, NY 14853-3501, USA
- Present address: Laboratoire Kastler Brossel, ENS-PSL Research University, CNRS, Sorbonne Université, Collège de France, Paris, France
| | - Rose Tatarsky
- Department of Neurobiology and Behavior, Cornell University, NY 14853-3501, USA
| | - Nilay Yapici
- Department of Neurobiology and Behavior, Cornell University, NY 14853-3501, USA
| | - Chris Xu
- School of Applied and Engineering Physics, Cornell University, NY 14853-3501, USA
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Kramer N, Tamir R, Ben‐Zvi O, Jacques SL, Loya Y, Wangpraseurt D. Efficient light‐harvesting of mesophotic corals is facilitated by coral optical traits. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Raz Tamir
- School of Zoology Tel‐Aviv University Tel Aviv Israel
- The Interuniversity Institute for Marine Sciences of Eilat Eilat Israel
| | - Or Ben‐Zvi
- School of Zoology Tel‐Aviv University Tel Aviv Israel
- The Interuniversity Institute for Marine Sciences of Eilat Eilat Israel
| | - Steven L. Jacques
- Department of Bioengineering University of Washington Seattle WA USA
| | - Yossi Loya
- School of Zoology Tel‐Aviv University Tel Aviv Israel
| | - Daniel Wangpraseurt
- Department of Nanoengineering University of California San Diego San Diego CA USA
- Department of Chemistry University of Cambridge Cambridge UK
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Optical investigation of bovine grey and white matters in visible and near-infrared ranges. POLISH JOURNAL OF MEDICAL PHYSICS AND ENGINEERING 2021. [DOI: 10.2478/pjmpe-2021-0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Introduction: Due to enormous interests for laser in medicine and biology, optical properties characterization of different tissue have be affecting in development processes. In addition, the optical properties of biological tissues could be influenced by storage methods. Thus, optical properties of bovine white and grey tissues preserved by formalin have been characterized over a wide wavelength spectrum varied between 440 nm and 1000 nm.
Materials and Methods: To that end, a single integrating sphere system was assembled for spectroscopic characterization and an inverse adding-doubling algorithm was used to retrieve optical coefficients, i.e. reduced scattering and absorption coefficients.
Results: White matter has shown a strong scattering property in comparison to grey matter. On the other hand, the grey matter has absorbed light extensively. In comparison, the reduced scattering profile for both tissue types turned out to be consistent with prior works that characterized optical coefficients in vivo. On the contrary, absorption coefficient behavior has a different feature.
Conclusion: Formalin could change the tissue’s optical properties because of the alteration of tissue’s structure and components. The absence of hemoglobin that seeps out due to the use of a formalin could reduce the absorption coefficient over the visible range. Both the water replacement by formalin could reduce the refractive index of a stored tissue and the absence of hemoglobin that scatters light over the presented wavelength range should diminish the reduced scattering coefficients over that wavelength range.
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Chin-Hao Chen R, Atry F, Richner T, Brodnick S, Pisaniello J, Ness J, Suminski AJ, Williams J, Pashaie R. A system identification analysis of optogenetically evoked electrocorticography and cerebral blood flow responses. J Neural Eng 2020; 17:056049. [PMID: 32299067 DOI: 10.1088/1741-2552/ab89fc] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE The main objective of this research was to study the coupling between neural circuits and the vascular network in the cortex of small rodents from system engineering point of view and generate a mathematical model for the dynamics of neurovascular coupling. The model was adopted to implement closed-loop blood flow control algorithms. APPROACH We used a combination of advanced technologies including optogenetics, electrocorticography, and optical coherence tomography to stimulate selected populations of neurons and simultaneously record induced electrocorticography and hemodynamic signals. We adopted system identification methods to analyze the acquired data and investigate the relation between optogenetic neural activation and consequential electrophysiology and blood flow responses. MAIN RESULTS We showed that the developed model, once trained by the acquired data, could successfully regenerate subtle spatio-temporal features of evoked electrocorticography and cerebral blood flow responses following an onset of optogenetic stimulation. SIGNIFICANCE The long term goal of this research is to open a new line for computational analysis of neurovascular coupling particularly in pathologies where the normal process of blood flow regulation in the central nervous system is disrupted including Alzheimer's disease.
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Affiliation(s)
- Rex Chin-Hao Chen
- Electrical Engineering, Computer Science Department, University of Wisconsin-Milwaukee, 3200N Cramer St., Milwaukee, WI, United States of America
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Tang Y, Yao J. 3D Monte Carlo simulation of light distribution in mouse brain in quantitative photoacoustic computed tomography. Quant Imaging Med Surg 2020; 11:1046-1059. [PMID: 33654676 DOI: 10.21037/qims-20-815] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background Photoacoustic computed tomography (PACT) detects light-induced ultrasound (US) waves to reconstruct the optical absorption contrast of the biological tissues. Due to its relatively deep penetration (several centimeters in soft tissue), high spatial resolution, and inherent functional sensitivity, PACT has great potential for imaging mouse brains with endogenous and exogenous contrasts, which is of immense interest to the neuroscience community. However, conventional PACT either assumes homogenous optical fluence within the brain or uses a simplified attenuation model for optical fluence estimation. Both approaches underestimate the complexity of the fluence heterogeneity and can result in poor quantitative imaging accuracy. Methods To optimize the quantitative performance of PACT, we explore for the first time 3D Monte Carlo (MC) simulation to study the optical fluence distribution in a complete mouse brain model. We apply the MCX MC simulation package on a digital mouse (Digimouse) brain atlas that has complete anatomy information. To evaluate the impact of the brain vasculature on light delivery, we also incorporate the whole-brain vasculature in the Digimouse atlas. k-wave toolbox was used to investigate the effect of inhomogeneous illumination on the reconstructed images and chromophore concentration estimation. Results The simulation results clearly show that the optical fluence in the mouse brain is heterogeneous at the global level and can decrease by a factor of five with increasing depth. Moreover, the strong absorption and scattering of the brain vasculature also induce the fluence disturbance at the local level. Conclusions Both global and local fluence heterogeneity contributes to the reduced quantitative accuracy of the reconstructed PACT images of mouse brain. Correcting the optical fluence distribution can improve the quantitative accuracy of PACT.
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Affiliation(s)
- Yuqi Tang
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Junjie Yao
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
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DePaoli D, Gasecka A, Bahdine M, Deschenes JM, Goetz L, Perez-Sanchez J, Bonin RP, De Koninck Y, Parent M, Côté DC. Anisotropic light scattering from myelinated axons in the spinal cord. NEUROPHOTONICS 2020; 7:015011. [PMID: 32206678 PMCID: PMC7063473 DOI: 10.1117/1.nph.7.1.015011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 01/14/2020] [Indexed: 06/10/2023]
Abstract
Optogenetics has become an integral tool for studying and dissecting the neural circuitries of the brain using optical control. Recently, it has also begun to be used in the investigation of the spinal cord and peripheral nervous system. However, information on these regions' optical properties is sparse. Moreover, there is a lack of data on the dependence of light propagation with respect to neural tissue organization and orientation. This information is important for effective simulations and optogenetic planning, particularly in the spinal cord where the myelinated axons are highly organized. To this end, we report experimental measurements for the scattering coefficient, validated with three different methods in both the longitudinal and radial directions of multiple mammalian spinal cords. In our analysis, we find that there is indeed a directional dependence of photon propagation when interacting with organized myelinated axons. Specifically, light propagating perpendicular to myelinated axons in the white matter of the spinal cord produced a measured reduced scattering coefficient ( μ s ' ) of 3.52 ± 0.1 mm - 1 , and light that was propagated along the myelinated axons in the white matter produced a measured μ s ' of 1.57 ± 0.03 mm - 1 , across the various species considered. This 50% decrease in scattering power along the myelinated axons is observed with three different measurement strategies (integrating spheres, observed transmittance, and punch-through method). Furthermore, this directional dependence in scattering power and overall light attenuation did not occur in the gray matter regions where the myelin organization is nearly random. The acquired information will be integral in preparing future light-transport simulations and in overall optogenetic planning in both the spinal cord and the brain.
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Affiliation(s)
- Damon DePaoli
- CERVO Brain Research Center, Québec City, Québec, Canada
- Center for Optics, Photonics and Lasers, Québec City, Québec, Canada
| | - Alicja Gasecka
- CERVO Brain Research Center, Québec City, Québec, Canada
- Center for Optics, Photonics and Lasers, Québec City, Québec, Canada
| | - Mohamed Bahdine
- CERVO Brain Research Center, Québec City, Québec, Canada
- Center for Optics, Photonics and Lasers, Québec City, Québec, Canada
| | - Jean M. Deschenes
- CERVO Brain Research Center, Québec City, Québec, Canada
- Center for Optics, Photonics and Lasers, Québec City, Québec, Canada
| | - Laurent Goetz
- CERVO Brain Research Center, Québec City, Québec, Canada
| | | | - Robert P. Bonin
- University of Toronto, Leslie Dan Faculty of Pharmacy, Toronto, Ontario, Canada
| | - Yves De Koninck
- CERVO Brain Research Center, Québec City, Québec, Canada
- Center for Optics, Photonics and Lasers, Québec City, Québec, Canada
| | - Martin Parent
- CERVO Brain Research Center, Québec City, Québec, Canada
| | - Daniel C. Côté
- CERVO Brain Research Center, Québec City, Québec, Canada
- Center for Optics, Photonics and Lasers, Québec City, Québec, Canada
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Sudakou A, Wojtkiewicz S, Lange F, Gerega A, Sawosz P, Tachtsidis I, Liebert A. Depth-resolved assessment of changes in concentration of chromophores using time-resolved near-infrared spectroscopy: estimation of cytochrome-c-oxidase uncertainty by Monte Carlo simulations. BIOMEDICAL OPTICS EXPRESS 2019; 10:4621-4635. [PMID: 31565513 PMCID: PMC6757481 DOI: 10.1364/boe.10.004621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
Time-resolved near-infrared spectroscopy (TR-NIRS) measurements can be used to recover changes in concentrations of tissue constituents ( Δ C ) by applying the moments method and the Beer-Lambert law. In this work we carried out the error propagation analysis allowing to calculate the standard deviations of uncertainty in estimation of the Δ C . Here, we show the process of choosing wavelengths for the evaluation of hemodynamic (oxy-, deoxyhemoglobin) and metabolic (cytochrome-c-oxidase (CCO)) responses within the brain tissue as measured with an in-house developed TR-NIRS multi-wavelength system, which measures at 16 consecutive wavelengths separated by 12.5 nm and placed between 650 and 950 nm. Data generated with Monte Carlo simulations on three-layered model (scalp, skull, brain) for wavelengths range from 650 to 950 nm were used to carry out the error propagation analysis for varying choices of wavelengths. For a detector with a spectrally uniform responsivity, the minimal standard deviation of the estimated changes in CCO within the brain layer, σ Δ C CCO brain = 0.40 µM, was observed for the 16 consecutive wavelengths from 725 to 912.5 nm. For realistic a detector model, i.e. the spectral responsivity characteristic is considered, the minimum, σ Δ C CCO brain = 0.47 µM, was observed at the 16 consecutive wavelengths from 688 to 875 nm. We introduce the method of applying the error propagation analysis to data as measured with spectral TR-NIRS systems to calculate uncertainty of recovery of tissue constituents concentrations.
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Affiliation(s)
- Aleh Sudakou
- Nalecz Institute of Biocybernetics and Biomedical Engineering Polish Academy of Sciences, Trojdena 4, 02-109 Warsaw, Poland
| | - Stanislaw Wojtkiewicz
- Nalecz Institute of Biocybernetics and Biomedical Engineering Polish Academy of Sciences, Trojdena 4, 02-109 Warsaw, Poland
- School of Computer Science, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Frédéric Lange
- Department of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, United Kingdom
| | - Anna Gerega
- Nalecz Institute of Biocybernetics and Biomedical Engineering Polish Academy of Sciences, Trojdena 4, 02-109 Warsaw, Poland
| | - Piotr Sawosz
- Nalecz Institute of Biocybernetics and Biomedical Engineering Polish Academy of Sciences, Trojdena 4, 02-109 Warsaw, Poland
| | - Ilias Tachtsidis
- Department of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, United Kingdom
| | - Adam Liebert
- Nalecz Institute of Biocybernetics and Biomedical Engineering Polish Academy of Sciences, Trojdena 4, 02-109 Warsaw, Poland
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20
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Xu Y, Long S, Yang Y, Zhou F, Dong N, Yan K, Wang B, Zeng Y, Du N, Li X, Chen WR. Mathematical simulation of temperature distribution in tumor tissue and surrounding healthy tissue treated by laser combined with indocyanine green. Theor Biol Med Model 2019; 16:12. [PMID: 31422770 PMCID: PMC6699130 DOI: 10.1186/s12976-019-0107-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 06/10/2019] [Indexed: 01/07/2023] Open
Abstract
Background Photothermal therapy is a local treatment method for cancer and the heat energy generated from it could destroy the tumor cells. This study is aimed to investigate the temperature distribution in tumor tissue and surrounding health tissue of tumor bearing mice applying mathematical simulation model. Tumor bearing mice treated by laser combined with or without indocyanine green. Monte Carlo method and the Pennes bio-heat equation were used to calculate the light distribution and heat energy. COMSOL Multiphysic was adopted to construct three dimensional temperature distribution model. Results This study revealed that the data calculated by simulation model is in good agreement with the surface temperature monitored by infrared thermometer. Effected by the optical parameters and boundary conditions of tissue, the highest temperature of tissue treated by laser combined with indocyanine green was about 65 °C which located in tumor tissue and the highest temperature of tissue treated by laser was about 43 °C which located under the tumor tissue. The temperature difference was about 20 °C. Temperature distribution in tissue was not uniform. The temperature difference in different parts of tumor tissue raised up to 15 °C. The temperature of tumor tissue treated by laser combined with indocyanine green was about 20 °C higher than that of the surrounding healthy tissue. Conclusions Reasonably good matching between the calculated temperature and the measured temperature was achieved, thus demonstrated great utility of our modeling method and approaches for deepening understand in the temperature distribution in tumor tissue and surrounding healthy tissue during the laser combined with photosensitizer. The simulation model could provide guidance and reference function for the effect of photothermal therapy. Electronic supplementary material The online version of this article (10.1186/s12976-019-0107-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuanyuan Xu
- Jinzhou Medical University, Jinzhou, 121000, China.,Department of Oncology, Graduate Training Base- Fourth Medical Center of Chinese PLA General Hospital of Jinzhou Medical University, Beijing, 100048, China
| | - Shan Long
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Yunning Yang
- Jinzhou Medical University, Jinzhou, 121000, China.,Department of Oncology, Graduate Training Base- Fourth Medical Center of Chinese PLA General Hospital of Jinzhou Medical University, Beijing, 100048, China
| | - Feifan Zhou
- Shenzhen University, Shenzhen, 518000, China
| | - Ning Dong
- Burns Institute, Fourth Medical Center of Chinese PLA General Hospital, Beijing, 100048, China
| | - Kesong Yan
- Department of laboratory animal, Fourth Medical Center of Chinese PLA General Hospital, Beijing, 100048, China
| | - Bo Wang
- Department of Oncology, Fourth Medical Center of Chinese PLA General Hospital, Beijing, 100048, China
| | - Yachao Zeng
- Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116000, Liaoning, China
| | - Nan Du
- Department of Oncology, Fourth Medical Center of Chinese PLA General Hospital, Beijing, 100048, China
| | - Xiaosong Li
- Department of Oncology, Fourth Medical Center of Chinese PLA General Hospital, Beijing, 100048, China.
| | - Wei R Chen
- Biophotonics Research Laboratory, Center for Interdisciplinary Biomedical Education and Research, College of Mathematics and Science, University of Central Oklahoma, Edmond, 73034, USA
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Advances in the simulation of light-tissue interactions in biomedical engineering. Biomed Eng Lett 2019; 9:327-337. [PMID: 31456892 DOI: 10.1007/s13534-019-00123-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 07/15/2019] [Accepted: 07/18/2019] [Indexed: 12/15/2022] Open
Abstract
Monte Carlo (MC) simulation for light propagation in scattering and absorbing media is the gold standard for studying the interaction of light with biological tissue and has been used for years in a wide variety of cases. The interaction of photons with the medium is simulated based on its optical properties and the original approximation of the scattering phase function. Over the past decade, with the new measurement geometries and recording techniques invented also the corresponding sophisticated methods for the description of the underlying light-tissue interaction taking into account realistic parameters and settings were developed. Applications, such as multiple scattering, optogenetics, optical coherence tomography, Raman spectroscopy, polarimetry and Mueller matrix measurement have emerged and are still constantly improved. Here, we review the advances and recent applications of MC simulation for the active field of the life sciences and the medicine pointing out the new insights enabled by the theoretical concepts.
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22
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Abdellah M, Hernando J, Eilemann S, Lapere S, Antille N, Markram H, Schürmann F. NeuroMorphoVis: a collaborative framework for analysis and visualization of neuronal morphology skeletons reconstructed from microscopy stacks. Bioinformatics 2019; 34:i574-i582. [PMID: 29949998 PMCID: PMC6022592 DOI: 10.1093/bioinformatics/bty231] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Motivation From image stacks to computational models, processing digital representations of neuronal morphologies is essential to neuroscientific research. Workflows involve various techniques and tools, leading in certain cases to convoluted and fragmented pipelines. The existence of an integrated, extensible and free framework for processing, analysis and visualization of those morphologies is a challenge that is still largely unfulfilled. Results We present NeuroMorphoVis, an interactive, extensible and cross-platform framework for building, visualizing and analyzing digital reconstructions of neuronal morphology skeletons extracted from microscopy stacks. Our framework is capable of detecting and repairing tracing artifacts, allowing the generation of high fidelity surface meshes and high resolution volumetric models for simulation and in silico imaging studies. The applicability of NeuroMorphoVis is demonstrated with two case studies. The first simulates the construction of three-dimensional profiles of neuronal somata and the other highlights how the framework is leveraged to create volumetric models of neuronal circuits for simulating different types of in vitro imaging experiments. Availability and implementation The source code and documentation are freely available on https://github.com/BlueBrain/NeuroMorphoVis under the GNU public license. The morphological analysis, visualization and surface meshing are implemented as an extensible Python API (Application Programming Interface) based on Blender, and the volume reconstruction and analysis code is written in C++ and parallelized using OpenMP. The framework features are accessible from a user-friendly GUI (Graphical User Interface) and a rich CLI (Command Line Interface). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marwan Abdellah
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
| | - Juan Hernando
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
| | - Stefan Eilemann
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
| | - Samuel Lapere
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
| | - Nicolas Antille
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
| | - Henry Markram
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
| | - Felix Schürmann
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
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Pimenta S, Pereira JP, Gomes NM, Ribeiro JF, Silva MF, Goncalves SB, Minas G, Correia JH. High-selectivity neural probe based on a Fabry-Perot optical filter and a CMOS silicon photodiodes array at visible wavelengths. JOURNAL OF BIOMEDICAL OPTICS 2018; 23:1-7. [PMID: 30350488 DOI: 10.1117/1.jbo.23.10.105004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 09/25/2018] [Indexed: 06/08/2023]
Abstract
This paper presents a silicon neural probe with a high-selectivity optical readout function and light emitting diodes for neurons photostimulation and fluorophore excitation. A high-selectivity Fabry-Perot optical filter on the top of a CMOS silicon photodiodes array can read the emitted fluorescence, which indicates the neurons physiological state. The design, fabrication, and characterization of the optical filter are presented. The SiO2 / TiO2 based optical filter thin films were deposited by RF sputtering. The performance of the optical filter deposited on the top of the silicon photodiodes array, implemented in the neural probe, was tested through in-vitro fluorescence measurements. The transmittance peak of the fabricated optical filter is 81.8% at 561 nm, with a full width at half maximum of 28 nm. The peak responsivity of the CMOS silicon photodiode with the optical filter deposited on its top is 273.6 mA / W at 578 nm. The in-vitro fluorescence measurements results show a CMOS photodiode current proportional to the fluorophore concentration with a good linearity (R2 = 0.9361). The results validate the use of the neural probe with the high-selectivity optical readout function to determine the presence of different fluorophore concentrations. The development of the device in a conventional CMOS process allows on-chip electronics readout.
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Affiliation(s)
- Sara Pimenta
- University of Minho, CMEMS-UMinho, Campus de Azurém, Guimarães, Portugal
| | - José P Pereira
- University of Minho, CMEMS-UMinho, Campus de Azurém, Guimarães, Portugal
| | - Nuno M Gomes
- University of Minho, CMEMS-UMinho, Campus de Azurém, Guimarães, Portugal
| | - João F Ribeiro
- University of Minho, CMEMS-UMinho, Campus de Azurém, Guimarães, Portugal
| | - Manuel F Silva
- University of Minho, CMEMS-UMinho, Campus de Azurém, Guimarães, Portugal
| | - Sandra B Goncalves
- University of Minho, CMEMS-UMinho, Campus de Azurém, Guimarães, Portugal
| | - Graca Minas
- University of Minho, CMEMS-UMinho, Campus de Azurém, Guimarães, Portugal
| | - José H Correia
- University of Minho, CMEMS-UMinho, Campus de Azurém, Guimarães, Portugal
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Atry F, Chen RCH, Pisaniello J, Brodnick S, Suminski AJ, Novello J, Ness J, Williams JC, Pashaie R. Optogenetic interrogation of neurovascular coupling in the cerebral cortex of transgenic mice. J Neural Eng 2018; 15:056033. [DOI: 10.1088/1741-2552/aad840] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Serruya MD, Harris JP, Adewole DO, Struzyna LA, Burrell JC, Nemes A, Petrov D, Kraft RH, Chen HI, Wolf JA, Cullen DK. Engineered Axonal Tracts as "Living Electrodes" for Synaptic-Based Modulation of Neural Circuitry. ADVANCED FUNCTIONAL MATERIALS 2018; 28:1701183. [PMID: 34045935 PMCID: PMC8152180 DOI: 10.1002/adfm.201701183] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Brain-computer interface and neuromodulation strategies relying on penetrating non-organic electrodes/optrodes are limited by an inflammatory foreign body response that ultimately diminishes performance. A novel "biohybrid" strategy is advanced, whereby living neurons, biomaterials, and microelectrode/optical technology are used together to provide a biologically-based vehicle to probe and modulate nervous-system activity. Microtissue engineering techniques are employed to create axon-based "living electrodes", which are columnar microstructures comprised of neuronal population(s) projecting long axonal tracts within the lumen of a hydrogel designed to chaperone delivery into the brain. Upon microinjection, the axonal segment penetrates to prescribed depth for synaptic integration with local host neurons, with the perikaryal segment remaining externalized below conforming electrical-optical arrays. In this paradigm, only the biological component ultimately remains in the brain, potentially attenuating a chronic foreign-body response. Axon-based living electrodes are constructed using multiple neuronal subtypes, each with differential capacity to stimulate, inhibit, and/or modulate neural circuitry based on specificity uniquely afforded by synaptic integration, yet ultimately computer controlled by optical/electrical components on the brain surface. Current efforts are assessing the efficacy of this biohybrid interface for targeted, synaptic-based neuromodulation, and the specificity, spatial density and long-term fidelity versus conventional microelectronic or optical substrates alone.
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Affiliation(s)
- Mijail D Serruya
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - James P Harris
- Center for Brain Injury & Repair, Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Neurotrauma, Neurodegeneration & Restoration, Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA 19104, USA
| | - Dayo O Adewole
- Center for Brain Injury & Repair, Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Neurotrauma, Neurodegeneration & Restoration, Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA 19104, USA; Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laura A Struzyna
- Center for Brain Injury & Repair, Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Neurotrauma, Neurodegeneration & Restoration, Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA 19104, USA; Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Justin C Burrell
- Center for Brain Injury & Repair, Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Neurotrauma, Neurodegeneration & Restoration, Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA 19104, USA
| | - Ashley Nemes
- Center for Brain Injury & Repair, Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Neurotrauma, Neurodegeneration & Restoration, Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA 19104, USA
| | - Dmitriy Petrov
- Center for Brain Injury & Repair, Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Neurotrauma, Neurodegeneration & Restoration, Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA 19104, USA
| | - Reuben H Kraft
- Computational Biomechanics Group, Department of Mechanical & Nuclear Engineering, Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16801, USA
| | - H Isaac Chen
- Center for Brain Injury & Repair, Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Neurotrauma, Neurodegeneration & Restoration, Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA 19104, USA
| | - John A Wolf
- Center for Brain Injury & Repair, Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Neurotrauma, Neurodegeneration & Restoration, Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA 19104, USA
| | - D Kacy Cullen
- Center for Brain Injury & Repair, Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Neurotrauma, Neurodegeneration & Restoration, Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA 19104, USA
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Lemaillet P, Cooksey CC, Hwang J, Wabnitz H, Grosenick D, Yang L, Allen DW. Correction of an adding-doubling inversion algorithm for the measurement of the optical parameters of turbid media. BIOMEDICAL OPTICS EXPRESS 2018; 9:55-71. [PMID: 29359087 PMCID: PMC5772589 DOI: 10.1364/boe.9.000055] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/16/2017] [Accepted: 11/19/2017] [Indexed: 05/22/2023]
Abstract
We present broadband measurements of the optical properties of tissue-mimicking solid phantoms using a single integrating sphere to measure the hemispherical reflectance and transmittance under a direct illumination at the normal incident angle. These measurements are traceable to reflectance and transmittance scales. An inversion routine using the output of the adding-doubling algorithm restricted to the reflectance and transmittance under a direct illumination was developed to produce the optical parameters of the sample along with an uncertainty budget at each wavelength. The results for two types of phantoms are compared to measurements by time-resolved approaches. The results between our method and these independent measurements agree within the estimated measurement uncertainties.
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Affiliation(s)
- Paul Lemaillet
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899,
USA
| | - Catherine C. Cooksey
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899,
USA
| | - Jeeseong Hwang
- National Institute of Standards and Technology, 325 Broadway Street, Boulder, CO 80305,
USA
| | - Heidrun Wabnitz
- Physikalisch-Technische Bundesanstalt (PTB), Abbestrasse 2-12, 10587 Berlin,
Germany
| | - Dirk Grosenick
- Physikalisch-Technische Bundesanstalt (PTB), Abbestrasse 2-12, 10587 Berlin,
Germany
| | - Lin Yang
- Physikalisch-Technische Bundesanstalt (PTB), Abbestrasse 2-12, 10587 Berlin,
Germany
| | - David W. Allen
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899,
USA
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Casas-Torremocha D, Clascá F, Núñez Á. Posterior Thalamic Nucleus Modulation of Tactile Stimuli Processing in Rat Motor and Primary Somatosensory Cortices. Front Neural Circuits 2017; 11:69. [PMID: 29021744 PMCID: PMC5623691 DOI: 10.3389/fncir.2017.00069] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/12/2017] [Indexed: 12/18/2022] Open
Abstract
Rodents move rhythmically their facial whiskers and compute differences between signals predicted and those resulting from the movement to infer information about objects near their head. These computations are carried out by a large network of forebrain structures that includes the thalamus and the primary somatosensory (S1BF) and motor (M1wk) cortices. Spatially and temporally precise mechanorreceptive whisker information reaches the S1BF cortex via the ventroposterior medial thalamic nucleus (VPM). Other whisker-related information may reach both M1wk and S1BF via the axons from the posterior thalamic nucleus (Po). However, Po axons may convey, in addition to direct sensory signals, the dynamic output of computations between whisker signals and descending motor commands. It has been proposed that this input may be relevant for adjusting cortical responses to predicted vs. unpredicted whisker signals, but the effects of Po input on M1wk and S1BF function have not been directly tested or compared in vivo. Here, using electrophysiology, optogenetics and pharmacological tools, we compared in adult rats M1wk and S1BF in vivo responses in the whisker areas of the motor and primary somatosensory cortices to passive multi-whisker deflection, their dependence on Po activity, and their changes after a brief intense activation of Po axons. We report that the latencies of the first component of tactile-evoked local field potentials in M1wk and S1BF are similar. The evoked potentials decrease markedly in M1wk, but not in S1BF, by injection in Po of the GABAA agonist muscimol. A brief high-frequency electrical stimulation of Po decreases the responsivity of M1wk and S1BF cells to subsequent whisker stimulation. This effect is prevented by the local application of omega-agatoxin, suggesting that it may in part depend on GABA release by fast-spiking parvalbumin (PV)-expressing cortical interneurons. Local optogenetic activation of Po synapses in different cortical layers also diminishes M1wk and S1BF responses. This effect is most pronounced in the superficial layers of both areas, known to be the main source and target of their reciprocal cortico-cortical connections.
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Affiliation(s)
- Diana Casas-Torremocha
- Department of Anatomy, Histology and Neuroscience, Faculty of Medicine, Autonomous University of Madrid, Madrid, Spain
| | - Francisco Clascá
- Department of Anatomy, Histology and Neuroscience, Faculty of Medicine, Autonomous University of Madrid, Madrid, Spain
| | - Ángel Núñez
- Department of Anatomy, Histology and Neuroscience, Faculty of Medicine, Autonomous University of Madrid, Madrid, Spain
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Abdellah M, Hernando J, Antille N, Eilemann S, Markram H, Schürmann F. Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies. BMC Bioinformatics 2017; 18:402. [PMID: 28929974 PMCID: PMC5606217 DOI: 10.1186/s12859-017-1788-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND We present a software workflow capable of building large scale, highly detailed and realistic volumetric models of neocortical circuits from the morphological skeletons of their digitally reconstructed neurons. The limitations of the existing approaches for creating those models are explained, and then, a multi-stage pipeline is discussed to overcome those limitations. Starting from the neuronal morphologies, we create smooth piecewise watertight polygonal models that can be efficiently utilized to synthesize continuous and plausible volumetric models of the neurons with solid voxelization. The somata of the neurons are reconstructed on a physically-plausible basis relying on the physics engine in Blender. RESULTS Our pipeline is applied to create 55 exemplar neurons representing the various morphological types that are reconstructed from the somatsensory cortex of a juvenile rat. The pipeline is then used to reconstruct a volumetric slice of a cortical circuit model that contains ∼210,000 neurons. The applicability of our pipeline to create highly realistic volumetric models of neocortical circuits is demonstrated with an in silico imaging experiment that simulates tissue visualization with brightfield microscopy. The results were evaluated with a group of domain experts to address their demands and also to extend the workflow based on their feedback. CONCLUSION A systematic workflow is presented to create large scale synthetic tissue models of the neocortical circuitry. This workflow is fundamental to enlarge the scale of in silico neuroscientific optical experiments from several tens of cubic micrometers to a few cubic millimeters. AMS SUBJECT CLASSIFICATION Modelling and Simulation.
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Affiliation(s)
- Marwan Abdellah
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland
| | - Juan Hernando
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland
| | - Nicolas Antille
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland
| | - Stefan Eilemann
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland
| | - Henry Markram
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland
| | - Felix Schürmann
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland.
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Epilepsy and optogenetics: can seizures be controlled by light? Clin Sci (Lond) 2017; 131:1605-1616. [DOI: 10.1042/cs20160492] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/30/2017] [Accepted: 04/13/2017] [Indexed: 01/12/2023]
Abstract
Over the past decade, ‘optogenetics’ has been consolidated as a game-changing tool in the neuroscience field, by allowing optical control of neuronal activity with high cell-type specificity. The ability to activate or inhibit targeted neurons at millisecond resolution not only offers an investigative tool, but potentially also provides a therapeutic intervention strategy for acute correction of aberrant neuronal activity. As efficient therapeutic tools are in short supply for neurological disorders, optogenetic technology has therefore spurred considerable enthusiasm and fostered a new wave of translational studies in neuroscience. Epilepsy is among the disorders that have been widely explored. Partial epilepsies are characterized by seizures arising from excessive excitatory neuronal activity that emerges from a focal area. Based on the constricted seizure focus, it appears feasible to intercept partial seizures by acutely shutting down excitatory neurons by means of optogenetics. The availability of both inhibitory and excitatory optogenetic probes, along with the available targeting strategies for respective excitatory or inhibitory neurons, allows multiple conceivable scenarios for controlling abnormal circuit activity. Several such scenarios have been explored in the settings of experimental epilepsy and have provided encouraging translational findings and revealed interesting and unexpected new aspects of epileptogenesis. However, it has also emerged that considerable challenges persist before clinical translation becomes feasible. This review provides a general introduction to optogenetics, and an overview of findings that are relevant for understanding how optogenetics may be utilized therapeutically as a highly innovative treatment for epilepsy.
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Suhan S, Ilona S, Chih-Chieh C, Isabelle D, Stéphane P, Antoine C, Claire M, Frédéric P. Experimental assessment of the safety and potential efficacy of high irradiance photostimulation of brain tissues. Sci Rep 2017; 7:43997. [PMID: 28276522 PMCID: PMC5343659 DOI: 10.1038/srep43997] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 02/02/2017] [Indexed: 01/09/2023] Open
Abstract
Optogenetics is widely used in fundamental neuroscience. Its potential clinical translation for brain neuromodulation requires a careful assessment of the safety and efficacy of repeated, sustained optical stimulation of large volumes of brain tissues. This study was performed in rats and not in non-human primates for ethical reasons. We studied the spatial distribution of light, potential damage, and non-physiological effects in vivo, in anesthetized rat brains, on large brain volumes, following repeated high irradiance photo-stimulation. We generated 2D irradiance and temperature increase surface maps based on recordings taken during optical stimulation using irradiance and temporal parameters representative of common optogenetics experiments. Irradiances of 100 to 600 mW/mm2 with 5 ms pulses at 20, 40, and 60 Hz were applied during 90 s. In vivo electrophysiological recordings and post-mortem histological analyses showed that high power light stimulation had no obvious phototoxic effects and did not trigger non-physiological functional activation. This study demonstrates the ability to illuminate cortical layers to a depth of several millimeters using pulsed red light without detrimental thermal damages.
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Affiliation(s)
- Senova Suhan
- Neurosurgery Department, Assistance Publique-Hôpitaux de Paris (APHP), Groupe Henri-Mondor Albert-Chenevier, PePsy department, Créteil, F-94000, France
- U955 INSERM IMRB eq.14 Université Paris 12 UPEC, Faculté de Médecine, F-94010 Créteil, France
| | - Scisniak Ilona
- IMNC, CNRS Univ. Paris Sud, Univ. Paris Saclay Orsay F-91405, France
- Faculty of Physics, Univ. Warsaw, P-02-093 Poland
| | - Chiang Chih-Chieh
- IMNC, CNRS Univ. Paris Sud, Univ. Paris Saclay Orsay F-91405, France
- Department of Biomedical Engineering and Environmental Sciences, National Tsing-Hua University, Hsinchu city, 300, Taiwan
| | - Doignon Isabelle
- Laboratory of Cellular interactions and liver physiopathology, INSERM, Univ. Paris-Sud, Univ. Paris Saclay, Orsay, F-91405 France
| | - Palfi Stéphane
- Neurosurgery Department, Assistance Publique-Hôpitaux de Paris (APHP), Groupe Henri-Mondor Albert-Chenevier, PePsy department, Créteil, F-94000, France
- U955 INSERM IMRB eq.14 Université Paris 12 UPEC, Faculté de Médecine, F-94010 Créteil, France
| | - Chaillet Antoine
- L2S, CentraleSupélec, Univ. Paris Saclay, Gif sur Yvette, F-91192 France
| | - Martin Claire
- IMNC, CNRS Univ. Paris Sud, Univ. Paris Saclay Orsay F-91405, France
- Univ. Paris Diderot, Sorbonne Paris Cité, Unité de Biologie Fonctionnelle et Adaptative, CNRS F-75205, Paris, France
| | - Pain Frédéric
- IMNC, CNRS Univ. Paris Sud, Univ. Paris Saclay Orsay F-91405, France
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Abdellah M, Bilgili A, Eilemann S, Shillcock J, Markram H, Schürmann F. Bio-physically plausible visualization of highly scattering fluorescent neocortical models for in silico experimentation. BMC Bioinformatics 2017; 18:62. [PMID: 28251871 PMCID: PMC5333179 DOI: 10.1186/s12859-016-1444-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Background We present a visualization pipeline capable of accurate rendering of highly scattering fluorescent neocortical neuronal models. The pipeline is mainly developed to serve the computational neurobiology community. It allows the scientists to visualize the results of their virtual experiments that are performed in computer simulations, or in silico. The impact of the presented pipeline opens novel avenues for assisting the neuroscientists to build biologically accurate models of the brain. These models result from computer simulations of physical experiments that use fluorescence imaging to understand the structural and functional aspects of the brain. Due to the limited capabilities of the current visualization workflows to handle fluorescent volumetric datasets, we propose a physically-based optical model that can accurately simulate light interaction with fluorescent-tagged scattering media based on the basic principles of geometric optics and Monte Carlo path tracing. We also develop an automated and efficient framework for generating dense fluorescent tissue blocks from a neocortical column model that is composed of approximately 31000 neurons. Results Our pipeline is used to visualize a virtual fluorescent tissue block of 50 μm3 that is reconstructed from the somatosensory cortex of juvenile rat. The fluorescence optical model is qualitatively analyzed and validated against experimental emission spectra of different fluorescent dyes from the Alexa Fluor family. Conclusion We discussed a scientific visualization pipeline for creating images of synthetic neocortical neuronal models that are tagged virtually with fluorescent labels on a physically-plausible basis. The pipeline is applied to analyze and validate simulation data generated from neuroscientific in silico experiments.
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Affiliation(s)
- Marwan Abdellah
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland
| | - Ahmet Bilgili
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland
| | - Stefan Eilemann
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland
| | - Julian Shillcock
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland
| | - Henry Markram
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland
| | - Felix Schürmann
- Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Biotech Campus, Chemin des Mines 9, Geneva, 1202, Switzerland.
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Azimipour M, Sheikhzadeh M, Baumgartner R, Cullen PK, Helmstetter FJ, Chang WJ, Pashaie R. Fluorescence laminar optical tomography for brain imaging: system implementation and performance evaluation. JOURNAL OF BIOMEDICAL OPTICS 2017; 22:16003. [PMID: 28056143 PMCID: PMC5997009 DOI: 10.1117/1.jbo.22.1.016003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 12/12/2016] [Indexed: 05/04/2023]
Abstract
We present our effort in implementing a fluorescence laminar optical tomography scanner which is specifically designed for noninvasive three-dimensional imaging of fluorescence proteins in the brains of small rodents. A laser beam, after passing through a cylindrical lens, scans the brain tissue from the surface while the emission signal is captured by the epi-fluorescence optics and is recorded using an electron multiplication CCD sensor. Image reconstruction algorithms are developed based on Monte Carlo simulation to model light–tissue interaction and generate the sensitivity matrices. To solve the inverse problem, we used the iterative simultaneous algebraic reconstruction technique. The performance of the developed system was evaluated by imaging microfabricated silicon microchannels embedded inside a substrate with optical properties close to the brain as a tissue phantom and ultimately by scanning brain tissue in vivo. Details of the hardware design and reconstruction algorithms are discussed and several experimental results are presented. The developed system can specifically facilitate neuroscience experiments where fluorescence imaging and molecular genetic methods are used to study the dynamics of the brain circuitries.
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Affiliation(s)
- Mehdi Azimipour
- University of Wisconsin–Milwaukee, Electrical and Computer Engineering Department, 3200 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Mahya Sheikhzadeh
- University of Wisconsin–Milwaukee, Electrical and Computer Engineering Department, 3200 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Ryan Baumgartner
- University of Wisconsin–Milwaukee, Electrical and Computer Engineering Department, 3200 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Patrick K. Cullen
- University of Wisconsin–Milwaukee, Psychology Department, 2441 East Hartford Avenue, 207 Garland Hall, Milwaukee, Wisconsin 53211, United States
| | - Fred J. Helmstetter
- University of Wisconsin–Milwaukee, Psychology Department, 2441 East Hartford Avenue, 207 Garland Hall, Milwaukee, Wisconsin 53211, United States
| | - Woo-Jin Chang
- University of Wisconsin–Milwaukee, Mechanical Engineering Department, 3200 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Ramin Pashaie
- University of Wisconsin–Milwaukee, Electrical and Computer Engineering Department, 3200 North Cramer Street, Milwaukee, Wisconsin 53211, United States
- Address all correspondence to: Ramin Pashaie, E-mail:
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Abstract
Optogenetic methods have been highly effective for suppressing neural activity and modulating behavior in rodents, but effects have been much smaller in primates, which have much larger brains. Here, we present a suite of technologies to use optogenetics effectively in primates and apply these tools to a classic question in oculomotor control. First, we measured light absorption and heat propagation in vivo, optimized the conditions for using the red-light-shifted halorhodopsin Jaws in primates, and developed a large-volume illuminator to maximize light delivery with minimal heating and tissue displacement. Together, these advances allowed for nearly universal neuronal inactivation across more than 10 mm3 of the cortex. Using these tools, we demonstrated large behavioral changes (i.e., up to several fold increases in error rate) with relatively low light power densities (≤100 mW/mm2) in the frontal eye field (FEF). Pharmacological inactivation studies have shown that the FEF is critical for executing saccades to remembered locations. FEF neurons increase their firing rate during the three epochs of the memory-guided saccade task: visual stimulus presentation, the delay interval, and motor preparation. It is unclear from earlier work, however, whether FEF activity during each epoch is necessary for memory-guided saccade execution. By harnessing the temporal specificity of optogenetics, we found that FEF contributes to memory-guided eye movements during every epoch of the memory-guided saccade task (the visual, delay, and motor periods).
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Gysbrechts B, Wang L, Trong NND, Cabral H, Navratilova Z, Battaglia F, Saeys W, Bartic C. Light distribution and thermal effects in the rat brain under optogenetic stimulation. JOURNAL OF BIOPHOTONICS 2016; 9:576-585. [PMID: 26192551 DOI: 10.1002/jbio.201500106] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 06/12/2015] [Accepted: 06/15/2015] [Indexed: 06/04/2023]
Abstract
Optical brain stimulation gained a lot of attention in neuroscience due to its superior cell-type specificity. In the design of illumination strategies, predicting the light propagation in a specific tissue is essential and requires knowledge of the optical properties of that tissue. We present the estimated absorption and reduced scattering in rodent brain tissue using non-destructive contact spatially resolved spectroscopy (cSRS). The obtained absorption and scattering in the cortex, hippocampus and striatum are similar, but lower than in the thalamus, leading to a less deep but broader light penetration profile in the thalamus. Next, the light distribution was investigated for different stimulation protocols relevant for fiber-optic based optogenetic experiments, using Monte Carlo simulation. A protocol specific analysis is proposed to evaluate the potential of thermally induced side effects.
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Affiliation(s)
- Barbara Gysbrechts
- Department of Physics and Astronomy, University of Leuven, Celestijnenlaan 200D, 3001, Leuven, Belgium.
| | - Ling Wang
- Department of Physics and Astronomy, University of Leuven, Celestijnenlaan 200D, 3001, Leuven, Belgium
| | - Nghia Nguyen Do Trong
- Department of Biosystems, University of Leuven, Kasteelpark Arenberg 30, 3001, Leuven, Belgium
| | - Henrique Cabral
- Donders Institute, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
| | - Zaneta Navratilova
- Donders Institute, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
| | - Francesco Battaglia
- Donders Institute, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
| | - Wouter Saeys
- Department of Biosystems, University of Leuven, Kasteelpark Arenberg 30, 3001, Leuven, Belgium
| | - Carmen Bartic
- Department of Physics and Astronomy, University of Leuven, Celestijnenlaan 200D, 3001, Leuven, Belgium
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35
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Realistic Numerical and Analytical Modeling of Light Scattering in Brain Tissue for Optogenetic Applications(1,2,3). eNeuro 2016; 3:eN-MNT-0059-15. [PMID: 26866055 PMCID: PMC4745178 DOI: 10.1523/eneuro.0059-15.2015] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 10/28/2015] [Accepted: 10/30/2015] [Indexed: 12/20/2022] Open
Abstract
In recent years, optogenetics has become a central tool in neuroscience research. Estimating the transmission of visible light through brain tissue is of crucial importance for controlling the activation levels of neurons in different depths, designing optical systems, and avoiding lesions from excessive power density. The Kubelka–Munk model and Monte Carlo simulations have previously been used to model light propagation through rodents' brain tissue, however, these prior attempts suffer from fundamental shortcomings. Here, we introduce and study two modified approaches for modeling the distributions of light emanating from a multimode fiber and scattering through tissue, using both realistic numerical Monte Carlo simulations and an analytical approach based on the beam-spread function approach. We demonstrate a good agreement of the new methods' predictions both with recently published data, and with new measurements in mouse brain cortical slices, where our results yield a new cortical scattering length estimate of ∼47 µm at λ = 473 nm, significantly shorter than ordinarily assumed in optogenetic applications.
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36
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Brake J, Jang M, Yang C. Analyzing the relationship between decorrelation time and tissue thickness in acute rat brain slices using multispeckle diffusing wave spectroscopy. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2016; 33:270-5. [PMID: 26831778 PMCID: PMC4783160 DOI: 10.1364/josaa.33.000270] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Novel techniques in the field of wavefront shaping have enabled light to be focused deep inside or through scattering media such as biological tissue. However, most of these demonstrations have been limited to thin, static samples since these techniques are very sensitive to changes in the arrangement of the scatterers within. As the samples of interest get thicker, the influence of the dynamic nature of the sample becomes even more pronounced and the window of time in which the wavefront solutions remain valid shrinks further. In this paper, we examine the time scales upon which this decorrelation happens in acute rat brain slices via multispeckle diffusing wave spectroscopy and investigate the relationship between this decorrelation time and the thickness of the sample using diffusing wave spectroscopy theory and Monte Carlo photon transport simulation.
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37
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Pawela C, DeYoe E, Pashaie R. Intracranial Injection of an Optogenetics Viral Vector Followed by Optical Cannula Implantation for Neural Stimulation in Rat Brain Cortex. Methods Mol Biol 2016; 1408:227-241. [PMID: 26965126 DOI: 10.1007/978-1-4939-3512-3_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Optogenetics is rapidly gaining acceptance as a preferred method to study specific neuronal cell types using light. Optogenetic neuromodulation requires the introduction of a cell-specific viral vector encoding for a light activating ion channel or ion pump and the utilization of a system to deliver light stimulation to brain. Here, we describe a two-part methodology starting with a procedure to inject an optogenetic AAV virus into rat cortex followed by a second procedure to surgically implant an optical cannula for light delivery to the deeper cortical layers.
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Affiliation(s)
- Christopher Pawela
- Biophysics Department, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Edgar DeYoe
- Radiology Department, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Ramin Pashaie
- Electrical Engineering Department, University of Wisconsin-Milwaukee, 3200 N. Cramer St., EMS 1181, Milwaukee, WI, 53211, USA.
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38
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Liu Y, Jacques SL, Azimipour M, Rogers JD, Pashaie R, Eliceiri KW. OptogenSIM: a 3D Monte Carlo simulation platform for light delivery design in optogenetics. BIOMEDICAL OPTICS EXPRESS 2015; 6:4859-70. [PMID: 26713200 PMCID: PMC4679260 DOI: 10.1364/boe.6.004859] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/03/2015] [Accepted: 11/09/2015] [Indexed: 05/07/2023]
Abstract
Optimizing light delivery for optogenetics is critical in order to accurately stimulate the neurons of interest while reducing nonspecific effects such as tissue heating or photodamage. Light distribution is typically predicted using the assumption of tissue homogeneity, which oversimplifies light transport in heterogeneous brain. Here, we present an open-source 3D simulation platform, OptogenSIM, which eliminates this assumption. This platform integrates a voxel-based 3D Monte Carlo model, generic optical property models of brain tissues, and a well-defined 3D mouse brain tissue atlas. The application of this platform in brain data models demonstrates that brain heterogeneity has moderate to significant impact depending on application conditions. Estimated light density contours can show the region of any specified power density in the 3D brain space and thus can help optimize the light delivery settings, such as the optical fiber position, fiber diameter, fiber numerical aperture, light wavelength and power. OptogenSIM is freely available and can be easily adapted to incorporate additional brain atlases.
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Affiliation(s)
- Yuming Liu
- Laboratory for Optical and Computational Instrumentation, Department of Biomedical Engineering, University of Wisconsin at Madison, 1675 Observatory Drive, Madison, WI 53706,
USA
| | - Steven L. Jacques
- Department of Biomedical Engineering, Oregon Health and Science University, 3303 SW Bond Ave, Portland, OR 97239,
USA
- Department of Dermatology, Oregon Health and Science University, 3303 SW Bond Ave, Portland, OR 97239,
USA
| | - Mehdi Azimipour
- Electrical Engineering Department, University of Wisconsin-Milwaukee, 3200 N Cramer St., Milwaukee, Wisconsin 53211,
USA
| | - Jeremy D. Rogers
- Laboratory for Optical and Computational Instrumentation, Department of Biomedical Engineering, University of Wisconsin at Madison, 1675 Observatory Drive, Madison, WI 53706,
USA
| | - Ramin Pashaie
- Electrical Engineering Department, University of Wisconsin-Milwaukee, 3200 N Cramer St., Milwaukee, Wisconsin 53211,
USA
| | - Kevin W. Eliceiri
- Laboratory for Optical and Computational Instrumentation, Department of Biomedical Engineering, University of Wisconsin at Madison, 1675 Observatory Drive, Madison, WI 53706,
USA
- Morgridge Institute for Research, 330 North Orchard Street, Madison, WI 53715,
USA
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39
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Transparent intracortical microprobe array for simultaneous spatiotemporal optical stimulation and multichannel electrical recording. Nat Methods 2015; 12:1157-62. [DOI: 10.1038/nmeth.3620] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 09/08/2015] [Indexed: 12/22/2022]
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40
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Abdala AP, Paton JFR, Smith JC. Defining inhibitory neurone function in respiratory circuits: opportunities with optogenetics? J Physiol 2015; 593:3033-46. [PMID: 25384785 PMCID: PMC4532524 DOI: 10.1113/jphysiol.2014.280610] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/30/2014] [Indexed: 12/22/2022] Open
Abstract
Pharmacological and mathematical modelling studies support the view that synaptic inhibition in mammalian brainstem respiratory circuits is essential for generating normal and stable breathing movements. GABAergic and glycinergic neurones are known components of these circuits but their precise functional roles have not been established, especially within key microcircuits of the respiratory pre-Bötzinger (pre-BötC) and Bötzinger (BötC) complexes involved in phasic control of respiratory pump and airway muscles. Here, we review briefly current concepts of relevant complexities of inhibitory synapses and the importance of synaptic inhibition in the operation of these microcircuits. We highlight results and limitations of classical pharmacological studies that have suggested critical functions of synaptic inhibition. We then explore the potential opportunities for optogenetic strategies that represent a promising new approach for interrogating function of inhibitory circuits, including a hypothetical wish list for optogenetic approaches to allow expedient application of this technology. We conclude that recent technical advances in optogenetics should provide a means to understand the role of functionally select and regionally confined subsets of inhibitory neurones in key respiratory circuits such as those in the pre-BötC and BötC.
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Affiliation(s)
- Ana Paula Abdala
- School of Physiology and Pharmacology, Bristol CardioVascular, Medical Science Building, University of BristolBristol, UK
| | - Julian F R Paton
- School of Physiology and Pharmacology, Bristol CardioVascular, Medical Science Building, University of BristolBristol, UK
| | - Jeffrey C Smith
- Cellular and Systems Neurobiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesda, MD, USA
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41
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Scattering of Sculpted Light in Intact Brain Tissue, with implications for Optogenetics. Sci Rep 2015; 5:11501. [PMID: 26108566 PMCID: PMC4480008 DOI: 10.1038/srep11501] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 05/27/2015] [Indexed: 11/08/2022] Open
Abstract
Optogenetics uses light to control and observe the activity of neurons, often using a focused laser beam. As brain tissue is a scattering medium, beams are distorted and spread with propagation through neural tissue, and the beam's degradation has important implications in optogenetic experiments. To address this, we present an analysis of scattering and loss of intensity of focused laser beams at different depths within the brains of zebrafish larvae. Our experimental set-up uses a 488 nm laser and a spatial light modulator to focus a diffraction-limited spot of light within the brain. We use a combination of experimental measurements of back-scattered light in live larvae and computational modelling of the scattering to determine the spatial distribution of light. Modelling is performed using the Monte Carlo method, supported by generalised Lorenz-Mie theory in the single-scattering approximation. Scattering in areas rich in cell bodies is compared to that of regions of neuropil to identify the distinct and dramatic contributions that cell nuclei make to scattering. We demonstrate the feasibility of illuminating individual neurons, even in nucleus-rich areas, at depths beyond 100 μm using a spatial light modulator in combination with a standard laser and microscope optics.
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Pashaie R, Baumgartner R, Richner TJ, Brodnick SK, Azimipour M, Eliceiri KW, Williams JC. Closed-Loop Optogenetic Brain Interface. IEEE Trans Biomed Eng 2015; 62:2327-37. [PMID: 26011877 DOI: 10.1109/tbme.2015.2436817] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This paper presents a new approach for implementation of closed-loop brain-machine interface algorithms by combining optogenetic neural stimulation with electrocorticography and fluorescence microscopy. We used a new generation of microfabricated electrocorticography (micro-ECoG) devices in which electrode arrays are embedded within an optically transparent biocompatible substrate that provides optical access to the brain tissue during electrophysiology recording. An optical setup was designed capable of projecting arbitrary patterns of light for optogenetic stimulation and performing fluorescence microscopy through the implant. For realization of a closed-loop system using this platform, the feedback can be taken from electrophysiology data or fluorescence imaging. In the closed-loop systems discussed in this paper, the feedback signal was taken from the micro-ECoG. In these algorithms, the electrophysiology data are continuously transferred to a computer and compared with some predefined spatial-temporal patterns of neural activity. The computer which processes the data also readjusts the duration and distribution of optogenetic stimulating pulses to minimize the difference between the recorded activity and the predefined set points so that after a limited period of transient response the recorded activity follows the set points. Details of the system design and implementation of typical closed-loop paradigms are discussed in this paper.
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43
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Wang K, Wang Q, Luo Q, Yang X. Fluorescence molecular tomography in the second near-infrared window. OPTICS EXPRESS 2015; 23:12669-12679. [PMID: 26074521 DOI: 10.1364/oe.23.012669] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Fluorescence molecular tomography (FMT), an in vivo noninvasive imaging technology, can provide localization and quantification information for deep fluorophores. Light at wavelengths in the near-infrared (NIR-I) window from 650 nm to 950 nm has conventionally been chosen for FMT. In this study, we introduced longer NIR wavelengths within the 1100 nm to 1400 nm range, known as the "second NIR spectral window" (NIR-II). A singular-value analysis method was used to demonstrate the utility and advantages of using the NIR-II for FMT, and experiments showed an improvement in the spatial resolution in phantom studies.
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44
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Azimipour M, Atry F, Pashaie R. Effect of blood vessels on light distribution in optogenetic stimulation of cortex. OPTICS LETTERS 2015; 40:2173-6. [PMID: 26393692 DOI: 10.1364/ol.40.002173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In this Letter, the impact of blood vessels on light distribution during photostimulation of cortical tissue in small rodents is investigated. Brain optical properties were extracted using a double-integrating sphere setup, and optical coherence tomography was used to image cortical vessels and capillaries to generate a three-dimensional angiogram of the cortex. By combining these two datasets, a complete volumetric structure of the cortical tissue was developed and linked to a Monte Carlo code which simulates light propagation in this inhomogeneous structure and illustrates the effect of blood vessels on the penetration depth and pattern preservation in optogenetic stimulation.
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45
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Atry F, Frye S, Richner TJ, Brodnick SK, Soehartono A, Williams J, Pashaie R. Monitoring Cerebral Hemodynamics Following Optogenetic Stimulation via Optical Coherence Tomography. IEEE Trans Biomed Eng 2015; 62:766-73. [DOI: 10.1109/tbme.2014.2364816] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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