1
|
Johnsen KA, Cruzado NA, Menard ZC, Willats AA, Charles AS, Markowitz JE, Rozell CJ. Bridging model and experiment in systems neuroscience with Cleo: the Closed-Loop, Electrophysiology, and Optophysiology simulation testbed. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.27.525963. [PMID: 39026717 PMCID: PMC11257437 DOI: 10.1101/2023.01.27.525963] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Systems neuroscience has experienced an explosion of new tools for reading and writing neural activity, enabling exciting new experiments such as all-optical or closed-loop control that effect powerful causal interventions. At the same time, improved computational models are capable of reproducing behavior and neural activity with increasing fidelity. Unfortunately, these advances have drastically increased the complexity of integrating different lines of research, resulting in the missed opportunities and untapped potential of suboptimal experiments. Experiment simulation can help bridge this gap, allowing model and experiment to better inform each other by providing a low-cost testbed for experiment design, model validation, and methods engineering. Specifically, this can be achieved by incorporating the simulation of the experimental interface into our models, but no existing tool integrates optogenetics, two-photon calcium imaging, electrode recording, and flexible closed-loop processing with neural population simulations. To address this need, we have developed Cleo: the Closed-Loop, Electrophysiology, and Optophysiology experiment simulation testbed. Cleo is a Python package enabling injection of recording and stimulation devices as well as closed-loop control with realistic latency into a Brian spiking neural network model. It is the only publicly available tool currently supporting two-photon and multi-opsin/wavelength optogenetics. To facilitate adoption and extension by the community, Cleo is open-source, modular, tested, and documented, and can export results to various data formats. Here we describe the design and features of Cleo, validate output of individual components and integrated experiments, and demonstrate its utility for advancing optogenetic techniques in prospective experiments using previously published systems neuroscience models.
Collapse
|
2
|
Tarvainen T, Cox B. Quantitative photoacoustic tomography: modeling and inverse problems. JOURNAL OF BIOMEDICAL OPTICS 2024; 29:S11509. [PMID: 38125717 PMCID: PMC10731766 DOI: 10.1117/1.jbo.29.s1.s11509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/19/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
Significance Quantitative photoacoustic tomography (QPAT) exploits the photoacoustic effect with the aim of estimating images of clinically relevant quantities related to the tissue's optical absorption. The technique has two aspects: an acoustic part, where the initial acoustic pressure distribution is estimated from measured photoacoustic time-series, and an optical part, where the distributions of the optical parameters are estimated from the initial pressure. Aim Our study is focused on the optical part. In particular, computational modeling of light propagation (forward problem) and numerical solution methodologies of the image reconstruction (inverse problem) are discussed. Approach The commonly used mathematical models of how light and sound propagate in biological tissue are reviewed. A short overview of how the acoustic inverse problem is usually treated is given. The optical inverse problem and methods for its solution are reviewed. In addition, some limitations of real-life measurements and their effect on the inverse problems are discussed. Results An overview of QPAT with a focus on the optical part was given. Computational modeling and inverse problems of QPAT were addressed, and some key challenges were discussed. Furthermore, the developments for tackling these problems were reviewed. Although modeling of light transport is well-understood and there is a well-developed framework of inverse mathematics for approaching the inverse problem of QPAT, there are still challenges in taking these methodologies to practice. Conclusions Modeling and inverse problems of QPAT together were discussed. The scope was limited to the optical part, and the acoustic aspects were discussed only to the extent that they relate to the optical aspect.
Collapse
Affiliation(s)
- Tanja Tarvainen
- University of Eastern Finland, Department of Technical Physics, Kuopio, Finland
| | - Ben Cox
- University College London, Department of Medical Physics and Biomedical Engineering, London, United Kingdom
| |
Collapse
|
3
|
Crowley J, Gordon GSD. Designing and simulating realistic spatial frequency domain imaging systems using open-source 3D rendering software. BIOMEDICAL OPTICS EXPRESS 2023; 14:2523-2538. [PMID: 37342713 PMCID: PMC10278632 DOI: 10.1364/boe.484286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 06/23/2023]
Abstract
Spatial frequency domain imaging (SFDI) is a low-cost imaging technique that maps absorption and reduced scattering coefficients, offering improved contrast for important tissue structures such as tumours. Practical SFDI systems must cope with various imaging geometries including imaging planar samples ex vivo, imaging inside tubular lumen in vivo e.g. for endoscopy, and measuring tumours or polyps of varying morphology. There is a need for a design and simulation tool to accelerate design of new SFDI systems and simulate realistic performance under these scenarios. We present such a system implemented using open-source 3D design and ray-tracing software Blender that simulates media with realistic absorption and scattering in a wide range of geometries. By using Blender's Cycles ray-tracing engine, our system simulates effects such as varying lighting, refractive index changes, non-normal incidence, specular reflections and shadows, enabling realistic evaluation of new designs. We first demonstrate quantitative agreement between Monte-Carlo simulated absorption and reduced scattering coefficients with those simulated from our Blender system, achieving 16 % discrepancy in absorption coefficient and 18 % in reduced scattering coefficient. However, we then show that using an empirically derived look-up table the errors reduce to 1 % and 0.7 % respectively. Next, we simulate SFDI mapping of absorption, scattering and shape for simulated tumour spheroids, demonstrating enhanced contrast. Finally we demonstrate SFDI mapping inside a tubular lumen, which highlighted a important design insight: custom look-up tables must be generated for different longitudinal sections of the lumen. With this approach we achieved 2 % absorption error and 2 % scattering error. We anticipate our simulation system will aid in the design of novel SFDI systems for key biomedical applications.
Collapse
Affiliation(s)
- Jane Crowley
- Optics & Photonics Group, Department of Electrical and
Electronic Engineering, University of Nottingham, Nottingham, United
Kingdom
| | - George S. D. Gordon
- Optics & Photonics Group, Department of Electrical and
Electronic Engineering, University of Nottingham, Nottingham, United
Kingdom
| |
Collapse
|
4
|
Guang Z, Ledwig P, Costa PC, Filan C, Robles FE. Optimization of a flexible fiber-optic probe for epi-mode quantitative phase imaging. OPTICS EXPRESS 2022; 30:17713-17729. [PMID: 36221587 PMCID: PMC9363029 DOI: 10.1364/oe.454997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Quantitative oblique back-illumination microscopy (qOBM) is an emerging label-free optical imaging technology that enables 3D, tomographic quantitative phase imaging (QPI) with epi-illumination in thick scattering samples. In this work, we present a robust optimization of a flexible, fiber-optic-based qOBM system. Our approach enables in silico optimization of the phase signal-to-noise-ratio over a wide parameter space and obviates the need for tedious experimental optimization which could easily miss optimal conditions. Experimental validations of the simulations are also presented and sensitivity limits for the probe are assessed. The optimized probe is light-weight (∼40g) and compact (8mm in diameter) and achieves a 2µm lateral resolution, 6µm axial resolution, and a 300µm field of view, with near video-rate operation (10Hz, limited by the camera). The phase sensitivity is <20nm for a single qOBM acquisition (at 10Hz) and a lower limit of ∼3 nm via multi-frame averaging. Finally, to demonstrate the utility of the optimized probe, we image (1) thick, fixed rat brain samples from a 9L gliosarcoma tumor model and (2) freshly excised human brain tissues from neurosurgery. Acquired qOBM images using the flexible fiber-optic probe are in excellent agreement with those from a free-space qOBM system (both in-situ), as well as with gold-standard histopathology slices (after tissue processing).
Collapse
Affiliation(s)
- Zhe Guang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Patrick Ledwig
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Paloma Casteleiro Costa
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Caroline Filan
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Francisco E. Robles
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| |
Collapse
|
5
|
Capart A, Metwally K, Bastiancich C, Da Silva A. Multiphysical numerical study of photothermal therapy of glioblastoma with photoacoustic temperature monitoring in a mouse head. BIOMEDICAL OPTICS EXPRESS 2022; 13:1202-1223. [PMID: 35414964 PMCID: PMC8973158 DOI: 10.1364/boe.444193] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/02/2022] [Accepted: 01/03/2022] [Indexed: 05/02/2023]
Abstract
This paper presents a multiphysical numerical study of a photothermal therapy performed on a numerical phantom of a mouse head containing a glioblastoma. The study has been designed to be as realistic as possible. Heat diffusion simulations were performed on the phantom to understand the temperature evolution in the mouse head and therefore in the glioblastoma. The thermal dose has been calculated and lesions caused by heat are shown. The thermal damage on the tumor has also been quantified. To improve the effectiveness of the therapy, the photoabsorber's concentration was increased locally, at the tumor site, to mimic the effect of using absorbing contrast agents such as nanoparticles. Photoacoustic simulations were performed in order to monitor temperature in the phantom: as the Grüneisen parameter changes with the temperature, the photoacoustic signal undergoes changes that can be linked to temperature evolution. These photoacoustic simulations were performed at different instants during the therapy and the evolution of the photoacoustic signal as a function of the spatio-temporal distribution of the temperature in the phantom was observed and quantified. We have developed in this paper a numerical tool that can be used to help defining key parameters of a photothermal therapy.
Collapse
Affiliation(s)
- Antoine Capart
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
| | - Khaled Metwally
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
- Aix Marseille Univ, CNRS, Centrale Marseille, LMA, Marseille, France
| | - Chiara Bastiancich
- Institute Neurophysiopathol, INP, CNRS, Aix-Marseille University, 13005 Marseille, France
| | - Anabela Da Silva
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
| |
Collapse
|
6
|
Acharya AR, Vandekerckhove B, Larsen LE, Delbeke J, Wadman WJ, Vonck K, Carette E, Meurs A, Vanfleteren J, Boon P, Missinne J, Raedt R. In vivoblue light illumination for optogenetic inhibition: effect on local temperature and excitability of the rat hippocampus. J Neural Eng 2021; 18. [PMID: 34951406 DOI: 10.1088/1741-2552/ac3ef4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/01/2021] [Indexed: 11/12/2022]
Abstract
Objective.The blue light-activated inhibitory opsin, stGtACR2, is gaining prominence as a neuromodulatory tool due its ability to shunt-inhibit neurons and is being frequently used inin vivoexperimentation. However, experiments involving stGtACR2 use longer durations of blue light pulses, which inadvertently heat up the local brain tissue and confound experimental results. Therefore, the heating effects of illumination parameters used forin vivooptogenetic inhibition must be evaluated.Approach.To assess blue light (473 nm)-induced heating of the brain, we used a computational model as well as direct temperature measurements using a fiber Bragg grating (FBG). The effects of different light power densities (LPDs) and pulse durations on evoked potentials (EP) recorded from dentate gyrus were assessed. For opsin-negative rats, LPDs between 127 and 636 mW mm-2and pulse durations between 20 and 5120 ms were tested while for stGtACR2 expressing rats, LPD of 127 mW mm-2and pulse durations between 20 and 640 ms were tested.Main results.Increasing LPDs and pulse durations logarithmically increased the peak temperature and significantly decreased the population spike (PS) amplitude and latencies of EPs. For a pulse duration of 5120 ms, the tissue temperature increased by 0.6 °C-3.4 °C. All tested LPDs decreased the PS amplitude in opsin-negative rats, but 127 mW mm-2had comparatively minimal effects and a significant effect of increasing light pulse duration was seen from 320 ms and beyond. This corresponded with an average temperature increase of 0.2 °C-1.1 °C at the recorded site. Compared to opsin-negative rats, illumination in stGtACR2-expressing rats resulted in much greater inhibition of EPs.Significance.Our study demonstrates that light-induced heating of the brain can be accurately measuredin vivousing FBG sensors. Such light-induced heating alone can affect neuronal excitability. Useful neuromodulation by the activation of stGtACR2 is still possible while minimizing thermal effects.
Collapse
Affiliation(s)
- Anirudh R Acharya
- 4Brain Team, Department of Head and Skin, Ghent University, 9000 Ghent, Belgium
| | - Bram Vandekerckhove
- Center for Microsystems Technology, Imec and Ghent University, 9000 Ghent, Belgium
| | - Lars Emil Larsen
- 4Brain Team, Department of Head and Skin, Ghent University, 9000 Ghent, Belgium
| | - Jean Delbeke
- 4Brain Team, Department of Head and Skin, Ghent University, 9000 Ghent, Belgium
| | - Wytse J Wadman
- 4Brain Team, Department of Head and Skin, Ghent University, 9000 Ghent, Belgium
| | - Kristl Vonck
- 4Brain Team, Department of Head and Skin, Ghent University, 9000 Ghent, Belgium
| | - Evelien Carette
- 4Brain Team, Department of Head and Skin, Ghent University, 9000 Ghent, Belgium
| | - Alfred Meurs
- 4Brain Team, Department of Head and Skin, Ghent University, 9000 Ghent, Belgium
| | - Jan Vanfleteren
- Center for Microsystems Technology, Imec and Ghent University, 9000 Ghent, Belgium
| | - Paul Boon
- 4Brain Team, Department of Head and Skin, Ghent University, 9000 Ghent, Belgium
| | - Jeroen Missinne
- Center for Microsystems Technology, Imec and Ghent University, 9000 Ghent, Belgium
| | - Robrecht Raedt
- 4Brain Team, Department of Head and Skin, Ghent University, 9000 Ghent, Belgium
| |
Collapse
|
7
|
Affiliation(s)
- Hui Liu
- Shanxi Eye Hospital 100 Fudong St, Liu Xiang Shang Quan Xinghualing District, Taiyuan 030002, China
| | - Juan Cheng
- Shanxi Eye Hospital 100 Fudong St, Liu Xiang Shang Quan Xinghualing District, Taiyuan 030002, China
| |
Collapse
|
8
|
Karadas M, Olsson C, Winther Hansen N, Perrier JF, Webb JL, Huck A, Andersen UL, Thielscher A. In-vitro Recordings of Neural Magnetic Activity From the Auditory Brainstem Using Color Centers in Diamond: A Simulation Study. Front Neurosci 2021; 15:643614. [PMID: 34054404 PMCID: PMC8155532 DOI: 10.3389/fnins.2021.643614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Magnetometry based on nitrogen-vacancy (NV) centers in diamond is a novel technique capable of measuring magnetic fields with high sensitivity and high spatial resolution. With the further advancements of these sensors, they may open up novel approaches for the 2D imaging of neural signals in vitro. In the present study, we investigate the feasibility of NV-based imaging by numerically simulating the magnetic signal from the auditory pathway of a rodent brainstem slice (ventral cochlear nucleus, VCN, to the medial trapezoid body, MNTB) as stimulated by both electric and optic stimulation. The resulting signal from these two stimulation methods are evaluated and compared. A realistic pathway model was created based on published data of the neural morphologies and channel dynamics of the globular bushy cells in the VCN and their axonal projections to the principal cells in the MNTB. The pathway dynamics in response to optic and electric stimulation and the emitted magnetic fields were estimated using the cable equation. For simulating the optic stimulation, the light distribution in brain tissue was numerically estimated and used to model the optogenetic neural excitation based on a four state channelrhodopsin-2 (ChR2) model. The corresponding heating was also estimated, using the bio-heat equation and was found to be low (<2°C) even at excessively strong optic signals. A peak magnetic field strength of ∼0.5 and ∼0.1 nT was calculated from the auditory brainstem pathway after electrical and optical stimulation, respectively. By increasing the stimulating light intensity four-fold (far exceeding commonly used intensities) the peak magnetic signal strength only increased to 0.2 nT. Thus, while optogenetic stimulation would be favorable to avoid artefacts in the recordings, electric stimulation achieves higher peak fields. The present simulation study predicts that high-resolution magnetic imaging of the action potentials traveling along the auditory brainstem pathway will only be possible for next generation NV sensors. However, the existing sensors already have sufficient sensitivity to support the magnetic sensing of cumulated neural signals sampled from larger parts of the pathway, which might be a promising intermediate step toward further maturing this novel technology.
Collapse
Affiliation(s)
- Mürsel Karadas
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Christoffer Olsson
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nikolaj Winther Hansen
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jean-François Perrier
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - James Luke Webb
- Department of Physics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alexander Huck
- Department of Physics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ulrik Lund Andersen
- Department of Physics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Axel Thielscher
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| |
Collapse
|
9
|
Hao Y, Thomas AM, Li N. Fully autonomous mouse behavioral and optogenetic experiments in home-cage. eLife 2021; 10:e66112. [PMID: 33944781 PMCID: PMC8116056 DOI: 10.7554/elife.66112] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/02/2021] [Indexed: 01/19/2023] Open
Abstract
Goal-directed behaviors involve distributed brain networks. The small size of the mouse brain makes it amenable to manipulations of neural activity dispersed across brain areas, but existing optogenetic methods serially test a few brain regions at a time, which slows comprehensive mapping of distributed networks. Laborious operant conditioning training required for most experimental paradigms exacerbates this bottleneck. We present an autonomous workflow to survey the involvement of brain regions at scale during operant behaviors in mice. Naive mice living in a home-cage system learned voluntary head-fixation (>1 hr/day) and performed difficult decision-making tasks, including contingency reversals, for 2 months without human supervision. We incorporated an optogenetic approach to manipulate activity in deep brain regions through intact skull during home-cage behavior. To demonstrate the utility of this approach, we tested dozens of mice in parallel unsupervised optogenetic experiments, revealing multiple regions in cortex, striatum, and superior colliculus involved in tactile decision-making.
Collapse
Affiliation(s)
- Yaoyao Hao
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
| | | | - Nuo Li
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
| |
Collapse
|
10
|
Zárate RV, Arancibia D, Fernández A, Signorelli JR, Larrondo LF, Andrés ME, Zamorano P. Optimization of the Light-On system in a lentiviral platform to a light-controlled expression of genes in neurons. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
11
|
Vandekerckhove B, Missinne J, Vonck K, Bauwens P, Verplancke R, Boon P, Raedt R, Vanfleteren J. Technological Challenges in the Development of Optogenetic Closed-Loop Therapy Approaches in Epilepsy and Related Network Disorders of the Brain. MICROMACHINES 2020; 12:38. [PMID: 33396287 PMCID: PMC7824489 DOI: 10.3390/mi12010038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 12/25/2022]
Abstract
Epilepsy is a chronic, neurological disorder affecting millions of people every year. The current available pharmacological and surgical treatments are lacking in overall efficacy and cause side-effects like cognitive impairment, depression, tremor, abnormal liver and kidney function. In recent years, the application of optogenetic implants have shown promise to target aberrant neuronal circuits in epilepsy with the advantage of both high spatial and temporal resolution and high cell-specificity, a feature that could tackle both the efficacy and side-effect problems in epilepsy treatment. Optrodes consist of electrodes to record local field potentials and an optical component to modulate neurons via activation of opsin expressed by these neurons. The goal of optogenetics in epilepsy is to interrupt seizure activity in its earliest state, providing a so-called closed-loop therapeutic intervention. The chronic implantation in vivo poses specific demands for the engineering of therapeutic optrodes. Enzymatic degradation and glial encapsulation of implants may compromise long-term recording and sufficient illumination of the opsin-expressing neural tissue. Engineering efforts for optimal optrode design have to be directed towards limitation of the foreign body reaction by reducing the implant's elastic modulus and overall size, while still providing stable long-term recording and large-area illumination, and guaranteeing successful intracerebral implantation. This paper presents an overview of the challenges and recent advances in the field of electrode design, neural-tissue illumination, and neural-probe implantation, with the goal of identifying a suitable candidate to be incorporated in a therapeutic approach for long-term treatment of epilepsy patients.
Collapse
Affiliation(s)
- Bram Vandekerckhove
- Center for Microsystems Technology, Imec and Ghent University, 9000 Ghent, Belgium; (B.V.); (J.M.); (P.B.); (R.V.)
| | - Jeroen Missinne
- Center for Microsystems Technology, Imec and Ghent University, 9000 Ghent, Belgium; (B.V.); (J.M.); (P.B.); (R.V.)
| | - Kristl Vonck
- 4Brain Team, Department of Head and Skin, Ghent University, 9000 Ghent, Belgium; (K.V.); (P.B.); (R.R.)
| | - Pieter Bauwens
- Center for Microsystems Technology, Imec and Ghent University, 9000 Ghent, Belgium; (B.V.); (J.M.); (P.B.); (R.V.)
| | - Rik Verplancke
- Center for Microsystems Technology, Imec and Ghent University, 9000 Ghent, Belgium; (B.V.); (J.M.); (P.B.); (R.V.)
| | - Paul Boon
- 4Brain Team, Department of Head and Skin, Ghent University, 9000 Ghent, Belgium; (K.V.); (P.B.); (R.R.)
| | - Robrecht Raedt
- 4Brain Team, Department of Head and Skin, Ghent University, 9000 Ghent, Belgium; (K.V.); (P.B.); (R.R.)
| | - Jan Vanfleteren
- Center for Microsystems Technology, Imec and Ghent University, 9000 Ghent, Belgium; (B.V.); (J.M.); (P.B.); (R.V.)
| |
Collapse
|
12
|
Abstract
Widefield fluorescence microscopy is used to monitor the spiking of populations of neurons in the brain. Widefield fluorescence can originate from indicator molecules at all depths in cortex and the relative contributions from somata, dendrites, and axons are often unknown. Here, I simulate widefield illumination and fluorescence collection and determine the main sources of fluorescence for several GCaMP mouse lines. Scattering strongly affects illumination and collection. One consequence is that illumination intensity is greatest ~300-400 µm below the pia, not at the brain surface. Another is that fluorescence from a source deep in cortex may extend across a diameter of 3-4 mm at the brain surface, severely limiting lateral resolution. In many mouse lines, the volume of tissue contributing to fluorescence extends through the full depth of cortex and fluorescence at most surface locations is a weighted average across multiple cortical columns and often more than one cortical area.
Collapse
Affiliation(s)
- Jack Waters
- Allen Institute for Brain ScienceSeattleUnited States
| |
Collapse
|
13
|
Leino AA, Lunttila T, Mozumder M, Pulkkinen A, Tarvainen T. Perturbation Monte Carlo Method for Quantitative Photoacoustic Tomography. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:2985-2995. [PMID: 32217473 DOI: 10.1109/tmi.2020.2983129] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Quantitative photoacoustic tomography aims at estimating optical parameters from photoacoustic images that are formed utilizing the photoacoustic effect caused by the absorption of an externally introduced light pulse. This optical parameter estimation is an ill-posed inverse problem, and thus it is sensitive to measurement and modeling errors. In this work, we propose a novel way to solve the inverse problem of quantitative photoacoustic tomography based on the perturbation Monte Carlo method. Monte Carlo method for light propagation is a stochastic approach for simulating photon trajectories in a medium with scattering particles. It is widely accepted as an accurate method to simulate light propagation in tissues. Furthermore, it is numerically robust and easy to implement. Perturbation Monte Carlo maintains this robustness and enables forming gradients for the solution of the inverse problem. We validate the method and apply it in the framework of Bayesian inverse problems. The simulations show that the perturbation Monte Carlo method can be used to estimate spatial distributions of both absorption and scattering parameters simultaneously. These estimates are qualitatively good and quantitatively accurate also in parameter scales that are realistic for biological tissues.
Collapse
|
14
|
Wangpraseurt D, Jacques S, Lyndby N, Holm JB, Pages CF, Kühl M. Microscale light management and inherent optical properties of intact corals studied with optical coherence tomography. J R Soc Interface 2020; 16:20180567. [PMID: 30958182 DOI: 10.1098/rsif.2018.0567] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Coral reefs are highly productive photosynthetic systems and coral optics studies suggest that such high efficiency is due to optimized light scattering by coral tissue and skeleton. Here, we characterize the inherent optical properties, i.e. the scattering coefficient, μs, and the anisotropy of scattering, g, of eight intact coral species using optical coherence tomography (OCT). Specifically, we describe light scattering by coral skeletons, coenoarc tissues, polyp tentacles and areas covered by fluorescent pigments (FP). Our results reveal that light scattering between coral species ranges from μs = 3 mm-1 ( Stylophora pistillata) to μs = 25 mm-1 ( Echinopora lamelosa) . For Platygyra pini, μs was 10-fold higher for tissue versus skeleton, while in other corals (e.g. Hydnophora pilosa) no difference was found between tissue and skeletal scattering. Tissue scattering was threefold enhanced in coenosarc tissues ( μs = 24.6 mm-1) versus polyp tentacles ( μs = 8.3 mm-1) in Turbinaria reniformis. FP scattering was almost isotropic when FP were organized in granule chromatophores ( g = 0.34) but was forward directed when FP were distributed diffusely in the tissue ( g = 0.96). Our study provides detailed measurements of coral scattering and establishes a rapid approach for characterizing optical properties of photosynthetic soft tissues via OCT in vivo.
Collapse
Affiliation(s)
- Daniel Wangpraseurt
- 1 Marine Biological Section, Department of Biology, University of Copenhagen , Strandpromenaden 5, 3000 Helsingør , Denmark.,2 Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge , UK.,3 Scripps Institution of Oceanography, University of California , San Diego, CA , USA
| | - Steven Jacques
- 4 Department of Biomedical Engineering, Tufts University , Medford, MA , USA
| | - Niclas Lyndby
- 1 Marine Biological Section, Department of Biology, University of Copenhagen , Strandpromenaden 5, 3000 Helsingør , Denmark
| | - Jacob Boiesen Holm
- 1 Marine Biological Section, Department of Biology, University of Copenhagen , Strandpromenaden 5, 3000 Helsingør , Denmark
| | | | - Michael Kühl
- 1 Marine Biological Section, Department of Biology, University of Copenhagen , Strandpromenaden 5, 3000 Helsingør , Denmark.,6 Climate Change Cluster, University of Technology Sydney , Ultimo, New South Wales 2007 , Australia
| |
Collapse
|
15
|
Weidner TCS, Vincenz D, Brocka M, Tegtmeier J, Oelschlegel AM, Ohl FW, Goldschmidt J, Lippert MT. Matching stimulation paradigms resolve apparent differences between optogenetic and electrical VTA stimulation. Brain Stimul 2020; 13:363-371. [DOI: 10.1016/j.brs.2019.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/15/2019] [Accepted: 11/06/2019] [Indexed: 10/25/2022] Open
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Li N, Chen S, Guo ZV, Chen H, Huo Y, Inagaki HK, Chen G, Davis C, Hansel D, Guo C, Svoboda K. Spatiotemporal constraints on optogenetic inactivation in cortical circuits. eLife 2019; 8:e48622. [PMID: 31736463 PMCID: PMC6892606 DOI: 10.7554/elife.48622] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/16/2019] [Indexed: 12/21/2022] Open
Abstract
Optogenetics allows manipulations of genetically and spatially defined neuronal populations with excellent temporal control. However, neurons are coupled with other neurons over multiple length scales, and the effects of localized manipulations thus spread beyond the targeted neurons. We benchmarked several optogenetic methods to inactivate small regions of neocortex. Optogenetic excitation of GABAergic neurons produced more effective inactivation than light-gated ion pumps. Transgenic mice expressing the light-dependent chloride channel GtACR1 produced the most potent inactivation. Generally, inactivation spread substantially beyond the photostimulation light, caused by strong coupling between cortical neurons. Over some range of light intensity, optogenetic excitation of inhibitory neurons reduced activity in these neurons, together with pyramidal neurons, a signature of inhibition-stabilized neural networks ('paradoxical effect'). The offset of optogenetic inactivation was followed by rebound excitation in a light dose-dependent manner, limiting temporal resolution. Our data offer guidance for the design of in vivo optogenetics experiments.
Collapse
Affiliation(s)
- Nuo Li
- Department of NeuroscienceBaylor College of MedicineHoustonUnited States
- Janelia Research CampusAshburnUnited States
| | - Susu Chen
- Janelia Research CampusAshburnUnited States
| | - Zengcai V Guo
- Janelia Research CampusAshburnUnited States
- School of MedicineTsinghua UniversityBeijingChina
| | - Han Chen
- School of MedicineTsinghua UniversityBeijingChina
| | - Yan Huo
- School of MedicineTsinghua UniversityBeijingChina
| | | | - Guang Chen
- Department of NeuroscienceBaylor College of MedicineHoustonUnited States
| | - Courtney Davis
- Department of NeuroscienceBaylor College of MedicineHoustonUnited States
- Janelia Research CampusAshburnUnited States
| | - David Hansel
- Center of Neurophysics, Physiology and Pathologies, CNRS-UMR8119ParisFrance
| | | | | |
Collapse
|
18
|
Ingusci S, Verlengia G, Soukupova M, Zucchini S, Simonato M. Gene Therapy Tools for Brain Diseases. Front Pharmacol 2019; 10:724. [PMID: 31312139 PMCID: PMC6613496 DOI: 10.3389/fphar.2019.00724] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 06/05/2019] [Indexed: 01/20/2023] Open
Abstract
Neurological disorders affecting the central nervous system (CNS) are still incompletely understood. Many of these disorders lack a cure and are seeking more specific and effective treatments. In fact, in spite of advancements in knowledge of the CNS function, the treatment of neurological disorders with modern medical and surgical approaches remains difficult for many reasons, such as the complexity of the CNS, the limited regenerative capacity of the tissue, and the difficulty in conveying conventional drugs to the organ due to the blood-brain barrier. Gene therapy, allowing the delivery of genetic materials that encodes potential therapeutic molecules, represents an attractive option. Gene therapy can result in a stable or inducible expression of transgene(s), and can allow a nearly specific expression in target cells. In this review, we will discuss the most commonly used tools for the delivery of genetic material in the CNS, including viral and non-viral vectors; their main applications; their advantages and disadvantages. We will discuss mechanisms of genetic regulation through cell-specific and inducible promoters, which allow to express gene products only in specific cells and to control their transcriptional activation. In addition, we will describe the applications to CNS diseases of post-transcriptional regulation systems (RNA interference); of systems allowing spatial or temporal control of expression [optogenetics and Designer Receptors Exclusively Activated by Designer Drugs (DREADDs)]; and of gene editing technologies (CRISPR/Cas9, Zinc finger proteins). Particular attention will be reserved to viral vectors derived from herpes simplex type 1, a potential tool for the delivery and expression of multiple transgene cassettes simultaneously.
Collapse
Affiliation(s)
- Selene Ingusci
- Department of Medical Sciences and National Institute of Neuroscience, University of Ferrara, Ferrara, Italy
| | - Gianluca Verlengia
- Department of Medical Sciences and National Institute of Neuroscience, University of Ferrara, Ferrara, Italy.,Division of Neuroscience, University Vita-Salute San Raffaele, Milan, Italy
| | - Marie Soukupova
- Department of Medical Sciences and National Institute of Neuroscience, University of Ferrara, Ferrara, Italy
| | - Silvia Zucchini
- Department of Medical Sciences and National Institute of Neuroscience, University of Ferrara, Ferrara, Italy.,Technopole of Ferrara, LTTA Laboratory for Advanced Therapies, Ferrara, Italy
| | - Michele Simonato
- Department of Medical Sciences and National Institute of Neuroscience, University of Ferrara, Ferrara, Italy.,Division of Neuroscience, University Vita-Salute San Raffaele, Milan, Italy
| |
Collapse
|
19
|
Marti D, Aasbjerg RN, Andersen PE, Hansen AK. MCmatlab: an open-source, user-friendly, MATLAB-integrated three-dimensional Monte Carlo light transport solver with heat diffusion and tissue damage. JOURNAL OF BIOMEDICAL OPTICS 2018; 23:1-6. [PMID: 30554503 DOI: 10.1117/1.jbo.23.12.121622] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/20/2018] [Indexed: 05/18/2023]
Abstract
While there exist many Monte Carlo (MC) programs for solving the radiative transfer equation (RTE) in biological tissues, we have identified a need for an open-source MC program that is sufficiently user-friendly for use in an education environment, in which detailed knowledge of compiling or UNIX command-line cannot be assumed. Therefore, we introduce MCmatlab, an open-source codebase thus far consisting of (a) a fast three-dimensional MC RTE solver and (b) a finite-element heat diffusion and Arrhenius-based thermal tissue damage simulator, both run in MATLAB. The kernel for both of these solvers is written in parallelized C and implemented as MATLAB MEX functions, combining the speed of C with the familiarity and versatility of MATLAB. We compare the RTE solver to Steven Jacques' mcxyz, which it is inspired by, and present example results generated by the thermal model. MCmatlab is easy to install and use and can be used by students and experienced researchers alike for simulating tissue light propagation and, optionally, thermal damage.
Collapse
Affiliation(s)
- Dominik Marti
- Technical University of Denmark, Department of Photonics Engineering, Roskilde, Denmark
| | - Rikke N Aasbjerg
- Technical University of Denmark, Department of Photonics Engineering, Roskilde, Denmark
| | - Peter E Andersen
- Technical University of Denmark, Department of Photonics Engineering, Roskilde, Denmark
| | - Anders K Hansen
- Technical University of Denmark, Department of Photonics Engineering, Roskilde, Denmark
| |
Collapse
|
20
|
Dubois A, Chiang CC, Smekens F, Jan S, Cuplov V, Palfi S, Chuang KS, Senova S, Pain F. Optical and thermal simulations for the design of optodes for minimally invasive optogenetics stimulation or photomodulation of deep and large cortical areas in non-human primate brain. J Neural Eng 2018; 15:065004. [PMID: 30190446 DOI: 10.1088/1741-2552/aadf97] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The use of optogenetics or photobiomodulation in non-human primate (NHP) requires the ability to noninvasively stimulate large and deep cortical brain tissues volumes. In this context, the optical and geometrical parameters of optodes are critical. Methods and general guidelines to optimize these parameters have to be defined. OBJECTIVE We propose the design of an optode for safe and efficient optical stimulation of a large volume of NHP cortex, down to 3-5 mm depths without inserting fibers into the cortex. APPROACH Monte Carlo simulations of optical and thermal transport have been carried out using the Geant4 application for tomographic emission (GATE) platform. Parameters such as the fiber diameter, numerical aperture, number of fibers and their geometrical arrangement have been studied. Optimal hardware parameters are proposed to obtain homogeneous fluence above the fluence threshold for opsin activation without detrimental thermal effects. MAIN RESULTS The simulations show that a large fiber diameter and a large numerical aperture are preferable since they allow limiting power concentration and hence the resulting thermal increases at the brain surface. To obtain a volume of 200-500 mm3 of brain tissues receiving a fluence above the opsin activation threshold for optogenetics or below a phototocixity threshold for photobiomodulation, a 4 fibers configuration is proposed. The optimal distance between the fibers was found to be 4 mm. A practical implementation of the optode has been performed and the corresponding fluence and thermal maps have been simulated. SIGNIFICANCE The present study defines a method to optimize the design of optode and the choice of stimulation parameters for optogenetics and more generally light delivery to deep and large volumes of tissues in NHP brain with a controlled irradiance dosimetry. The general guidelines are the use of silica fibers with a large numerical aperture and a large diameter. The combination of several fibers is required if large volumes need to be stimulated while avoiding thermal effects.
Collapse
Affiliation(s)
- A Dubois
- IMNC, CNRS, Université Paris-Sud, Université Paris Saclay, Orsay F-91405, France
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
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]
|
22
|
Boros ÖC, Horváth ÁC, Beleznai S, Sepsi Ö, Lenk S, Fekete Z, Koppa P. Optical and thermal modeling of an optrode microdevice for infrared neural stimulation. APPLIED OPTICS 2018; 57:6952-6957. [PMID: 30129582 DOI: 10.1364/ao.57.006952] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/16/2018] [Indexed: 06/08/2023]
Abstract
Infrared neural stimulation is a promising medical technique using pulsed infrared light for generating temperature-controlled firing of neurons. A combined optical and thermal model of a stimulating microtool-or so-called optrode-has been developed to investigate the amount, the spatial distribution, and the temporal behavior of the thermal excitation. Ray tracing and Fourier optics were used to describe the propagation and scattering of light in the optrode, and the finite element method was applied to model heat transfer. The scattered intensity distribution profiles were calculated based on measured surface roughness of the device and were integrated into the ray optics model. As a validation of the optical model, the simulated and measured values of the light efficiency of the microoptical system are compared. The temperature rise of the brain tissue during the infrared stimulation was estimated using the combined model. Using 30 mW total power and a single 100 ms pulse, the excitation resulted in a temperature rise of 3°C of the brain tissue. The spatial and temporal distributions of the tissue temperature are discussed in the paper. The proposed combined model is an efficient tool for the investigation and optimization of the stimulation process and for further development of the optrode configuration.
Collapse
|
23
|
Shuaib A, Bourisly AK. Photobiomodulation Optimization for Spinal Cord Injury Rat Phantom Model. Transl Neurosci 2018; 9:67-71. [PMID: 29967691 PMCID: PMC6024694 DOI: 10.1515/tnsci-2018-0012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/24/2018] [Indexed: 12/20/2022] Open
Abstract
Spinal Cord Injury (SCI) causes interruption along the severed axonal tract(s) resulting in complete or partial loss of sensation and motor function. SCI can cause tetraplegia or paraplegia. Both these conditions can have lifelong excessive medical costs, as well as can reduce life expectancy. Preclinical research showed that Photobiomodulation therapy (PBMT), also known as Low-level laser (light) therapy (LLLT), possesses reparative and regenerative capabilities that have the potential to be used as a complimentary or supplementary SCI therapy. Despite the promising effects of PBMT, there are still no standardized irradiation parameters (i.e. different wavelengths, power, fluence, irradiance, beam type, beam diameters, and irradiation time) and there is also a lack of standardized experimental protocol(s), which makes it difficult to compare different studies. It is, nonetheless, essential to standardize such irradiation parameters in order to provide better PBMTs. The aim of this study, therefore, is to evaluate the delivery of light in a 3D voxelated SCI rat model for PBMT using different irradiation parameters (wavelengths: 660, 810, and 980 nm; beam types: Gaussian and Flat beam; and beam diameters: 0.04-1.2 cm) using Monte Carlo simulation. This study also aids in providing standardization for preclinical research for PBMT, which will eventually translate into clinical standardization upon clinical research studies and results.
Collapse
Affiliation(s)
- Ali Shuaib
- Biomedical Engineering Unit, Department of Physiology, Faculty of Medicine, Kuwait University, Kuwait city, Kuwait
| | - Ali K Bourisly
- Biomedical Engineering Unit, Department of Physiology, Faculty of Medicine, Kuwait University, Kuwait city, Kuwait
| |
Collapse
|
24
|
Wiegert JS, Mahn M, Prigge M, Printz Y, Yizhar O. Silencing Neurons: Tools, Applications, and Experimental Constraints. Neuron 2017; 95:504-529. [PMID: 28772120 DOI: 10.1016/j.neuron.2017.06.050] [Citation(s) in RCA: 173] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 12/16/2022]
Abstract
Reversible silencing of neuronal activity is a powerful approach for isolating the roles of specific neuronal populations in circuit dynamics and behavior. In contrast with neuronal excitation, for which the majority of studies have used a limited number of optogenetic and chemogenetic tools, the number of genetically encoded tools used for inhibition of neuronal activity has vastly expanded. Silencing strategies vary widely in their mechanism of action and in their spatial and temporal scales. Although such manipulations are commonly applied, the design and interpretation of neuronal silencing experiments present unique challenges, both technically and conceptually. Here, we review the most commonly used tools for silencing neuronal activity and provide an in-depth analysis of their mechanism of action and utility for particular experimental applications. We further discuss the considerations that need to be given to experimental design, analysis, and interpretation of collected data. Finally, we discuss future directions for the development of new silencing approaches in neuroscience.
Collapse
Affiliation(s)
- J Simon Wiegert
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, Falkenried 94, 20251 Hamburg, Germany
| | - Mathias Mahn
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Matthias Prigge
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoav Printz
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ofer Yizhar
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|
25
|
Periyasamy V, Pramanik M. Advances in Monte Carlo Simulation for Light Propagation in Tissue. IEEE Rev Biomed Eng 2017; 10:122-135. [PMID: 28816674 DOI: 10.1109/rbme.2017.2739801] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Monte Carlo (MC) simulation for light propagation in tissue is the gold standard for studying the light propagation in biological tissue and has been used for years. Interaction of photons with a medium is simulated based on its optical properties. New simulation geometries, tissue-light interaction methods, and recording techniques recently have been designed. Applications, such as whole mouse body simulations for fluorescence imaging, eye modeling for blood vessel imaging, skin modeling for terahertz imaging, and human head modeling for sinus imaging, have emerged. Here, we review the technical advances and recent applications of MC simulation.
Collapse
|
26
|
Simmons ZJ, Rogers JD. Microscope objective based 4 π spectroscopic tissue scattering goniometry. BIOMEDICAL OPTICS EXPRESS 2017; 8:3828-3841. [PMID: 28856053 PMCID: PMC5560844 DOI: 10.1364/boe.8.003828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 07/12/2017] [Indexed: 06/07/2023]
Abstract
The measurement of optical scattering as a function of angle, goniometry, can provide a wealth of information about tissue. The goniometry technique described here measures the intensity profile at the pupil planes of two microscope objectives with a scattering sample between them. The maximum observable scattering angle is extended by employing off-axis illumination. This configuration permits several advantages including: i) rapid measurement of scattering into 4π sr to characterize the entire scattering phase function in isotropic tissue, ii) sensitivity to axially asymmetric scattering from anisotropic fibrous tissue, iii) selective interrogation of small regions within spatially inhomogenous tissue, iv) concurrent measurement of scattering coefficient μs , and v) measurement of wavelength dependent scattering properties via spectrally tunable source. The instrument is validated by comparing measurements of microsphere suspensions to the Mie scattering solution. Instrument capabilities are demonstrated with samples of rat brain and mouse eye tissues.
Collapse
Affiliation(s)
- Z. J. Simmons
- Department of Biomedical Engineering, University of Wisconsin–Madison, 1550 Engineering Drive, Madison, WI 53706,
USA
- McPherson Eye Research Institute, University of Wisconsin–Madison, 1111 Highland Avenue, WIMR 9433, Madison, WI 53705,
USA
| | - J. D. Rogers
- Department of Biomedical Engineering, University of Wisconsin–Madison, 1550 Engineering Drive, Madison, WI 53706,
USA
- McPherson Eye Research Institute, University of Wisconsin–Madison, 1111 Highland Avenue, WIMR 9433, Madison, WI 53705,
USA
| |
Collapse
|
27
|
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: 38] [Impact Index Per Article: 5.4] [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.
Collapse
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
| |
Collapse
|
28
|
Nikolic K, Evans BD, Andras P, Yakovlev A, Degenaar P. Optogenetics in Silicon: A Neural Processor for Predicting Optically Active Neural Networks. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2017; 11:15-27. [PMID: 28113518 DOI: 10.1109/tbcas.2016.2571339] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We present a reconfigurable neural processor for real-time simulation and prediction of opto-neural behaviour. We combined a detailed Hodgkin-Huxley CA3 neuron integrated with a four-state Channelrhodopsin-2 (ChR2) model into reconfigurable silicon hardware. Our architecture consists of a Field Programmable Gated Array (FPGA) with a custom-built computing data-path, a separate data management system and a memory approach based router. Advancements over previous work include the incorporation of short and long-term calcium and light-dependent ion channels in reconfigurable hardware. Also, the developed processor is computationally efficient, requiring only 0.03 ms processing time per sub-frame for a single neuron and 9.7 ms for a fully connected network of 500 neurons with a given FPGA frequency of 56.7 MHz. It can therefore be utilized for exploration of closed loop processing and tuning of biologically realistic optogenetic circuitry.
Collapse
|
29
|
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.
Collapse
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:
| |
Collapse
|
30
|
Song Y, Garcia S, Frometa Y, Ramella-Roman JC, Soltani M, Almadi M, Riera JJ, Lin WC. Quantitative assessment of hemodynamic and structural characteristics of in vivo brain tissue using total diffuse reflectance spectrum measured in a non-contact fashion. BIOMEDICAL OPTICS EXPRESS 2017; 8:78-103. [PMID: 28101403 PMCID: PMC5231317 DOI: 10.1364/boe.8.000078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/03/2016] [Accepted: 11/08/2016] [Indexed: 05/03/2023]
Abstract
Here we present a new methodology that investigates the intrinsic structural and hemodynamic characteristics of in vivo brain tissue, in a non-contact fashion, and can be easily incorporated in an intra-operative environment. Within this methodology, relative total diffuse reflectance spectra (RTD(λ)) were acquired from targets using a hybrid spectroscopy imaging system. A spectral interpretation algorithm was subsequently applied to RTD(λ) to retrieve optical properties related to the compositional and structural characteristics of each target. Estimation errors of the proposed methodology were computationally evaluated using a Monte Carlo simulation model for photon migration under various conditions. It was discovered that this new methodology could handle moderate noise and achieve very high accuracy, but only if the refractive index of the target is known. The accuracy of the technique was also validated using a series of tissue phantom studies, and consistent and accurate estimates of μs'(λ)/μa(λ) were obtained from all the phantoms tested. Finally, a small-scale animal study was conducted to demonstrate the clinical utility of the reported method, wherein a forepaw stimulation model was utilized to induce transient hemodynamic responses in somatosensory cortices. With this approach, significant stimulation-related changes (p < 0.001) in cortical hemodynamic and structural characteristics were successfully measured.
Collapse
|
31
|
Shin Y, Yoo M, Kim HS, Nam SK, Kim HI, Lee SK, Kim S, Kwon HS. Characterization of fiber-optic light delivery and light-induced temperature changes in a rodent brain for precise optogenetic neuromodulation. BIOMEDICAL OPTICS EXPRESS 2016; 7:4450-4471. [PMID: 27895987 PMCID: PMC5119587 DOI: 10.1364/boe.7.004450] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/04/2016] [Accepted: 10/04/2016] [Indexed: 06/06/2023]
Abstract
Understanding light intensity and temperature increase is of considerable importance in designing or performing in vivo optogenetic experiments. Our study describes the optimal light power at target depth in the rodent brain that would maximize activation of light-gated ion channels while minimizing temperature increase. Monte Carlo (MC) simulations of light delivery were used to provide a guideline for suitable light power at a target depth. In addition, MC simulations with the Pennes bio-heat model using data obtained from measurements with a temperature-measuring cannula having 12.3 mV/°C of thermoelectric sensitivity enabled us to predict tissue heating of 0.116 °C/mW on average at target depth of 563 μm and specifically, a maximum mean plateau temperature increase of 0.25 °C/mW at 100 μm depth for 473 nm light. Our study will help to improve the design and performance of optogenetic experiments while avoiding potential over- and under-illumination.
Collapse
Affiliation(s)
- Younghoon Shin
- Department of Biomedical Science and Engineering, and Gwangju Institute of Science and Technology (GIST), 123 Cheomdan-Gwagiro, Buk-Gu, Gwangju 61005, South Korea
| | - Minsu Yoo
- Graduate Program in Computational Neuroscience, University of Chicago, Chicago, Illinois 60637, USA
| | - Hyung-Sun Kim
- Korea Institute of Toxicology (KIT), 141 Gajeong-Ro, Yuseong-Gu, Daejon 34114, South Korea
| | - Sung-Ki Nam
- Department of Mechanical Engineering, Gwangju Institute of Science and Technology (GIST), 123 Cheomdan-Gwagiro, Buk-Gu, Gwangju 61005, South Korea
| | - Hyoung-Ihl Kim
- Department of Biomedical Science and Engineering, and Gwangju Institute of Science and Technology (GIST), 123 Cheomdan-Gwagiro, Buk-Gu, Gwangju 61005, South Korea
| | - Sun-Kyu Lee
- Department of Mechanical Engineering, Gwangju Institute of Science and Technology (GIST), 123 Cheomdan-Gwagiro, Buk-Gu, Gwangju 61005, South Korea
| | - Sohee Kim
- Department of Robotics Engineering, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, South Korea
| | - Hyuk-Sang Kwon
- Department of Biomedical Science and Engineering, and Gwangju Institute of Science and Technology (GIST), 123 Cheomdan-Gwagiro, Buk-Gu, Gwangju 61005, South Korea
- Department of Mechanical Engineering, Gwangju Institute of Science and Technology (GIST), 123 Cheomdan-Gwagiro, Buk-Gu, Gwangju 61005, South Korea
| |
Collapse
|
32
|
Park DW, Brodnick SK, Ness JP, Atry F, Krugner-Higby L, Sandberg A, Mikael S, Richner TJ, Novello J, Kim H, Baek DH, Bong J, Frye ST, Thongpang S, Swanson KI, Lake W, Pashaie R, Williams JC, Ma Z. Fabrication and utility of a transparent graphene neural electrode array for electrophysiology, in vivo imaging, and optogenetics. Nat Protoc 2016; 11:2201-2222. [DOI: 10.1038/nprot.2016.127] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/19/2016] [Indexed: 11/09/2022]
|
33
|
Evans BD, Jarvis S, Schultz SR, Nikolic K. PyRhO: A Multiscale Optogenetics Simulation Platform. Front Neuroinform 2016; 10:8. [PMID: 27148037 PMCID: PMC4834562 DOI: 10.3389/fninf.2016.00008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 02/19/2016] [Indexed: 01/07/2023] Open
Abstract
Optogenetics has become a key tool for understanding the function of neural circuits and controlling their behavior. An array of directly light driven opsins have been genetically isolated from several families of organisms, with a wide range of temporal and spectral properties. In order to characterize, understand and apply these opsins, we present an integrated suite of open-source, multi-scale computational tools called PyRhO. The purpose of developing PyRhO is three-fold: (i) to characterize new (and existing) opsins by automatically fitting a minimal set of experimental data to three-, four-, or six-state kinetic models, (ii) to simulate these models at the channel, neuron and network levels, and (iii) provide functional insights through model selection and virtual experiments in silico. The module is written in Python with an additional IPython/Jupyter notebook based GUI, allowing models to be fit, simulations to be run and results to be shared through simply interacting with a webpage. The seamless integration of model fitting algorithms with simulation environments (including NEURON and Brian2) for these virtual opsins will enable neuroscientists to gain a comprehensive understanding of their behavior and rapidly identify the most suitable variant for application in a particular biological system. This process may thereby guide not only experimental design and opsin choice but also alterations of the opsin genetic code in a neuro-engineering feed-back loop. In this way, we expect PyRhO will help to significantly advance optogenetics as a tool for transforming biological sciences.
Collapse
Affiliation(s)
- Benjamin D Evans
- Centre for Bio-Inspired Technology, Institute of Biomedical Engineering, Department of Electrical and Electronic Engineering, Imperial College London London, UK
| | - Sarah Jarvis
- Centre for Neurotechnology, Institute of Biomedical Engineering, Department of Bioengineering, Imperial College London London, UK
| | - Simon R Schultz
- Centre for Neurotechnology, Institute of Biomedical Engineering, Department of Bioengineering, Imperial College London London, UK
| | - Konstantin Nikolic
- Centre for Bio-Inspired Technology, Institute of Biomedical Engineering, Department of Electrical and Electronic Engineering, Imperial College London London, UK
| |
Collapse
|
34
|
Glaser AK, Chen Y, Liu JT. Fractal propagation method enables realistic optical microscopy simulations in biological tissues. OPTICA 2016; 3:861-869. [PMID: 28983499 PMCID: PMC5626453 DOI: 10.1364/optica.3.000861] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Current simulation methods for light transport in biological media have limited efficiency and realism when applied to three-dimensional microscopic light transport in biological tissues with refractive heterogeneities. We describe here a technique which combines a beam propagation method valid for modeling light transport in media with weak variations in refractive index, with a fractal model of refractive index turbulence. In contrast to standard simulation methods, this fractal propagation method (FPM) is able to accurately and efficiently simulate the diffraction effects of focused beams, as well as the microscopic heterogeneities present in tissue that result in scattering, refractive beam steering, and the aberration of beam foci. We validate the technique and the relationship between the FPM model parameters and conventional optical parameters used to describe tissues, and also demonstrate the method's flexibility and robustness by examining the steering and distortion of Gaussian and Bessel beams in tissue with comparison to experimental data. We show that the FPM has utility for the accurate investigation and optimization of optical microscopy methods such as light-sheet, confocal, and nonlinear microscopy.
Collapse
Affiliation(s)
- Adam K. Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Corresponding author:
| | - Ye Chen
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Jonathan T.C. Liu
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| |
Collapse
|