All-Optical Methods to Study Neuronal Function

Preface to the Series
Preface
Contents
Contributors
Chapter 1: Optical Manipulation and Recording of Neural Activity with Wavefront Engineering
1 Introduction
2 State-of-the-art Technologies for All-Optical Neurophysiology
2.1 Photophysical Properties of Common Molecular Tools Used for All-Optical Neurophysiology
2.2 Combining Molecular Tools for All-Optical Neurophysiology Experiments
2.2.1 Expressing Molecular Tools in Specific Populations of Neurons for All-Optical Neurophysiology Experiments
2.3 State-of-the-art Two-Photon Excitation Approaches for All-Optical Neurophysiology
3 Implementation of Methods
3.1 Laser Sources
3.2 Beam Shaping with Generalized Phase Contrast
3.3 Implementing Temporal Focusing
3.4 Preparation of Organotypic Hippocampal Slice Cultures
3.4.1 Solutions
3.4.2 Equipment
3.4.3 Bulk Infection
3.4.4 Troubleshooting
3.4.5 What Is Essential on the Day of Experiment?
4 Notes
5 Outlook
References
Chapter 2: Balancing the Fluorescence Imaging Budget for All-Optical Neurophysiology Experiments
1 Introduction
2 Key Challenges to Imaging Neuronal Activity
2.1 Challenge 1: Brains Are Three-Dimensional
2.2 Challenge 2: (Most) Brains Scatter Light
3 Signal-to-Noise Ratio Is King: Fluorescence Budget
4 Choosing a Fluorescent Indicator
4.1 Temporal Considerations
4.2 Membrane Potential vs. Calcium
4.3 Spectral Considerations
4.4 Fluorophore Spatial Distribution
5 SNR and Imaging Modality
5.1 Fluorescence Excitation
5.1.1 Fluorescence Excitation Volume, VFl
5.1.2 Fluorescence Integration Time, Δt
5.2 Fluorescence Detection
5.2.1 Single-Channel Detectors
5.2.2 Multi-channel Detectors
6 Summary of Key Points
7 Notes
References
Chapter 3: Light-Based Neuronal Circuit Probing in Living Brains at High Resolution: Constraints and Layouts for Integrating N...
1 Introduction
2 Methods
2.1 Molecular and Technical Constraints
2.2 Absorption Characteristics and Its Impact
2.3 Photocurrent Integration and Spurious Opsin Activation
2.4 Off-Target Activation and Somatic Opsin Targeting
3 Hardware Implementations for 3D Recordings of Neuronal Activity
3.1 Remote Configurations for 3D Beam Scanning
3.2 Methods for Scanning the Sample Along the Lateral Dimension
3.3 Methods for Scanning the Sample Along the Longitudinal Dimension
4 Hardware Implementations for 3D Modulation of Neuronal Activity
4.1 The General Features of a Photostimulation Train
4.2 Sequential 3D Photostimulation
4.3 Parallel 3D Photostimulation
5 Setting Up an All-Optical 3D Investigation System
5.1 The Hardware Integration
5.2 Beam Co-registration Procedures
5.3 Spatial Uniformity and Addressable Field of View
6 Notes
7 Conclusions
References
Chapter 4: High-Speed All-Optical Neural Interfaces with 3D Temporally Focused Holography
1 Introduction
2 Methods
2.1 3D-SHOT Optical System Design
2.1.1 3D-SHOT Design Parameters
2.1.2 Implementation Guidelines for 3D-SHOT
2.2 Characterization and Performance Metrics for 3D-SHOT
2.2.1 Scanless 2P Optogenetics Using 3D-SHOT
2.2.2 3D-SHOT Photostimulation with Single-Neuron Resolution
2.2.3 Spatially Precise Remote Control with 3D-SHOT
2.2.4 Volumetric Optogenetics at High Spatial Resolution
2.3 Calibration of 3D-SHOT with Imaging System
2.4 Comparison of Opsins for Precise Activation of Activity
3 Conclusion
References
Chapter 5: An All-Optical Physiology Pipeline Toward Highly Specific and Artifact-Free Circuit Mapping
1 Introduction
2 Experimental Framework
3 Technical Framework for Functional Neuronal Circuit Mapping
4 Somatic Calcium Influx as Correlate of Suprathreshold Neuronal Activity
4.1 Two-photon Raster Scanning
4.2 One-photon Miniature Microscope Full-Field Imaging via GRIN Lens
5 The Principles of Optogenetic Manipulation Methods in a Nutshell
5.1 One-photon Raster Scan Opsin Excitation
5.2 Two-photon Raster Scan Opsin Excitation
5.3 Two-photon Scanless Opsin Excitation via CGH
5.4 One-photon Miniature Microscopes with GRIN Lenses
6 Everything You Always Wanted to Know About All-Optical Data Processing But Were Afraid to Ask
6.1 Roadmap for Processing All-Optical Data
6.1.1 System Integration
6.1.2 Image Data Acquisition
6.1.3 Segmentation
6.1.4 Trace Extraction
6.1.5 Artifact Removal
6.1.6 Event-Related Binarization
6.1.7 Connectivity Analysis
6.2 Toward Cross-Talk-Free Experimental Designs
6.2.1 Assessing the Impact of Continuous Illumination for Calcium Imaging on Opsin Excitation
6.2.2 Increasing the Spectral Separation Between Opsin and Indicator to Minimize Optogenetic Stimulation Artifacts on the Imag...
7 Outlook
8 Notes
References
Chapter 6: Spatial and Temporal Considerations of Optogenetic Tools in an All-Optical Single-Beam Experiment
1 Introduction
1.1 Optogenetic Tools for All-Optical Experiments
2 All-Optical Single-Beam Experiments
3 Temporal Considerations of Actuator Kinetics in Single-Beam All-Optical Experiments
4 Spatial Consideration of Optogenetic Tools in a Single-Beam All-Optical Experiment
Note 1: Beyond Temporal and Spatial Constraints: Ion Permeability
Note 2: Beyond Temporal and Spatial Constraints: Spectral Consideration
5 Summary
References
Chapter 7: Miniature Multiphoton Microscopes for Recording Neural Activity in Freely Moving Animals
1 Introduction
2 Background
2.1 Optical Design Considerations for Miniature 2P Microscopes
2.2 Optical Design Considerations for Axial Scanning with a Tunable Lens
2.3 Cranial Windows
2.4 Gradient-Refractive Index (GRIN) Lenses
2.5 Fiber-Coupling of Excitation Laser
2.6 Coherent Imaging Fiber Bundles (CIFB)
2.7 Ultrafast Laser-Pulse Propagation Through Fiber
2.8 Tunable Focus by Liquid Lens Technology
3 Methods
3.1 Overall System Design
3.1.1 Laser-Source
3.1.2 Spectral and Temporal Pulse Pre-compensation
3.1.3 2P-LSM Bench-Top System
3.1.4 2P-FCM Miniature Optical System Design
3.1.5 3D-Printed Miniature Head-Mount Design
3.2 Test Sample Preparation
3.3 Mouse Imaging Setup
3.4 Image Processing
3.5 Testing and Calibration of Resolution, Magnification, and Axial Scan Range
4 Discussion
4.1 2P-FCM Imaging Capabilities
4.1.1 3D Imaging
4.1.2 Tilted-Field Imaging
4.1.3 Multi-Color Imaging
4.2 2P-FCM Imaging In Vivo
4.2.1 2P-FCM In Vivo Mouse Imaging Through Cranial Window
4.2.2 2P-FCM In Vivo Mouse Imaging in Deep Brain Regions Through GRIN Lens
5 Materials
6 Notes
6.1 Optimizing Alignment into Single Mode Fiber
6.2 Setup and Alignment of the Grating Pair Compressor
6.3 Optimizing Imaging Through Coherent Fiber Bundle
6.4 Installing the Pedestal for the 2P-FCM on the Cranium
7 Conclusions
References
Untitled
Chapter 8: Optogenetics and Light-Sheet Microscopy
1 Imaging Translucent Organisms
1.1 Light-Sheet Technologies
1.1.1 Light-Sheet Configurations
1.1.2 Engineering Illumination Improves Resolution and Photodamage
1.2 Design Choices
1.2.1 Prioritize Scale, Resolution, or Speed
1.2.2 Type of Photostimulation
1.2.3 One Photon or Two?
2 Materials
2.1 Light-Sheet Module
2.2 2P-CGH Module
2.3 Sample Preparation
3 Methods
3.1 Microscope Alignment
3.1.1 Align the Light-Sheet Module
3.1.2 Align the 2P-CGH Module
3.1.3 Registration Between Light-Sheet Module and 2P-CGH Module
3.2 Workflow of Light-Sheet Optogenetics Experiment
3.2.1 Imaging Larval Zebrafish
3.2.2 Analysis of Large-Scale Ca2+ Data Set
3.3 Choice of CGH Algorithm
3.4 Effect of Aberrations on CGH
4 Summary
5 Notes
References
Chapter 9: Widefield Multiphoton Imaging at Depth with Temporal Focusing
1 Introduction
2 Methods
2.1 Temporal Focusing
2.2 Single-Pixel Detection
2.2.1 Compressive Sensing
2.3 TRAFIX
2.3.1 Setup
2.3.2 Imaging
2.3.3 Hybrid Demixing
3 Future Prospects
4 Summary
5 Notes
References
Chapter 10: High-Speed Neural Imaging with Synaptic Resolution: Bessel Focus Scanning Two-Photon Microscopy and Optical-Sectio...
1 Introduction
2 Bessel Focus Scanning Two-Photon Fluorescence Microscopy
2.1 Background
2.1.1 Multiphoton Excitation
2.1.2 Challenges of Volumetric Imaging with Multiphoton Microscopy
2.1.3 Bessel Focus Scanning Technology
2.2 Materials and Equipment
2.3 Methods
2.3.1 Two-Photon Fluorescence Microscope
2.3.2 Design and Setup of a Bessel Focus Module
2.3.3 Design of a Bessel Module
Generation of Annular Illumination with an SLM (Adapted from Ref.)
Generation of Annular Illumination with an Axicon
Calculation of Two-Photon Excitation PSF
Design of the Annular Aperture Mask in an SLM-Based Bessel Module (Adapted from Ref.)
Design of an Axicon-Based Bessel Module
2.3.4 Alignment of Bessel Module (Adapted from Ref.)
Installation of the Optical Components
Gross Alignment of the Bessel and Gaussian Beam Paths
Fine Alignment
2.3.5 Results and Data Analysis
2.4 Notes
3 Widefield Fluorescence Microscopy with Optical Sectioning
3.1 Background
3.2 Material and Equipment
3.2.1 Optical Components
3.2.2 Fixed Mouse Brain Slices Preparation
3.2.3 Drosophila Larvae Preparation
3.3 Methods
3.3.1 SIM Setup
Laser Beam Multiplexing, Shuttering, and Expansion
Beam Modulation Module
Maximizing Diffraction Efficiency and Pattern Contrast at the Sample Plane
Fine Alignment
3.3.2 SIM Detection Path
3.3.3 Optical-Sectioning Widefield Imaging and Its Application Examples
Refined OS-SIM Reconstruction Method
Fast Functional Imaging Using OS-SIM
Parameter Selection in Image Reconstruction
Other Optical Sectioning Reconstruction Methods
Other Considerations for In Vivo Imaging
4 Discussion
References
Chapter 11: Optical and Analytical Methods to Visualize and Manipulate Cortical Ensembles and Behavior
1 Introduction
2 Implementation of Simultaneous Two-Photon Imaging and Two-Photon Optogenetics
2.1 Background
2.1.1 Light-Sensitive Sensors and Actuators of Neuronal Activity
2.1.2 One-Photon and Multiphoton Excitation
2.1.3 Basic Setup of Multiphoton Microscope
2.2 Simultaneous Two-Photon Imaging and Two-Photon Optogenetics
2.2.1 Overall Consideration
2.2.2 Holographic Illumination
2.2.3 Spiral Scan Versus Scanless Approach in Holographic Photostimulation
2.2.4 Detailed Implementation of the Microscope for Simultaneous Two-Photon Imaging and Two-Photon Holographic Photostimulation
3 Identification and Targeting of Neuronal Ensembles Related to Behavior
3.1 Background
3.1.1 Multidimensional Reduction Techniques Applied to Population Recordings
3.1.2 Targeting Visualized Neuronal Populations with Two-Photon Optogenetics
3.2 Implementation of Analytical Methods to Recall Neuronal Ensembles Relevant to a Learned Behavior
3.2.1 Motion Correction, Identification of Neurons, and Spike Extraction
3.2.2 Binary Arrays from Inferred Activity
3.2.3 Multidimensional Population Vectors Defining Neuronal Ensembles
3.2.4 Similarity Measurements on Population Vectors
3.2.5 Identification of Neuronal Ensembles from Population Vectors
3.2.6 Pattern Completion Properties of Neuronal Ensembles
3.2.7 Recalling Neuronal Ensembles Related to Behavior
4 Considerations for the Implementation of a Visually Guided Go/No-Go Task
5 Notes
6 Outlook
References
Chapter 12: Illuminating Neural Computation Using Precision Optogenetics-Controlled Synthetic Perception
1 Introduction
2 Paradigms for Psychophysical Measurement of Synthetic Perception
2.1 Using Detection to Test the Relevance of Neural Codes
2.2 Technical Implementation of Detection Experiments
2.3 Measuring Perceptual Distance of Synthetic Percepts
2.4 Technical Implementation of Perceptual Distance Experiments
3 Validating Precise Manipulation
3.1 Characterizing the Scale and Timing of Response to Stimulation
3.2 Registration Between Photostimulation and Imaging, and In Situ Evaluation of Targeting
3.3 Assessing the Reliability of Behavioral Readout
4 Notes
5 Outlook
References
Chapter 13: Spectrally Focused Stimulated Raman Scattering (sf-SRS) Microscopy for Label-Free Investigations of Molecular Mech...
1 Introduction
1.1 Stimulated Raman Spectroscopy (SRS)
1.2 Spectral Resolution and the Role of the Pulse Duration, Chirping and Delay in SRS
1.3 Spectrally Focused SRS: The General Hardware Layout
1.4 Application Perspectives
2 Materials
3 Methods
3.1 Main Components for Integrating sf-SRS in a Multiphoton Microscope
3.2 Methods for Spectral Tuning of the System and Its Optimization: Pulse Chirp and Delay Control
3.3 Methods for Optimal Signal Detection: Differential Detection
4 Notes
4.1 Signal-to-Noise Ratio of SRS Images
4.2 Strategies for Ensuring Optimal Spatio-Temporal Overlap Between Pump and Stokes Beams
4.3 Optimizing the Beam Modulation Frequency and Depth
References
Index