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Intro; Supervisor's Foreword; Reference; Abstract; Publications Related to this Thesis; Acknowledgements; Contents; Abbreviations; 1 Introduction; References; 2 Light Scattering in Brain Tissue Using Monte Carlo Method; 2.1 Monte Carlo Method and Our Model; 2.1.1 Introduction to Monte Carlo; 2.1.2 Complexity of Models and the Monte Carlo Solution; 2.2 Details of Monte Carlo Method Code Writing for Scattering in Brain Tissue; 2.3 Results of Monte Carlo Method; 2.4 Conclusion; References; 3 Scattering in Zebrafish Brain for Optogenetics
3.1 Description of Set-Up to Study Light Scattering in Brain Tissue3.1.1 Introduction to Spatial Light Modulators (SLM); 3.1.2 Experimental Set-Up for Studies of Scattering; 3.2 Experimental Measurements; 3.2.1 Experimental Procedures; 3.2.2 Measurements; 3.3 Comparing Monte Carlo Method with Experimental Measurements; 3.4 Conclusions; References; 4 Optical Systems to Decode Brain Activity; 4.1 Fluorescent Proteins and the Development of GECIs; 4.2 Imaging Neuronal Activity; 4.3 The Advantages of Combining Optical Systems; 4.4 Building of the Optogenetics System
4.4.1 Presentation of the Optogenetics System4.4.2 Set-Up Improvements Using SLM Flexibility; 4.4.3 Stimulation of Specific Brain Regions and Deduction of Brain Circuitry; 4.5 Conclusions; References; 5 Investigation of Optical Properties of Otoliths with Optical Trapping; 5.1 Description of the Vestibular System; 5.1.1 Necessity of a Non-invasive System; 5.1.2 Structure of the Anterior Otolith; 5.2 Optical Trapping for Otolith Manipulation; 5.2.1 Introduction to Optical Trapping; 5.2.2 Investigation of the Possibility of Otolith Manipulation; 5.2.3 Manipulation of Free Otolith
5.3 Force Measurement with Optical Trapping5.3.1 Introduction to Light Deflection Method; 5.3.2 Experimental Otolith Scanning and Force Measurements; 5.4 Discussion; References; 6 Optical Manipulation of Otoliths In-Vivo; 6.1 Experimental Set-Up; 6.2 Measuring Behavioural Responses as a Result of Otolith Manipulation; 6.2.1 Experimental Procedures; 6.2.2 Behavioural Responses to Otolith Trapping; 6.2.3 Tail and Eyes Movements in the Literature; 6.3 Set Up Improvements for Calcium Imaging; 6.3.1 Details of ETL Functionning and Performances
6.4 Calcium Imaging: Mapping Out Responses to Acceleration6.4.1 Past Relevant Studies on Brain Activity in Zebrafish; 6.4.2 Experimental Procedure; 6.4.3 Preliminary Results; 6.5 Discussion; References; 7 Conclusion
3.1 Description of Set-Up to Study Light Scattering in Brain Tissue3.1.1 Introduction to Spatial Light Modulators (SLM); 3.1.2 Experimental Set-Up for Studies of Scattering; 3.2 Experimental Measurements; 3.2.1 Experimental Procedures; 3.2.2 Measurements; 3.3 Comparing Monte Carlo Method with Experimental Measurements; 3.4 Conclusions; References; 4 Optical Systems to Decode Brain Activity; 4.1 Fluorescent Proteins and the Development of GECIs; 4.2 Imaging Neuronal Activity; 4.3 The Advantages of Combining Optical Systems; 4.4 Building of the Optogenetics System
4.4.1 Presentation of the Optogenetics System4.4.2 Set-Up Improvements Using SLM Flexibility; 4.4.3 Stimulation of Specific Brain Regions and Deduction of Brain Circuitry; 4.5 Conclusions; References; 5 Investigation of Optical Properties of Otoliths with Optical Trapping; 5.1 Description of the Vestibular System; 5.1.1 Necessity of a Non-invasive System; 5.1.2 Structure of the Anterior Otolith; 5.2 Optical Trapping for Otolith Manipulation; 5.2.1 Introduction to Optical Trapping; 5.2.2 Investigation of the Possibility of Otolith Manipulation; 5.2.3 Manipulation of Free Otolith
5.3 Force Measurement with Optical Trapping5.3.1 Introduction to Light Deflection Method; 5.3.2 Experimental Otolith Scanning and Force Measurements; 5.4 Discussion; References; 6 Optical Manipulation of Otoliths In-Vivo; 6.1 Experimental Set-Up; 6.2 Measuring Behavioural Responses as a Result of Otolith Manipulation; 6.2.1 Experimental Procedures; 6.2.2 Behavioural Responses to Otolith Trapping; 6.2.3 Tail and Eyes Movements in the Literature; 6.3 Set Up Improvements for Calcium Imaging; 6.3.1 Details of ETL Functionning and Performances
6.4 Calcium Imaging: Mapping Out Responses to Acceleration6.4.1 Past Relevant Studies on Brain Activity in Zebrafish; 6.4.2 Experimental Procedure; 6.4.3 Preliminary Results; 6.5 Discussion; References; 7 Conclusion