Importance of defocus correction for high-NA OCT and OCM

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Table of contents

1 Introduction
1.1 We want to image the brain
1.2 Optical aberrations cause imperfect imaging
1.3 Aberrations can be thought of as a phase term on the wavefront
1.4 Many imaging systems can be limited by aberrations
1.4.1 Wide-field microscopy
1.4.2 Confocal microscopy
1.4.3 Two-photon microscopy
1.4.4 Structured illumination microscopy
1.4.5 PALM/FPALM/STORM
1.4.6 Stimulated emission depletion
1.4.7 Optical coherence tomography
1.5 Astronomy uses direct wavefront measurement
1.5.1 Why direct wavefront sensing is hard in microscopy
1.6 The sample refractive index sets the scale for aberrations
1.7 Our refractive index measurements led us to develop deep-OCM
1.8 Deep rat brain imaging is limited by aberrations
1.9 Image analysis allows indirect wavefront measurement
1.9.1 Metric-based, imaging-model-agnostic methods
1.9.2 Metric-based modal wavefront sensing
1.9.3 Pupil segmentation
1.9.4 Phase diversity
2 Deep-OCM
2.1 Details of the setup
2.2 Animal preparation and treatment
2.3 High-speed in vivo rat brain imaging shows blood flow
2.4 Importance of defocus correction for high-NA OCT and OCM
3 Myelin imaging with deep-OCM
3.1 Deep-OCM shows myelin
3.1.1 Sensitivity to fiber orientation
3.2 Imaging myelin fibers in vivo in cortex
3.3 Myelin imaging in the peripheral nervous system
3.4 Discussion
4 Rat brain refractive index
4.1 Introduction
4.2 Measuring refractive index using high-NA OCT
4.2.1 OCT signal strength is sensitive to refractive-index-induced defocus
4.2.2 Dispersion and high NA complicate the refractive index measurement
4.2.3 Modeling the image formation process in high-NA OCT
4.2.4 Assuming a dispersion function allows calculation of the refractive index .
4.2.5 Choosing a suitable metric increases penetration depth
4.3 Results
4.3.1 Rat brain refractive index as a function of rat age
4.3.2 Importance of dispersion and high NA
4.4 Discussion
4.4.1 A model of defocus in OCT taking high NA and dispersion into account
4.4.2 Value and (non-)dependence of brain refractive index
4.4.3 Limits to the measuring precision
4.4.4 Potential systematic errors
4.4.5 Comparison with recent measurements
5 Consequences of brain refractive index mismatch for two-photon microscopy
5.1 Discussion
6 Maximum-A-Posteriori Focus and Stigmation (MAPFoSt)
6.1 Introduction
6.2 Materials and methods
6.2.1 The MAPFoSt algorithm
6.2.2 Data analysis
6.2.3 Experiments
6.2.4 Simulating image pairs
6.3 Results
6.3.1 Simulations show bias-free aberration estimation
6.3.2 SEM imaging experiments
6.4 Discussion
7 General Discussion
7.1 Correcting aberrations adds complexity
7.2 Defocus correction in high-NA OCM is worth it
7.3 Two-photon rat-brain imaging suffers from spherical aberration
7.4 The race is still on
8 Acknowledgements
9 Appendices
9.1 Deep-OCM motor placement
9.2 Derivations for MAPFoSt
9.2.1 Calculating the MTF and its derivatives
9.2.2 Calculating the MAPFoSt posterior and profile posterior
9.3 The heuristic SEM autofocus and auto-stigmation algorithm
9.4 Modal wavefront sensing for SEM
10 Literature
11 List of Acronyms
12 French summary / Résumé substantiel de cette thèse