Adaptive Optics for Biological Imaging

Adaptive Optics for Biological Imaging......Page 4
Contents......Page 8
Foreword......Page 10
Preface......Page 12
Editor......Page 14
Contributors......Page 16
Section I: Principles......Page 18
1.1 Introduction......Page 20
1.2.2 Maxwell’s Equations and the Plane Wave Solutions......Page 21
1.3.1 Dispersion and Refraction......Page 23
1.3.2 Polarization......Page 25
1.3.3 Optical Path Length, Geometric Rays, and Diffraction......Page 26
1.3.4 Photons, Scattering, Energy, and Momentum......Page 29
1.4.1 Huygens Wavelets......Page 31
1.4.2 Computer Simulation of Wave Propagation......Page 33
1.5.1 Ray Tracing......Page 35
1.5.2 Lagrange Invariant......Page 37
1.5.4 Diffraction Limit......Page 38
1.5.5 Depth of Field......Page 39
1.5.6 Rayleigh Range......Page 40
1.6 Image Formation and Analysis......Page 41
References......Page 44
2.2 Reflection......Page 46
2.3 Refraction......Page 48
2.4 Paraxial Lens Equation......Page 49
2.5 Thin Lens Equation......Page 51
2.6 Magnification......Page 56
2.7 Aberrations......Page 57
References......Page 58
3.2 Diffraction of Light......Page 60
3.3 Amplitude PSF of a Thin Lens......Page 62
3.4 Effective PSF and Image Formation in a Confocal Microscope......Page 63
3.5 PSF for an Ideal Lens and Diffraction Limited Imaging......Page 64
Bibliography......Page 65
Section II: Methods......Page 66
4.1 Introduction: Why Measure Specimen-Induced Aberration?......Page 68
4.2 Definition of Aberrations......Page 69
4.3 Zernike Mode Analysis of the Aberrated Wavefront......Page 70
4.5 Effect of Aberrations on the Imaging Quality of the Confocal Microscope......Page 72
4.6 Experimental System for Aberration Measurement......Page 74
4.7 Data Acquisition......Page 76
4.8 Phase Extraction......Page 77
4.9 Results for Aberration Measurements at Low Numerical Aperture......Page 78
4.10 Setup for Large Numerical Aperture, Specimens Investigated, and Data Acquisition......Page 83
4.11 Example Results for High Numerical Aperture......Page 84
4.12 Simulation of the Zernike Modal Correction......Page 85
4.13 Wavefront Quality Characterization......Page 86
4.14 Which Level of Correction Is Sensible?......Page 87
4.15 Effect of the Numerical Aperture on Aberrations......Page 88
4.16 Discussion and Conclusion......Page 89
References......Page 90
5.2 Problem Description......Page 92
5.4 Relation between Zernike Aberration Modes and Geometric Distortion......Page 94
5.5 Results and Discussion......Page 95
References......Page 98
6.1 Introduction......Page 100
6.2 Wavefront Aberration Simulation for a Spherical Object......Page 101
6.3 Modeling of an Oocyte Cell and Comparison to Experimental Results......Page 104
6.4 Wavefront Aberration Simulation for a Cylindrical Object......Page 107
6.5 Optical Fiber Simulation and Comparison to Experimental Results......Page 108
References......Page 110
7.1.1 Wavefront Sensing......Page 112
7.1.1.3 Pyramid Sensor......Page 113
7.1.2.1 Deformable Mirrors......Page 114
7.2 Biological Imaging in the Eye......Page 115
7.2.1 Adaptive Optics Ophthalmoscope......Page 116
7.2.3 Multiconjugate Adaptive Optics for Wide Field of View......Page 117
7.3.1 Wavefront Sensorless......Page 118
7.3.2 Wavefront Sensors and Guide Stars......Page 119
References......Page 121
8.1 Introduction......Page 126
8.2 Liquid Crystal Spatial Light Modulators......Page 127
8.3 History of Deformable Mirrors in Adaptive Optics......Page 130
8.4 Specifications for Deformable Mirrors......Page 133
8.4.1 Figure of Merit for Adaptive Optics System Performance......Page 137
8.4.2 Deformable Mirror Requirements......Page 138
8.5 Conventional Deformable Mirrors Using Piezoelectric and Electrostrictive Actuators......Page 142
8.6 Microelectromechanical System Deformable Mirrors......Page 144
8.6.1 Microelectromechanical System Polysilicon Surface Micromachining Fabrication Process......Page 145
8.6.2 Electrostatic Actuation......Page 146
8.6.3 Mechanical Restoring Force......Page 149
8.6.4 Electrostatically Actuated Membrane Mirrors......Page 151
8.6.6 Electrostatically Actuated Continuous Facesheet Microelectromechanical System Mirrors......Page 153
8.6.7 Electrostatically Actuated Segmented Facesheet Microelectromechanical System Mirrors......Page 156
8.8 High-Stroke, High-Order Microelectromechanical System Mirrors......Page 157
8.9 Comparison of Microelectromechanical System Mirrors......Page 162
8.10 Microelectromechanical System Mirror Solutions......Page 163
References......Page 164
9.1 Introduction......Page 168
9.2 Adaptive Optics Optical System Design Considerations......Page 169
9.3 Optical Aberrations......Page 172
9.4 Optomechanics......Page 174
9.4.4 Optical Subsystem, Cages, Rails, and Stages......Page 175
9.5.2 Use Mechanical Constraints......Page 177
9.5.4 Establish Optical Axis and Line of Sight......Page 178
9.6.1 Point Source with a Single-Mode Optical Fiber......Page 179
9.6.2 Alignment Sources......Page 180
9.6.3 Shearing Interferometer......Page 181
9.6.6 Iris (Diaphragm)......Page 182
9.7.2 Shack–Hartmann Wavefront Sensor Subassembly......Page 183
9.7.3 Pupil Plane Camera......Page 185
9.7.4 Photomultiplier Tube Pinhole Adjustment......Page 186
9.8 Assembly Procedures for an AO System......Page 187
9.9 Optical System Performance Improvement/Troubleshooting......Page 188
9.10 Understanding Alignment Penalties......Page 189
References......Page 190
Section III: Applications, Part 1: Indirect\rWavefront Sensing......Page 192
10.1 Introduction......Page 194
10.2 Indirect Wavefront Sensing......Page 195
10.3 Modal Representation of Aberrations......Page 197
10.5 Measurement of a Single Mode......Page 198
10.6 Measurement of Multiple Modes......Page 199
10.7 Example of a Sensorless Adaptive System......Page 200
10.8 Derivation of Optimal Modes......Page 202
10.9 An Empirical Approach for the Derivation of Optimal Modes......Page 203
10.10 Orthogonalization of Modes......Page 204
Acknowledgments......Page 205
References......Page 206
11.1 Introduction......Page 208
11.1.1 Basics of Nonlinear Imaging......Page 209
11.1.2 Sources of Aberration......Page 210
11.2.1 Basic Beam-Scanned System......Page 211
11.2.2 Incorporation of the Adaptive Optic Element: Pre- and Postscanning......Page 212
11.2.3 Adaptive Optical Element......Page 214
11.2.4 Practical System......Page 216
11.3.1 Image-Based Metrics and Optimization Algorithms......Page 217
11.3.2 Results......Page 219
11.3.3 Three-Dimensional Optimization Methods......Page 221
References......Page 223
12.1 Introduction......Page 226
12.1.2 Two-Photon Fluorescence Excitation and Emission......Page 227
12.1.3 Optical Resolution and Tissue Optical Aberrations......Page 228
12.2 Background......Page 229
12.3 Method......Page 230
12.3.1 Stochastic Parallel Gradient Descent Algorithm with Zernike Polynomial Basis......Page 231
12.3.2 Metric Selection for Stochastic Parallel Gradient Descent Algorithm......Page 233
12.3.3 Application of Stochastic Parallel Gradient Decent Algorithm with Zernike Polynomial Basis......Page 235
12.4 Optical System Design......Page 237
12.5.1 Point Spread Function Quantification......Page 239
12.5.2 Mouse Bone-Marrow Imaging with Adaptive Optics......Page 241
12.6 Critical Discussion......Page 243
12.7 Summary......Page 244
References......Page 245
13.1 Introduction......Page 248
13.2 Adaptive Optical Two-Photon Microscopy Using Pupil Segmentation......Page 249
13.3 Experimental Setup......Page 253
13.4.1 System Aberration......Page 254
13.4.2 Nonbiological Samples......Page 256
13.4.3 Biological Sample Examples......Page 257
13.5.1 Pupil Segmentation Strategy......Page 260
13.5.2 Phase Measurement vs Phase Reconstruction......Page 262
13.5.3 Field Dependence and Averaged Correction......Page 263
13.5.5 Application to Superresolution Point-Scanning: STED......Page 264
13.5.6 Zonal-Based Approaches for Scattering Control......Page 265
References......Page 266
Section III: Applications, Part 2: Direct\rWavefront Sensing......Page 268
14.1 Introduction......Page 270
14.2 Background/Prior Work: Coherence Gating......Page 271
14.3 Background/Prior Work: Wavefront Sensing Using a Shack-Hartmann Sensor......Page 274
14.4.1 Basic Coherence-Gated Wavefront Sensing Setup......Page 275
14.4.2 Virtual Shack-Hartmann Sensor......Page 278
14.4.3 Measurement Procedure......Page 279
14.5.1 Experimental Implementation......Page 280
14.5.2 In Vivo Adaptive Correction......Page 282
14.5.3 Speckle Size and Multiple Scattering......Page 283
14.6 Critical Discussion......Page 284
14.7 Conclusions......Page 285
References......Page 286
15.1 Introduction......Page 288
15.1.1 Sources of Aberrations in Microscopy......Page 290
15.1.2 Earlier Correction Approaches......Page 292
15.2 Microscope Design......Page 293
15.2.2 Simulation of Microscope and Sample Configurations......Page 295
15.3.1 Open-Loop Correction of Depth Aberration......Page 299
15.3.2 Focusing......Page 302
15.3.3 Deconvolution......Page 304
15.3.5 Phase Retrieval......Page 305
15.3.5.1 Phase Retrieval from Biological Samples......Page 309
15.3.6 Phase Diversity......Page 310
15.4 Conclusions......Page 311
References......Page 312
16.1 Introduction......Page 316
16.2.3 Application of Confocal Detection to Select Reflected Light Signals from the Focal Plane......Page 317
16.2.4 Overall Instrument Configuration......Page 318
16.3.1 Signal Loss Due to Aberrations as a Function of Imaging Depth......Page 320
16.3.2 Point Spread Function Degradation Due to Aberrations as a Function of Imaging Depth......Page 322
16.3.3 Mouse-Tongue-Muscle Imaging Using Adaptive Optics–Compensated Two-Photon Microscopy......Page 323
16.3.4 Mouse-Heart-Muscle Imaging Using Adaptive Optics–Compensated Two-P\rhoton Microscopy......Page 325
16.3.5 Neuronal Imaging in Mouse-Brain Slices Using Adaptive Optics–Compensated Two-Photon Microscopy......Page 326
16.4 Conclusions......Page 328
References......Page 329
17.1 Introduction......Page 332
17.1.1 Fluorescent Beads......Page 333
17.1.2 Shack-Hartmann Wavefront Sensor......Page 334
17.1.3 Cross-Correlation Centroiding......Page 335
17.1.4 Reconstruction......Page 336
17.2 AO Wide-Field Microscope......Page 337
17.2.1 Fluorescent Microsphere Reference Beacons (Guide Stars)......Page 338
17.2.2 Wavefront Measurements......Page 339
17.2.3 Wavefront Corrections......Page 342
17.2.4 The Isoplanatic Angle and Half-Width......Page 344
17.3 AO Confocal Fluorescence Microscope......Page 345
17.3.1 Optical Setup......Page 347
17.3.2 Results for Fixed Mouse-Brain Tissue......Page 348
17.3.2.2 Confocal Imaging with Wavefront Compensation......Page 349
17.3.2.3 Comparison between a Commercial Confocal Microscope and the AO Confocal Microscope......Page 351
17.4.1 Method......Page 352
17.5 Discussion and Conclusion......Page 356
References......Page 359
Index......Page 362
Color Insert......Page 378