A fast-Fourier-transform method of topography and interferometry is proposed. By computer processing of a noncontour type of fringe pattern, automatic discrimination is achieved between elevation and depression of the object or wave-front form, which has not been possible by the fringe-contour-generation techniques. The method has advantages over moire topography and conventional fringe-contour interferometry in both accuracy and sensitivity. Unlike fringe-scanning techniques, the method is easy to apply because it uses no moving components.

Fourier-transform method of fringe-pattern analysis for computer-based topography and interferometry

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Principles Of Optics Electromagnetic Theory Of Propagation Interference And Diffraction Of Light

Our understanding of the cellular implementation of systems-level neural processes like action, thought and emotion has been limited by the availability of tools to interrogate specific classes of neural cells within intact, living brain tissue. Here we identify and develop an archaeal light-driven chloride pump (NpHR) from Natronomonas pharaonis for temporally precise optical inhibition of neural activity. NpHR allows either knockout of single action potentials, or sustained blockade of spiking. NpHR is compatible with ChR2, the previous optical excitation technology we have described, in that the two opposing probes operate at similar light powers but with well-separated action spectra. NpHR, like ChR2, functions in mammals without exogenous cofactors, and the two probes can be integrated with calcium imaging in mammalian brain tissue for bidirectional optical modulation and readout of neural activity. Likewise, NpHR and ChR2 can be targeted together to Caenorhabditis elegans muscle and cholinergic motor neurons to control locomotion bidirectionally. NpHR and ChR2 form a complete system for multimodal, high-speed, genetically targeted, all-optical interrogation of living neural circuits.

Multimodal fast optical interrogation of neural circuitry

Course Description This is an advanced course in which we explore the field of Statistical Optics. Topics covered include such subjects as the statistical properties of natural (thermal) and laser light, spatial and temporal coherence, effects of partial coherence on optical imaging instruments, effects on imaging due to randomly inhomogeneous media, and a statistical treatment of the detection of light. Development of this more comprehensive model of the behavior of light draws upon the use of tools traditionally available to the electrical engineer, such as linear system theory and the theory of stochastic processes.

http://ieeexplore.ieee.org/iel5/3/23094/01073023.pdf

Statistical optics

A self-scanned 1024 element photodiode array and minicomputer are used to measure the phase (wavefront) in the interference pattern of an interferometer to lambda/100. The photodiode array samples intensities over a 32 x 32 matrix in the interference pattern as the length of the reference arm is varied piezoelectrically. Using these data the minicomputer synchronously detects the phase at each of the 1024 points by a Fourier series method and displays the wavefront in contour and perspective plot on a storage oscilloscope in less than 1 min (Bruning et al. Paper WE16, OSA Annual Meeting, Oct. 1972). The array of intensities is sampled and averaged many times in a random fashion so that the effects of air turbulence, vibrations, and thermal drifts are minimized. Very significant is the fact that wavefront errors in the interferometer are easily determined and may be automatically subtracted from current or subsequent wavefrots. Various programs supporting the measurement system include software for determining the aperture boundary, sum and difference of wavefronts, removal or insertion of tilt and focus errors, and routines for spatial manipulation of wavefronts. FFT programs transform wavefront data into point spread function and modulus and phase of the optical transfer function of lenses. Display programs plot these functions in contour and perspective. The system has been designed to optimize the collection of data to give higher than usual accuracy in measuring the individual elements and final performance of assembled diffraction limited optical systems, and furthermore, the short loop time of a few minutes makes the system an attractive alternative to constraints imposed by test glasses in the optical shop.

Digital wavefront measuring interferometer for testing optical surfaces and lenses

Fourier Ptychography is a new computational microscopy technique that achieves gigapixel images with both wide field of view and high resolution in both phase and amplitude. The hardware setup involves a simple replacement of the microscope's illumination unit with a programmable LED array, allowing one to flexibly pattern illumination angles without any moving parts. In previous work, a series of low-resolution images was taken by sequentially turning on each single LED in the array, and the data were then combined to recover a bandwidth much higher than the one allowed by the original imaging system. Here, we demonstrate a multiplexed illumination strategy in which multiple randomly selected LEDs are turned on for each image. Since each LED corresponds to a different area of Fourier space, the total number of images can be significantly reduced, without sacrificing image quality. We demonstrate this method experimentally in a modified commercial microscope. Compared to sequential scanning, our multiplexed strategy achieves similar results with approximately an order of magnitude reduction in both acquisition time and data capture requirements.

/pdf/multiplexed-coded-illumination-for-fourier-ptychography-with-139xpi0ny9.pdf

Multiplexed coded illumination for Fourier Ptychography with an LED array microscope.

Realizing high resolution across large volumes is challenging for 3D imaging techniques with high-speed acquisition. Here, we describe a new method for 3D intensity and phase recovery from 4D light field measurements, achieving enhanced resolution via Fourier ptychography. Starting from geometric optics light field refocusing, we incorporate phase retrieval and correct diffraction artifacts. Further, we incorporate dark-field images to achieve lateral resolution beyond the diffraction limit of the objective (5× larger NA) and axial resolution better than the depth of field, using a low-magnification objective with a large field of view. Our iterative reconstruction algorithm uses a multislice coherent model to estimate the 3D complex transmittance function of the sample at multiple depths, without any weak or single-scattering approximations. Data are captured by an LED array microscope with computational illumination, which enables rapid scanning of angles for fast acquisition. We demonstrate the method with thick biological samples in a modified commercial microscope, indicating the technique’s versatility for a wide range of applications.

/pdf/3d-intensity-and-phase-imaging-from-light-field-measurements-3ok644fypp.pdf

3D intensity and phase imaging from light field measurements in an LED array microscope

We demonstrate a compact, easy-to-build computational camera for single-shot three-dimensional (3D) imaging. Our lensless system consists solely of a diffuser placed in front of an image sensor. Every point within the volumetric field-of-view projects a unique pseudorandom pattern of caustics on the sensor. By using a physical approximation and simple calibration scheme, we solve the large-scale inverse problem in a computationally efficient way. The caustic patterns enable compressed sensing, which exploits sparsity in the sample to solve for more 3D voxels than pixels on the 2D sensor. Our 3D reconstruction grid is chosen to match the experimentally measured two-point optical resolution, resulting in 100 million voxels being reconstructed from a single 1.3 megapixel image. However, the effective resolution varies significantly with scene content. Because this effect is common to a wide range of computational cameras, we provide a new theory for analyzing resolution in such systems.

DiffuserCam: lensless single-exposure 3D imaging

We demonstrate a method for improving the accuracy of phase retrieval based on the Transport of Intensity equation by using intensity measurements at multiple planes to estimate and remove the artifacts due to higher order axial derivatives. We suggest two similar methods of higher order correction, and demonstrate their ability for accurate phase retrieval well beyond the ‘linear’ range of defocus that TIE imaging traditionally requires. Computation is fast and efficient, and sensitivity to noise is reduced by using many images.

Transport of Intensity phase-amplitude imaging with higher order intensity derivatives

Fourier ptychography is a new computational microscopy technique that provides gigapixel-scale intensity and phase images with both wide field-of-view and high resolution. By capturing a stack of low-resolution images under different illumination angles, an inverse algorithm can be used to computationally reconstruct the high-resolution complex field. Here, we compare and classify multiple proposed inverse algorithms in terms of experimental robustness. We find that the main sources of error are noise, aberrations and mis-calibration (i.e. model mis-match). Using simulations and experiments, we demonstrate that the choice of cost function plays a critical role, with amplitude-based cost functions performing better than intensity-based ones. The reason for this is that Fourier ptychography datasets consist of images from both brightfield and darkfield illumination, representing a large range of measured intensities. Both noise (e.g. Poisson noise) and model mis-match errors are shown to scale with intensity. Hence, algorithms that use an appropriate cost function will be more tolerant to both noise and model mis-match. Given these insights, we propose a global Newton’s method algorithm which is robust and accurate. Finally, we discuss the impact of procedures for algorithmic correction of aberrations and mis-calibration.

Laura Waller

Papers

Multiplexed coded illumination for Fourier Ptychography with an LED array microscope.

3D intensity and phase imaging from light field measurements in an LED array microscope

DiffuserCam: lensless single-exposure 3D imaging

Transport of Intensity phase-amplitude imaging with higher order intensity derivatives

Experimental robustness of Fourier ptychography phase retrieval algorithms