The Application of Preconditioned Alternating Direction Method of Multipliers in Depth from Focal Stack

Post capture refocusing effect in smartphone cameras is achievable by using focal stacks. However, the accuracy of this effect is totally dependent on the combination of the depth layers in the stack. The accuracy of the extended depth of field effect in this application can be improved significantly by computing an accurate depth map which has been an open issue for decades. To tackle this issue, in this paper, a framework is proposed based on Preconditioned Alternating Direction Method of Multipliers (PADMM) for depth from the focal stack and synthetic defocus application. In addition to its ability to provide high structural accuracy and occlusion handling, the optimization function of the proposed method can, in fact, converge faster and better than state of the art methods. The evaluation has been done on 21 sets of focal stacks and the optimization function has been compared against 5 other methods. Preliminary results indicate that the proposed method has a better performance in terms of structural accuracy and optimization in comparison to the current state of the art methods.Comment: 15 pages, 8 figure

Real-time optical manipulation of cardiac conduction in intact hearts

Optogenetics has provided new insights in cardiovascular research, leading to new methods for cardiac pacing, resynchronization therapy and cardioversion. Although these interventions have clearly demonstrated the feasibility of cardiac manipulation, current optical stimulation strategies do not take into account cardiac wave dynamics in real time. Here, we developed an all‐optical platform complemented by integrated, newly developed software to monitor and control electrical activity in intact mouse hearts. The system combined a wide‐field mesoscope with a digital projector for optogenetic activation. Cardiac functionality could be manipulated either in free‐run mode with submillisecond temporal resolution or in a closed‐loop fashion: a tailored hardware and software platform allowed real‐time intervention capable of reacting within 2 ms. The methodology was applied to restore normal electrical activity after atrioventricular block, by triggering the ventricle in response to optically mapped atrial activity with appropriate timing. Real‐time intraventricular manipulation of the propagating electrical wavefront was also demonstrated, opening the prospect for real‐time resynchronization therapy and cardiac defibrillation. Furthermore, the closed‐loop approach was applied to simulate a re‐entrant circuit across the ventricle demonstrating the capability of our system to manipulate heart conduction with high versatility even in arrhythmogenic conditions. The development of this innovative optical methodology provides the first proof‐of‐concept that a real‐time optically based stimulation can control cardiac rhythm in normal and abnormal conditions, promising a new approach for the investigation of the (patho)physiology of the heart

Spectral pre-modulation of training examples enhances the spatial resolution of the Phase Extraction Neural Network (PhENN)

The Phase Extraction Neural Network (PhENN) is a computational architecture, based on deep machine learning, for lens-less quantitative phase retrieval from raw intensity data. PhENN is a deep convolutional neural network trained through examples consisting of pairs of true phase objects and their corresponding intensity diffraction patterns; thereafter, given a test raw intensity pattern PhENN is capable of reconstructing the original phase object robustly, in many cases even for objects outside the database where the training examples were drawn from. Here, we show that the spatial frequency content of the training examples is an important factor limiting PhENN's spatial frequency response. For example, if the training database is relatively sparse in high spatial frequencies, as most natural scenes are, PhENN's ability to resolve fine spatial features in test patterns will be correspondingly limited. To combat this issue, we propose "flattening" the power spectral density of the training examples before presenting them to PhENN. For phase objects following the statistics of natural scenes, we demonstrate experimentally that the spectral pre-modulation method enhances the spatial resolution of PhENN by a factor of 2.Comment: 12 pages, 10 figure

Accelerated Modeling of Near and Far-Field Diffraction for Coronagraphic Optical Systems

Accurately predicting the performance of coronagraphs and tolerancing optical surfaces for high-contrast imaging requires a detailed accounting of diffraction effects. Unlike simple Fraunhofer diffraction modeling, near and far-field diffraction effects, such as the Talbot effect, are captured by plane-to-plane propagation using Fresnel and angular spectrum propagation. This approach requires a sequence of computationally intensive Fourier transforms and quadratic phase functions, which limit the design and aberration sensitivity parameter space which can be explored at high-fidelity in the course of coronagraph design. This study presents the results of optimizing the multi-surface propagation module of the open source Physical Optics Propagation in PYthon (POPPY) package. This optimization was performed by implementing and benchmarking Fourier transforms and array operations on graphics processing units, as well as optimizing multithreaded numerical calculations using the NumExpr python library where appropriate, to speed the end-to-end simulation of observatory and coronagraph optical systems. Using realistic systems, this study demonstrates a greater than five-fold decrease in wall-clock runtime over POPPY's previous implementation and describes opportunities for further improvements in diffraction modeling performance.Comment: Presented at SPIE ASTI 2018, Austin Texas. 11 pages, 6 figure

Accurate position tracking of optically trapped live cells

Optical trapping is a powerful tool in Life Science research and is becoming common place in many microscopy laboratories and facilities. There is a growing need to directly trap the cells of interest rather than introduce beads to the sample that can affect the fundamental biological functions of the sample and impact on the very properties the user wishes to observe and measure. However, instabilities while tracking large inhomogeneous objects, such as cells, can make tracking position, calibrating trap strength and making reliable measurements challenging. These instabilities often manifest themselves as cell roll or re-orientation and can occur as a result of viscous drag forces and thermal convection, as well as spontaneously due to Brownian forces. In this paper we discuss and mathematically model the cause of this roll and present several experimental approaches for tackling these issues, including using a novel beam profile consisting of three closely spaced traps and tracking a trapped object by analysing fluorescence images. The approaches presented here trap T cells which form part of the adaptive immune response system, but in principle can be applied to a wide range of samples where the size and inhomogeneous nature of the trapped object can hinder particle tracking experiments

Roadmap on structured light

Structured light refers to the generation and application of custom light fields. As the tools and technology to create and detect structured light have evolved, steadily the applications have begun to emerge. This roadmap touches on the key fields within structured light from the perspective of experts in those areas, providing insight into the current state and the challenges their respective fields face. Collectively the roadmap outlines the venerable nature of structured light research and the exciting prospects for the future that are yet to be realized.Peer ReviewedPostprint (published version

Tight focusing of plane waves from micro-fabricated spherical mirrors

We derive a formula for the light field of a monochromatic plane wave that is truncated and reflected by a spherical mirror. Our formula is valid even for deep mirrors, where the aperture radius approaches the radius of curvature. We apply this result to micro-fabricated mirrors whose size scales are in the range of tens to hundreds of wavelengths, and show that sub-wavelength spot sizes can be achieved. This opens up the possibility of scalable arrays of tightly focused optical dipole traps without the need for high-performance optical systems.Comment: 8 pages, 5 color figures, 1 .sty file; changes made in response to referee comments; published in Optics Expres

Holographic optical trapping

Holographic optical tweezers use computer-generated holograms to create arbitrary three-dimensional configurations of single-beam optical traps useful for capturing, moving and transforming mesoscopic objects. Through a combination of beam-splitting, mode forming, and adaptive wavefront correction, holographic traps can exert precisely specified and characterized forces and torques on objects ranging in size from a few nanometers to hundreds of micrometers. With nanometer-scale spatial resolution and real-time reconfigurability, holographic optical traps offer extraordinary access to the microscopic world and already have found applications in fundamental research and industrial applications.Comment: 8 pages, 7 figures, invited contribution to Applied Optics focus issue on Digital Holograph