Accurate Light Field Depth Estimation with Superpixel Regularization over Partially Occluded Regions

Depth estimation is a fundamental problem for light field photography applications. Numerous methods have been proposed in recent years, which either focus on crafting cost terms for more robust matching, or on analyzing the geometry of scene structures embedded in the epipolar-plane images. Significant improvements have been made in terms of overall depth estimation error; however, current state-of-the-art methods still show limitations in handling intricate occluding structures and complex scenes with multiple occlusions. To address these challenging issues, we propose a very effective depth estimation framework which focuses on regularizing the initial label confidence map and edge strength weights. Specifically, we first detect partially occluded boundary regions (POBR) via superpixel based regularization. Series of shrinkage/reinforcement operations are then applied on the label confidence map and edge strength weights over the POBR. We show that after weight manipulations, even a low-complexity weighted least squares model can produce much better depth estimation than state-of-the-art methods in terms of average disparity error rate, occlusion boundary precision-recall rate, and the preservation of intricate visual features

Modelling of optical traps for aerosols

Experimental observations suggest that there are differences between the behavior of particles optically trapped in air and trapped in a liquid phase. We present a modified version of Mie Debye Spherical Aberration theory to numerically simulate such optical system in attempt to explain and predict these effects. The model incorporates Mie scattering and focussing of the trapping beam through media of stratified refractive index. Our results show a geometrical optics approach cannot correctly describe our system and that spherical aberration must be included. We successfully qualitatively explain the observed phenomena and those of other authors, before discussing the limits of our experimental techniques and methods to improve it. We draw the important conclusion that when optically trapping aerosols the system does not behave as a true `optical tweezers', varying between levitation and single beam gradient force trapping depending on particle and beam parameters

Interferometric detection and enumeration of viral particles using Si-based microfluidics

Single-particle interferometric reflectance imaging sensor enables optical visualization and characterization of individual nanoparticles without any labels. Using this technique, we have shown end-point and real-time detection of viral particles using laminate-based active and passive cartridge configurations. Here, we present a new concept for low-cost microfluidic integration of the sensor chips into compact cartridges through utilization of readily available silicon fabrication technologies. This new cartridge configuration will allow simultaneous detection of individual virus binding events on a 9-spot microarray, and provide the needed simplicity and robustness for routine real-time operation for discrete detection of viral particles in a multiplex format.This work was supported in part by a research contract with the ASELSAN Research Center, Ankara, Turkey, and in part by the European Union's Horizon 2020 FET Open program under Grant 766466-INDEX. (ASELSAN Research Center, Ankara, Turkey; 766466-INDEX - European Union's Horizon 2020 FET Open program)First author draf

Optically-controlled platforms for transfection and single- and sub-cellular surgery

Improving the resolution of biological research to the single- or sub-cellular level is of critical importance in a wide variety of processes and disease conditions. Most obvious are those linked to aging and cancer, many of which are dependent upon stochastic processes where individual, unpredictable failures or mutations in individual cells can lead to serious downstream conditions across the whole organism. The traditional tools of biochemistry struggle to observe such processes: the vast majority are based upon ensemble approaches analysing the properties of bulk populations, which means that the detail about individual constituents is lost. What are required, then, are tools with the precision and resolution to probe and dissect cells at the single-micron scale: the scale of the individual organelles and structures that control their function. In this review, we highlight the use of highly-focused laser beams to create systems providing precise control and specificity at the single cell or even single micron level. The intense focal points generated can directly interact with cells and cell membranes, which in conjunction with related modalities such as optical trapping provide a broad platform for the development of single and sub-cellular surgery approaches. These highly tuneable tools have demonstrated delivery or removal of material from cells of interest, but can simultaneously excite fluorescent probes for imaging purposes or plasmonic structures for very local heating. We discuss both the history and recent applications of the field, highlighting the key findings and developments over the last 40 years of biophotonics researc