Surface Plasmon Fluorescence Microscopy: Characteristics and Application to Bioimaging

Ph.DDOCTOR OF PHILOSOPH

Wide-field extended-resolution fluorescence microscopy with standing surface-plasmon-resonance waves

The resolution of conventional SPR imaging has been limited by the diffraction nature of light. A wide-field extended-resolution optical imaging technique, standing-wave surface plasmon resonance fluorescence (SW-SPRF) microscopy, has been developed. Based on evanescent SPR standing waves, SW-SPRF provides lateral resolution approaching 100 nm and offers the advantages of significant signal enhancement and background noise reduction. SW-SPRF has the potential for sensitive biomolecular detection, nanoscale imaging, and lithographic applications

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Ladder queue: An O(1) priority queue structure for large-scale discrete event simulation

10.1145/1103323.1103324ACM Transactions on Modeling and Computer Simulation153175-204ATMC

Surface-plasmon-coupled emission microscopy with a spiral phase plate

The surface plasmon-coupled emission microscope provides high sensitivity for surface imaging. However, it suffers from a distorted donut-shape point-spread function (PSF). Here we report an effective yet simple method to correct for the distortion by introducing a spiral phase plate. This modification converts the donut PSF into one that is single lobed, which is preferable for imaging. The optical performance of the system is characterized and compared with previous publications. This technique provides more than twofold lateral resolution enhancement

A Code Generation Framework for Targeting Optimized Library Calls for Multiple Platforms

Directive-based programming approaches such as OpenMP and OpenACC have gained popularity due to their ease of programming. These programming models typically involve adding compiler directives to code sections such as loops in order to parallelize them for execution on multicore CPUs or GPUs. However, one problem with this approach is that existing compilers generate code directly from the annotated sections and do not make use of hardware-specific architectural features. As a result, the generated code is unable to fully exploit the capabilities of the underlying hardware. Alternatively, we propose a code generation framework in which linear algebraic operations in the annotated codes are recognized, extracted and mapped to optimized vendor-provided platform-specific library calls. We demonstrate that such an approach can result in better performance in the generated code compared to those which are generated by existing compilers. This is substantiated by experimental results on multicore CPUs and GPUs.ASTAR (Agency for Sci., Tech. and Research, S’pore)Accepted versio

Surface-plasmon-coupled emission microscopy with a spiral phase plate

10.1364/OL.35.000517Optics Letters354517-519OPLE

Optimizing and auto-tuning iterative stencil loops for GPUs with the in-plane method

10.1109/IPDPS.2013.79Proceedings - IEEE 27th International Parallel and Distributed Processing Symposium, IPDPS 2013452-46