An LED-Based structured illumination microscope using a digital micromirror device and GPU accelerated image reconstruction

Abstract

When combined with computational approaches, fluorescence imaging becomes one of the most powerful tools in biomedical research. It is possible to achieve resolution figures beyond the diffraction limit, and improve the performance and flexibility of high-resolution imaging systems with techniques such as structured illumination microscopy (SIM) reconstruction. In this study, the hardware and software implementation of an LED-based super-resolution imaging system using SIM employing GPU accelerated parallel image reconstruction is presented. The sample is illuminated with two-dimensional sinusoidal patterns with various orientations and lateral phase shifts generated using a digital micromirror device (DMD). SIM reconstruction is carried out in frequency space using parallel CUDA kernel functions. Furthermore, a general purpose toolbox for the parallel image reconstruction algorithm and an infrastructure that allows all users to perform parallel operations on images without developing any CUDA kernel code is presented. The developed image reconstruction algorithm was run separately on a CPU and a GPU. Two different SIM reconstruction algorithms have been developed for the CPU as mono-thread CPU algorithm and multi-thread OpenMP CPU algorithm. SIM reconstruction of 1024 × 1024 px images was achieved in 1.49 s using GPU computation, indicating an enhancement by ∼28 and ∼20 in computation time when compared with mono-thread CPU computation and multi-thread OpenMP CPU computation, respectively.

Correlative single-molecule and structured illumination microscopy of fast dynamics at the plasma membrane

“…Although recent developments demonstrate, for example, scanner-based systems [67] or fiber optic configurations [68] to achieve fast TIRF-SIM, these systems are more complex to synchronize or less versatile, respectively, to achieve multimodal multi-color high-speed imaging. Recently, digital mirror devices (DMDs) are a promising alternative to SLMs for high-speed SIM applications [69][70][71][72][73], but robust multi-color applications with more than two colors are still challenging. Furthermore, new developments in image denoising will provide more opportunities to apply fast SIM in biological samples [53,74].…”

Open-source microscope add-on for structured illumination microscopy

“…LCOS are most commonly used for SLM-based pattern generation due to their high level of performance. The use of DMDs for SIM 33 – 36 would be an alternative. They are more cost-effective and the implementation of the timing scheme is less difficult.…”