An LED-Based Structured Illumination Microscope Using A Digital Micromirror Device And GPU Accelerated Image Reconstruction

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 superresolution 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

Fabrication and Characterization of Large Numerical Aperture, High-Resolution Optical Fiber Bundles Based on High-Contrast Pairs of Soft Glasses for Fluorescence Imaging

Fabrication and characterization of flexible optical fiber bundles (FBs) with inhouse synthesized high-index and low-index thermally matched glasses are presented. The FBs composed of around 15000 single-core fibers with pixel sizes between 1.1 and 10 μm are fabricated using the stack-and-draw technique from sets of thermally matched zirconiumsilicate ZR3, borosilicate SK222, sodium-silicate K209, and F2 glasses. With high refractive index contrast pair of glasses ZR3/SK222 and K209/F2, FBs with numerical apertures (NAs) of 0.53 and 0.59 are obtained, respectively. Among the studied glass materials, ZR3, SK222, and K209 are in-house synthesized, while F2 is commercially acquired. Seven different FBs with varying pixel sizes and bundle diameters are characterized. Brightfield imaging of a micro-ruler and a Convallaria majalis sample and fluorescence imaging of a dye-stained paper tissue and a cirrhotic mice liver tissue are demonstrated using these FBs, demonstrating their good potential for microendoscopic imaging. Brightfield and fluorescence imaging performance of the studied FBs are compared. For both sets of glass compositions, good imaging performance is observed for FBs, with core diameter and core-to-core distance values larger than 1.6 μm and 2.3 μm, respectively. FBs fabricated with K209/F2 glass pairs revealed better performance in fluorescence imaging due to their higher NA of 0.59

Image Reconstruction in Frequency Space using Sinusoidal Illumination Patterns

Yapılandırılmı¸s Aydınlatma Desenleri (Structured Illumination Patterns) mikroskobik görüntülemede, kırımın limitinin (diffraction limit) a¸sılarak süper çözünürlüklü görüntünün elde edilmesini sa˘glamak için kullanılan bir görüntüleme tekni- ˘gidir. Mikroskobik görüntülemede, görüntülenmek istenen örnek üzerine yansıtılan ı¸sık iki boyutlu sinüs aydınlatma desenleri ¸seklinde modüle edilir ve ham görüntünün elde edilmesi sa˘glanır. Bu teknik kullanılarak ham görüntülere frekans uzayında uygulanan görüntü yenide yapılandırma algoritması ile nihai görüntünün çözünürlü˘günün iki kata kadar artması sa˘glanmı¸s olur. Bu çalı¸smada, öncelikle yüksek çözünürlüklü hedef görüntünün elde edilmesi için bir test görüntüsü yapılandırılmı¸s aydınlatma desenleri (iki boyutlu sinüzoidal görüntü olarak) ile moire giri¸sim deseni olu¸sturacak ¸sekilde konvolüsyon çarpımına u˘gratılmı¸stır.Daha sonra yapılandırılmı¸s aydınlatma mikroskobisi tekni˘gi algoritmasının adımları anlatılmı¸stır. Son olarak frekans uzayında görüntü yeniden yapılandırma (image reconstruction) için gerekli algoritma geli¸stirilmi¸s ve sonuçlar gösterilmi¸stir.Structured Illumination Patterns is an imaging technique used in microscopic imaging to achieve super-resolution image by exceeding the diffraction limit. In microscopic imaging, the light projected onto the sample to be imaged is modulated into two dimensional sinusoidal illumination patterns and the raw image is obtained. By using this technique, the image reconstruction algorithm applied to the raw images in the frequency space is provided to increase the resolution of the final image up to two times. In this study, to obtain the high resolution target image, convolution multiplication of the structured illumination patterns with a test image is applied and a moire fringe pattern is formed as a result of this product. Next, the steps of the structured illumination microscopy technique algorithm are described. Finally, the algorithm for image reconstruction in frequency space has been developed and the results are shown