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

Farklı ortamlar arası geçiş sırasında foton momentum değişiminin açılı cam fiber elyafı üzerinden interferometrik ölçümü.

There is a long standing dilemma about the value of photon momentum in dielectric media. Two rivaling views differ on both the magnitude and the direction of momentum but both are seemingly sound from a theoretical standpoint. Experimental work done also has evidence favoring both Abraham and Minkowski theories with different experiments supporting one of them. Aim of this thesis is to measure the deflection of a silica fiber filament with an angled end face and measure the displacement resulting from the momentum transfer between the fiber and air interface. The results found are within the error margins predicted by the Minkowski theory. Since the error margins are relatively large, the results are not conclusive enough to disprove the Abraham theory, however they are in strong favor of the Minkowski theory. M.S. - Master of Scienc

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

An LED-based super resolution GPU implemented structured illumination microscope

Fluorescence imaging of sub-cellular structures with sizes below the di raction limit is vital in understanding cellular processes. Relying on exciting the sample with di erent illumination patterns and image processing for the elimination of background uorescence, Structured Illumination Microscopy (SIM) provides imaging capability beyond di raction limit using relatively simple optical setups. Here, we present a laser-free, DLP projector-based, and GPU-implemented SIM super resolution microscope. Sub-di ractive biological structures were imaged with a lateral resolution of 150 nm. The microscopy system is LED-based and entirely home-built which enables customizable operation at a low cost

Coalescence of few layer graphene grains grown by chemical vapor deposition and their stacking sequence

Few layer graphene is attractive due to its extraordinary electronic and optical properties, which are strongly influenced by the orientation between the layers called as stacking sequence. It is challenging to synthesize high quality large size single or multi layer graphene crystals on the metal catalyst using chemical vapor deposition technique. The present work is about synthesis of few layer graphene grains on platinum foil using ambient pressure chemical together vapor deposition technique. The main focus is how the different grains coalesced and maintain the stacking sequence. Different characterization techniques are used to analyze the grains when they are in the process of merging to make a bigger grain. Scanning electron microscopy clearly shows different stacking sequences and merging of different nucleation sites of different grains. Interestingly, different stacking sequences are observed during the process of coalescence of grains. Raman spectroscopy gives accurate information about the number of layers and their stacking sequence. We observed Bernal AB and twisted layer stacking in the grains when they were combining together to grow into a bigger size. The full width at half maximum (FWHM) value of 2D Raman peaks appeared in the range of 52-69 cm(-1) which shows an increase from the value of single layer graphene (30.18 cm(-1)) and identifies Bernal stacking in grains. For twisted stacking FWHM values lie in the range of 19-32 cm(-1).Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) ; European Union (EU

Three-dimensional imaging of cleared human liver tissues reveals extensive fibrosis heterogeneity in non-alcoholic fatty liver disease

Background and aims: Liver fibrosis is a dynamic process of fibrogenesis and fibrolysis traditionally evaluated by liver biopsy. Accurate assessment of hepatic fibrosis is vital for optimal biomarker and drug development in the era of NASH clinical trials. The limitations of biopsy-based fibrosis staging include semi-quantitative assessment, sampling, and observer variability. In this study, we aimed to perform 3D imaging of optically transparent whole liver biopsy samples by light sheet fluorescence microscopy (LSFM) to quantify extra-cellular matrix proteins