Researcher:
Özgönül, Ekin

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Ekin

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Özgönül

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Özgönül, Ekin

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2020 - 20225

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Researcher Of Publications: search.filters.isAuthorOfPublication.cc20edf1-4abd-4c8d-ad09-265ac9ff5a1c

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    Image reconstruction in frequency space using sinusoidal illumination patterns
    (IEEE, 2020) Aydın, Musa; Department of Physics; N/A; N/A; Department of Physics; Kiraz, Alper; Uysallı, Yiğit; Özgönül, Ekin; Morova, Berna; Faculty Member; PhD Student; PhD Student; Researcher; Department of Physics; College of Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; 22542; N/A; N/A; N/A
    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.
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    Three-dimensional imaging of cleared human liver tissues reveals extensive fibrosis heterogeneity in non-alcoholic fatty liver disease
    (Elsevier, 2022) Ulukan, Burge; Tas, Yagmur Cetin; Morova, Berna; Aydin, Musa; Uysalli, Erkan, Mert; Karahuseyinoglu, Sercin; Yurdaydin, Cihan; Akyildiz, Murat; Sheth, Abhishek; Kirimlioglu, Hale; Dayangac, Murat; Ferhanoglu, Onur; Kiraz, Alper; Zeybel, Mujdat; N/A; N/A; N/A; N/A; N/A; N/A; Department of Physics; N/A; N/A; N/A; N/A; Özdemir, Yasemin Gürsoy; Yiğit Alpdoğan, Buket; Özgönül, Ekin; Yaman, Ömer; Morova, Berna; Uysallı, Yiğit; Kiraz, Alper; Taş, Yağmur Çetin; Demirtaş, Elif; Karahüseyinoğlu, Serçin; Zeybel, Müjdat; Faculty Member; Researcher; PhD Student; PhD Student; Researcher; PhD Student; Faculty Member; Researcher; Master Student; Faculty Member; Faculty Member; Department of Physics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); N/A; School of Medicine; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; N/A; Graduate School of Sciences and Engineering; College of Sciences; School of Medicine; Graduate School of Health Sciences; School of Medicine; School of Medicine; 170592; N/A; N/A; N/A; N/A; N/A; 22542; N/A; N/A; 110772; 214694
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    An LED-based super resolution GPU implemented structured illumination microscope
    (Spie-Int Soc Optical Engineering, 2020) Aydin, Musa; N/A; N/A; N/A; Department of Physics; Uysallı, Yiğit; Özgönül, Ekin; Morova, Berna; Kiraz, Alper; PhD Student; PhD Student; Researcher; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; N/A; College of Sciences; N/A; N/A; N/A; 22542
    Fluorescence imaging of sub-cellular structures with sizes below the diffraction limit is vital in understanding cellular processes. Relying on exciting the sample with different illumination patterns and image processing for the elimination of background fluorescence, Structured Illumination Microscopy (SIM) provides imaging capability beyond diffraction limit using relatively simple optical setups. Here, we present a laser-free, DLP projector-based, and GPU-implemented SIM super resolution microscope. Sub-diffractive biological structures were imaged with a lateral resolution of similar to 150 nm. The microscopy system is LED-based and entirely home-built which enables customizable operation at a low cost.
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    Image reconstruction in frequency space using sinusoidal illumination patterns
    (Institute of Electrical and Electronics Engineers Inc., 2020) Aydın, Musa; Department of Physics; N/A; N/A; N/A; Kiraz, Alper; Morova, Berna; Özgönül, Ekin; Uysallı, Yiğit; Faculty Member; Researcher; PhD Student; PhD Student; Department of Physics; N/A; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); N/A; N/A; College of Sciences; N/A; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; 22542; N/A; N/A; N/A
    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 nal 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.
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    PublicationOpen Access
    An LED-Based structured illumination microscope using a digital micromirror device and GPU accelerated image reconstruction
    (Public Library of Science, 2022) Aydın, Musa; Doğan, Buket; Department of Physics; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Kiraz, Alper; Karalar, Elif Nur Fırat; Morova, Berna; Uysallı, Yiğit; Özgönül, Ekin; Faculty Member; Researcher; PhD Student; PhD Student; Department of Physics; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; 22542; 206349; N/A; N/A; N/A
    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.