Researcher:
Aygün, Uğur

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PhD Student

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Uğur

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Aygün

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Aygün, Uğur

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2014 - 201952020 - 20234

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Researcher Of Publications: search.filters.isAuthorOfPublication.2d5edc12-a936-4f97-8711-fe7e7ba998b9

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Now showing 1 - 9 of 9
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    Label-free and high-throughput detection of biomolecular interactions using a flatbed scanner biosensor
    (Amer Chemical Soc, 2017) Avci, Oguzhan; Seymour, Elif; Unlu, M. Selim; Ozkumur, Ayca Yalcin; N/A; Department of Electrical and Electronics Engineering; Aygün, Uğur; Ürey, Hakan; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; N/A; 8579
    Fluorescence based microarray detection systems provide sensitive measurements; however, variation of probe immobilization and poor repeatability negatively affect the final readout, and thus quantification capability of these systems. Here, we demonstrate a label-free and high-throughput optical biosensor that can be utilized for calibration of fluorescence microarrays. The sensor employs a commercial flatbed scanner, and we demonstrate transformation of this low cost (similar to 100 USD) system into an Interferometric Reflectance Imaging Sensor through hardware and software modifications. Using this sensor, we report detection of DNA hybridization and DNA directed antibody immobilization on label-free microarrays with a noise floor of similar to 30 pg/mm(2), and a scan speed of 5 s (50 s for 10 frames averaged) for a 2 mm X 2 mm area. This novel system may be used as a standalone label-free sensor especially in low-resource settings, as well as for quality control and calibration of microarrays in existing fluorescence-based DNA and protein detection platforms.
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    High-speed broadband FTIR system using MEMS
    (Optical Soc Amer, 2014) Stehle, Jean-Louis; N/A; N/A; Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; N/A; Department of Electrical and Electronics Engineering; Ayerden, Nadire Pelin; Aygün, Uğur; Holmstrom, Sven; Ölçer, Selim; Can, Başarbatu; Ürey, Hakan; Master Student; PhD Student; Researcher; Other; Master Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; N/A; N/A; N/A; 8579
    Current Fourier transform infrared spectroscopy (FTIR) systems have very good spectral resolution, but are bulky, sensitive to vibrations, and slow. We developed a new FTIR system using a microelectromechanical system (MEMS)-based lamellar grating interferometer that is fast, compact, and achromatic (i.e., does not require a beam splitter). The MEMS device has > 10 mm(2) active surface area, up to +/- 325 mu m mechanical displacement, and a 343 Hz resonant operation frequency. The system uses a 5 MHz bandwidth custom infrared (IR) detector and a small emission area custom blackbody source to achieve fast interferogram acquisition and compact form factor. Effects of lamellar grating period, detector size, laser reference, apodization, and averaging of data on the spectral resolution are discussed. The measurement time ranges from 1.5 to 100 ms depending on the averaging time. In the target range of 2.5-16 mu m (625- 4000 cm(-1)) a spectral resolution of 15-20 cm(-1) is demonstrated. The measurements are shown to be stable over a long time. (C) 2014 Optical Society of America
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    Label-free imaging of exosomes using depth scanning correlation (DSC) interferometric microscopy
    (Spie-Int Soc Optical Engineering, 2020) Ozkumur, Ayca Yalcin; Durmus, Naside Gozde; Demirci, Utkan; N/A; Department of Electrical and Electronics Engineering; Aygün, Uğur; Ürey, Hakan; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; N/A; 8579
    Direct visualization and characterization of nanosized biological particles such as viruses, vesicles and protein aggregates are important for various applications in medicine. Specifically, exosomes (30-150 nm in diameter) gained huge interest due to their potential role as a biomarker in cancer diagnosis and prognosis, however direct detection of these particles is challenging due to their small size. Interferometric microscopy allows detection of these particles without using any labels. We show that visibility of nanoparticles can be enhanced in interferometric microscopy by utilizing defocused images. In this paper, with the proposed method Depth Scanning Correlation, we demonstrate label-free detection of individual exosomes isolated from breast cancer cell culture isolated by using Exosome Total Isolation Chip (ExoTIC). Proposed imaging system combined with an isolation tool, can be used in a wide range of applications, where label-free detection of single biological nanoparticles is needed.
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    PublicationOpen Access
    Dynamic accommodation measurement using Purkinje reflections and ML algorithms
    (Society of Photo-optical Instrumentation Engineers (SPIE), 2023) Department of Electrical and Electronics Engineering; N/A; Aygün, Uğur; Şahin, Afsun; Ürey, Hakan; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; School of Medicine; N/A; N/A; N/A; 171267; 8579
    We developed a prototype device for dynamic gaze and accommodation measurements based on 4 Purkinje reflections (PR) suitable for use in AR and ophthalmology applications. PR1&2 and PR3&4 are used for accurate gaze and accommodation measurements, respectively. Our eye-model was developed in Zemax and matches the experiments well. Our model predicts the accommodation from 25cm to infinity (<4 diopters) with better than 0,25D accuracy. We performed repeatability tests and obtained accurate gaze and accommodation estimations using 15 subjects. We are generating a large synthetic data set using physically accurate models and machine learning algorithms.
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    PublicationOpen Access
    Wearable multi-color RAPD screening device
    (Society of Photo-optical Instrumentation Engineers (SPIE), 2023) Department of Electrical and Electronics Engineering; Aygün, Uğur; Şahin, Afsun; Ürey, Hakan; Hasanreisoğlu, Murat; Kavaklı, Koray; Küçüködük, Abdullah; Faculty Member; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; School of Medicine; Koç University Hospital; N/A; N/A; 171267; 8579; 182001; N/A; N/A; N/A; N/A; N/A
    In this work, we developed a wearable, head-mounted device that automatically calculates the precise Relative Afferent Pupillary Defect (RAPD) value of a patient. The device consists of two RGB LEDs, two infrared cameras, and one microcontroller. In the RAPD test, the parameters like LED on-off durations, brightness level, and color of the light can be controlled by the user. Upon data acquisition, a computational unit processes the data, calculates the RAPD score and visualizes the test results with a user-friendly interface. Multiprocessing methods used on GUI to optimize the processing pipeline. We have shown that our head-worn instrument is easy to use, fast, and suitable for early-diagnostics and screening purposes for various neurological conditions such as RAPD, glaucoma, asymmetric glaucoma, and anisocoria.
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    PublicationOpen Access
    Artificial eye model and holographic display based IOL simulator
    (Society of Photo-optical Instrumentation Engineers (SPIE), 2023) N/A; Department of Electrical and Electronics Engineering; N/A; Şahin, Afsun; Ürey, Hakan; Aygün, Uğur; Kavaklı, Koray; Akyazı, Deniz; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; School of Medicine; College of Engineering; Graduate School of Sciences and Engineering; 171267; 8579; N/A; N/A; N/A
    Cataract is a common ophthalmic disease in which a cloudy area is formed in the lens of the eye and requires surgical removal and replacement of eye lens. Careful selection of the intraocular lens (IOL) is critical for the post-surgery satisfaction of the patient. Although there are various types of IOLs in the market with different properties, it is challenging for the patient to imagine how they will perceive the world after the surgery. We propose a novel holographic vision simulator which utilizes non-cataractous regions on eye lens to allow the cataract patients to experience post-operative visual acuity before surgery. Computer generated holography display technology enables to shape and steer the light beam through the relatively clear areas of the patient’s lens. Another challenge for cataract surgeries is to match the right patient with the right IOL. To evaluate various IOLs, we developed an artificial human eye composed of a scleral lens, a glass retina, an iris, and a replaceable IOL holder. Next, we tested different IOLs (monofocal and multifocal) by capturing real-world scenes to demonstrate visual artifacts. Then, the artificial eye was implemented in the benchtop holographic simulator to evaluate various IOLs using different light sources and holographic contents.
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    PublicationOpen Access
    Low cost flatbed scanner label-free biosensor
    (Society of Photo-optical Instrumentation Engineers (SPIE), 2016) Avcı, Oğuzhan; Seymour, Elif; Sevenler, Derin D.; Ünlü, M. Selim; Özkumur, Ayça Yalçın; Department of Electrical and Electronics Engineering; Aygün, Uğur; Ürey, Hakan; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; N/A; 8579
    In this paper, we demonstrate utilization of a commercial flatbed document scanner as a label-free biosensor for high-throughput imaging of DNA and protein microarrays. We implemented an interferometric sensing technique through use of a silicon/oxide layered substrate, and easy to implement hardware modifications such as re-aligning moving parts and inserting a custom made sample plate. With a cost as low as 100USD, powered by a USB cable, and scan speed of 30 seconds for a 4mm x 4 mm area with similar to 10 mu m lateral resolution, the presented system offers a super low cost, easy to use alternative to commercially available label-free systems.
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    PublicationOpen Access
    Label-free detection of nanoparticles using depth scanning correlation interferometric microscopy
    (Nature Publishing Group (NPG), 2019) Özkümür, Ayça Yalçın; Department of Electrical and Electronics Engineering; Aygün, Uğur; Ürey, Hakan; Faculty Member; Department of Electrical and Electronics Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; N/A; 8579
    Single particle level visualization of biological nanoparticles such as viruses and exosomes is challenging due to their small size and low dielectric contrast. Fluorescence based methods are highly preferred, however they require labelling which may perturb the functionality of the particle of interest. On the other hand, wide-field interferometric microscopy can be used to detect sub-diffraction limited nanoparticles without using any labels. Here we demonstrate that utilization of defocused images enhances the visibility of nanoparticles in interferometric microscopy and thus improves the detectable size limit. With the proposed method termed as Depth Scanning Correlation (DSC) Interferometric Microscopy, we experimentally demonstrate the detection of sub-35nm dielectric particles without using any labels. Furthermore, we demonstrate direct detection of single exosomes. This label-free and high throughput nanoparticle detection technique can be used to sense and characterize biological particles over a range between a few tens to a few hundred nanometers, where conventional methods are insufficient.
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    PublicationOpen Access
    Author correction: label-free detection of nanoparticles using depth scanning correlation interferometric microscopy
    (Nature Publishing Group (NPG), 2019) Department of Electrical and Electronics Engineering; Aygün, Uğur; Ürey, Hakan; Faculty Member; Department of Electrical and Electronics Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; N/A; 8579