<?xml version="1.0" encoding="utf-8" standalone="yes"?><rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom"><channel><title>Phi-X</title><link>https://biocil.github.io/tr/</link><description>Recent content on Phi-X</description><generator>Hugo</generator><language>tr-TR</language><lastBuildDate>Sat, 31 Oct 2026 00:00:00 +0000</lastBuildDate><atom:link href="https://biocil.github.io/tr/index.xml" rel="self" type="application/rss+xml"/><item><title>Nicel faz ve dijital holografik mikroskopi</title><link>https://biocil.github.io/tr/research/phase-imaging/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/research/phase-imaging/</guid><description>Saydam bir hücre ışığın parlaklığını pek değiştirmez ama onu geciktirir. Eksen dışı dijital holografik mikroskopi bu gecikmeyi girişim saçakları olarak kaydeder ve optik kalınlıktaki nanometre düzeyindeki değişimlere duyarlı bir faz haritasına çevirir.</description></item><item><title>Holotomografi: üç boyutta kırılma indisi</title><link>https://biocil.github.io/tr/research/holotomography/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/research/holotomography/</guid><description>Birçok aydınlatma açısından hologram kaydetmek, bir numunenin 3B kırılma indisini geri kazanmamızı sağlar: canlı nöronlardaki nano ölçekli yapılardan beyin dokusundaki miyeline kadar, hiçbir boya kullanmadan.</description></item><item><title>Polarizasyona duyarlı holografi</title><link>https://biocil.github.io/tr/research/polarization/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/research/polarization/</guid><description>Kolajenden miyeline kadar birçok biyolojik yapı çift kırıcıdır. Polarizasyon holografik mikroskobumuz, bir numunenin tam Jones matrisini iki kamera pozundan geri kazanır ve gecikme ile hızlı eksen yönelimi haritalarını verir.</description></item><item><title>Artırılmış gerçeklik mikroskopisi için optik hesaplama</title><link>https://biocil.github.io/tr/research/optical-computing/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/research/optical-computing/</guid><description>Görüntüleri sonradan bilgisayarda işlemek yerine işin bir kısmını optiğe bırakıyoruz. Uzaysal ışık modülatöründe gösterilen optimize edilmiş bir faz deseni, seçilen hedefleri doğrudan mikroskobun canlı görüntüsünde vurgular.</description></item><item><title>Laboratuvar ve klinik için cihazlar</title><link>https://biocil.github.io/tr/research/instruments/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/research/instruments/</guid><description>Nicel görüntülemeyi ihtiyaç duyulan yere yaklaştıran donanımlar tasarlıyoruz: inkübatöre entegre holografik görüntülemeden kompakt spektrometrelere ve mikroskop otomatik odaklamasına kadar.</description></item><item><title>Upcoming talk at SPIE Photonics West 2027</title><link>https://biocil.github.io/tr/post/20261031/</link><pubDate>Sat, 31 Oct 2026 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20261031/</guid><description>Fatih Toy will present our latest polarization holography work in the Quantitative Phase Imaging XIII conference.</description></item><item><title>Mohammad Hussein accepted for a research internship at KAUST</title><link>https://biocil.github.io/tr/post/20261030/</link><pubDate>Fri, 30 Oct 2026 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20261030/</guid><description>After completing his MSc, Mohammad has been accepted for a research internship at King Abdullah University of Science and Technology (KAUST).</description></item><item><title>Design and Development of an Incubator with Integrated Imaging for Live Mammalian Cell Monitoring</title><link>https://biocil.github.io/tr/student_projects/incubator-imaging/</link><pubDate>Thu, 01 Oct 2026 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/student_projects/incubator-imaging/</guid><description>&lt;p&gt;A senior-year graduation project in Biomedical Engineering at Istanbul Medipol University (2026–2027), supervised by Fatih Toy. The team is designing and building an incubator that keeps mammalian cells under culture conditions while imaging them, so that living cells can be followed over time without being taken out of their environment.&lt;/p&gt;</description></item><item><title>Maha Sahloul’s poster at Frontiers in Optics + Laser Science 2026</title><link>https://biocil.github.io/tr/post/20261001/</link><pubDate>Thu, 01 Oct 2026 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20261001/</guid><description>We presented Maha Sahloul’s poster at FiO LS 2026, Optica’s annual meeting, in Rochester, New York.</description></item><item><title>TÜBİTAK–NARD bilateral project on polarization holography concluded</title><link>https://biocil.github.io/tr/post/20260915/</link><pubDate>Tue, 15 Sep 2026 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20260915/</guid><description>Our project with colleagues in Moldova on polarization-sensitive holographic microscopy has come to an end.</description></item><item><title>Our AR microscopy paper is on the cover of Optics Continuum</title><link>https://biocil.github.io/tr/post/20260815/</link><pubDate>Sat, 15 Aug 2026 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20260815/</guid><description>Maha Sahloul’s paper on all-optical target highlighting was selected for the cover of Optics Continuum, Volume 5, Issue 8.</description></item><item><title>Mohammad Hussein defends his MSc thesis</title><link>https://biocil.github.io/tr/post/20260813/</link><pubDate>Thu, 13 Aug 2026 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20260813/</guid><description>Mohammad M. T. R. Hussein defended his MSc thesis on polarization-sensitive digital holographic microscopy with structured illumination.</description></item><item><title>All-optical target highlighting for AR microscopy out in Optics Continuum</title><link>https://biocil.github.io/tr/post/20260806/</link><pubDate>Thu, 06 Aug 2026 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20260806/</guid><description>Maha Sahloul’s paper, with Kaan Akşit of UCL, highlights selected objects in a microscope’s live view using precomputed phase masks on a spatial light modulator.</description></item><item><title>Label-free holotomographic imaging of brain myelin</title><link>https://biocil.github.io/tr/publication/2026_scirep_oguz/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2026_scirep_oguz/</guid><description>Here we introduce a rapid, label-free approach that combines holotomographic imaging with a point-spread-function-aware model to infer axon diameter, myelin sheath thickness and g-ratio in mouse corpus-callosum cryosections.</description></item><item><title>Label-free holotomography of brain myelin accepted in Scientific Reports</title><link>https://biocil.github.io/tr/post/20260729/</link><pubDate>Wed, 29 Jul 2026 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20260729/</guid><description>With the Kerman lab, we show that holotomography can image myelin in brain tissue without staining.</description></item><item><title>All-optical selective target highlighting for augmented reality microscopy</title><link>https://biocil.github.io/tr/publication/2026_optcon_sahloul/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2026_optcon_sahloul/</guid><description>We introduce an all-optical alternative by proposing a new phase optimization scheme integrated into AR microscopes. By leveraging the inherent shift-invariant property of Fourier optical systems, our phase masks maintain a selective augmentation of the target object during in-plane translations within the field of view (FoV) without explicit tracking algorithms. Our results demonstrate selective target highlighting based on object size or shape, enabling continuous real-time observation in microscopy systems.</description></item><item><title>Dual-shot polarization DHM published in Biomedical Optics Express</title><link>https://biocil.github.io/tr/post/20260313/</link><pubDate>Fri, 13 Mar 2026 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20260313/</guid><description>Mohammad Hussein’s paper shows how to recover the full-field Jones matrix of a sample from just two holograms.</description></item><item><title>Dual-shot polarization digital holographic microscopy with phase bias equalization for full-field Jones matrix imaging</title><link>https://biocil.github.io/tr/publication/2026_bopex_hussein/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2026_bopex_hussein/</guid><description>To suppress inter-shot phase drift, we propose a phase bias equalization that leverages isotropic reference regions to align complex phases across Jones elements. Experiments on biaxially oriented polypropylene (BOPP) films yield retardance and fast axis maps in agreement. Imaging of mouse brain sections and human cornea further demonstrates robust visualization of anisotropic microstructures.</description></item><item><title>Research visit to the Institute of Applied Physics in Chișinău</title><link>https://biocil.github.io/tr/post/20250914/</link><pubDate>Sun, 14 Sep 2025 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20250914/</guid><description>Fatih Toy spent a week in the partner lab in Moldova within our TÜBİTAK–NARD bilateral project.</description></item><item><title>Best poster award, third place, FOTONİK 2025</title><link>https://biocil.github.io/tr/funding/fotonik-2025/</link><pubDate>Fri, 12 Sep 2025 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/funding/fotonik-2025/</guid><description>&lt;p&gt;For the poster &lt;em&gt;Enhancing Jones Matrix Reconstruction in Polarization DHM via Phase Bias Equalization&lt;/em&gt;. &lt;a href="https://biocil.github.io/tr/post/20250912/"&gt;News item&lt;/a&gt;&lt;/p&gt;</description></item><item><title>Mohammad Hussein wins third place in the FOTONİK 2025 poster award</title><link>https://biocil.github.io/tr/post/20250912/</link><pubDate>Fri, 12 Sep 2025 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20250912/</guid><description>Mohammad’s poster on phase bias equalization for polarization DHM won third place in the best poster competition at FOTONİK 2025.</description></item><item><title>Two posters at FOTONİK 2025</title><link>https://biocil.github.io/tr/post/20250912b/</link><pubDate>Fri, 12 Sep 2025 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20250912b/</guid><description>Mohammad Hussein and Maha Sahloul presented their work at FOTONİK 2025, the national optics and photonics workshop at Koç University.</description></item><item><title>Veronica Cazac from IAP Moldova visits the lab</title><link>https://biocil.github.io/tr/post/20250629/</link><pubDate>Sun, 29 Jun 2025 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20250629/</guid><description>Our partner from the Institute of Applied Physics in Chișinău spent a week working with us in Istanbul.</description></item><item><title>PhoBioS COST Action meeting in Linares, Spain</title><link>https://biocil.github.io/tr/post/20250218/</link><pubDate>Tue, 18 Feb 2025 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20250218/</guid><description>We presented a poster at the management committee meeting of COST Action CA21159 PhoBioS at the University of Jaén.</description></item><item><title>Working visit to the Institute of Applied Physics in Chișinău</title><link>https://biocil.github.io/tr/post/20250202/</link><pubDate>Sun, 02 Feb 2025 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20250202/</guid><description>Fatih Toy spent a week at our partner institute in Moldova within the TÜBİTAK–NARD bilateral project.</description></item><item><title>Elena Achimova and Vladimir Abaskin visit Medipol</title><link>https://biocil.github.io/tr/post/20241107/</link><pubDate>Thu, 07 Nov 2024 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20241107/</guid><description>Our partners from the Institute of Applied Physics in Chișinău spent two weeks with us in Istanbul.</description></item><item><title>Microscope with autofocus system</title><link>https://biocil.github.io/tr/publication/wo2024208601/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/wo2024208601/</guid><description>A microscope apparatus (2) for imaging a sample (5) positioned on a substrate (3) of a sample holder (1), the microscope comprising a sample stage (16) on which the sample holder is mounted, a light collecting device (38), an imaging sensor (12), and an autofocus system (8) that serves to focus an image of the sample on the imaging sensor. The autofocus system (8) is positioned below the sample stage and comprises a light beam emitter (22) emitting an autofocus light beam (13), and a beam steering system (24) configured to direct and reflect the autofocus light beam (13) off a bottom side of the substrate (3) of the sample holder positioned on the sample stage (16) and onto a light sensor (40) comprised in the autofocus system or onto the imaging sensor (12), the beam steering system configured to adjust a translational position and an angle of the autofocus light beam output by the beam steering system.</description></item><item><title>TÜBA GEBİP annual evaluation meeting in Erzurum</title><link>https://biocil.github.io/tr/post/20240705/</link><pubDate>Fri, 05 Jul 2024 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20240705/</guid><description>Fatih Toy attended the Turkish Academy of Sciences’ annual GEBİP evaluation meeting at Atatürk University.</description></item><item><title>Visualizing hydrogen peroxide and nitric oxide dynamics in endothelial cells using multispectral imaging under controlled oxygen conditions</title><link>https://biocil.github.io/tr/publication/2024_frbm_altun/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2024_frbm_altun/</guid><description>Our results demonstrate that under ambient oxygen conditions, H2O2 exhibited no significant influence on NO production. Subsequent exploration under physiological normoxia (5 kPa O2) revealed distinct oxidative stress levels characterized by reduced basal HyPer7 signals, enhanced H2O2 scavenging kinetics, and altered responses to pharmacological treatment.</description></item><item><title>Smartphone-based holographic blood analyser</title><link>https://biocil.github.io/tr/student_projects/inline_kramer/</link><pubDate>Wed, 15 May 2024 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/student_projects/inline_kramer/</guid><description/></item><item><title>Polarization-sensitive DHM with singular structured illumination for biomedical applications</title><link>https://biocil.github.io/tr/funding/123n774/</link><pubDate>Mon, 15 Jan 2024 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/funding/123n774/</guid><description>&lt;p&gt;The project brought together our lab and colleagues in Moldova to develop polarization-sensitive digital holographic microscopy. It was financed under the 4th joint call of TÜBİTAK and NARD.&lt;/p&gt;&#10;&lt;h2 id="outputs"&gt;Outputs&lt;/h2&gt;&#10;&lt;ul&gt;&#10;&lt;li&gt;&lt;a href="https://biocil.github.io/tr/publication/2026_bopex_hussein/"&gt;Dual-shot polarization DHM for full-field Jones matrix imaging&lt;/a&gt;, Biomedical Optics Express 2026&lt;/li&gt;&#10;&lt;li&gt;&lt;a href="https://biocil.github.io/tr/publication/2026_optcon_sahloul/"&gt;All-optical selective target highlighting for augmented-reality microscopy&lt;/a&gt;, Optics Continuum 2026 (&lt;a href="https://biocil.github.io/tr/projects/target-highlighting/"&gt;project page&lt;/a&gt;, &lt;a href="https://opticapublishing.figshare.com/articles/journal_contribution/Supplementary_document_for_All-Optical_Selective_Target_Highlighting_for_Augmented_Reality_Microscopy_-_7967150_pdf/32886380?file=67315379"&gt;supplementary material&lt;/a&gt;)&lt;/li&gt;&#10;&lt;/ul&gt;&#10;&lt;p&gt;&lt;img src="https://biocil.github.io/funding/123n774/setup.png" alt="Optical setup of the augmented-reality microscope"&gt;&lt;/p&gt;</description></item><item><title>TÜBA GEBİP annual evaluation meeting in Mersin</title><link>https://biocil.github.io/tr/post/20231117/</link><pubDate>Fri, 17 Nov 2023 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20231117/</guid><description>Fatih Toy attended the Turkish Academy of Sciences’ annual GEBİP evaluation meeting at Mersin University.</description></item><item><title>A photolithography method and system</title><link>https://biocil.github.io/tr/publication/wo2023172228/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/wo2023172228/</guid><description>A photolithography method characterized by steps of providing a target phase, transmitting a beam from an EM radiation source (9) to a spatial light modulator (3) and the beam reflected from the spatial light modulator (3) to a sample (5), dividing a beam provided by a light source (10) into two as an object wave (7) and a reference wave (8) and transmitting the object wave (7) to the sample (5), merging and sending the object wave (7) went through the sample (5) and the reference wave (8) to an image receiving element (1) and obtaining a phase image, comparing the phase image and the target phase and the quantizing the phase image to create a new image for the spatial light modulator (3), if a difference between the phase image and the target phase is above a predetermined value.</description></item><item><title>Best poster award, second place, FOTONİK 2023</title><link>https://biocil.github.io/tr/funding/fotonik-2023/</link><pubDate>Fri, 08 Sep 2023 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/funding/fotonik-2023/</guid><description>&lt;p&gt;For the poster &lt;em&gt;Holotomographic Imaging of Myelinated Axons in the CNS&lt;/em&gt;. &lt;a href="https://biocil.github.io/tr/post/20230908/"&gt;News item&lt;/a&gt;&lt;/p&gt;</description></item><item><title>Tuba Oğuz wins a poster award at FOTONİK 2023</title><link>https://biocil.github.io/tr/post/20230908/</link><pubDate>Fri, 08 Sep 2023 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20230908/</guid><description>Tuba Oğuz’s poster on holotomographic imaging of myelinated axons won a prize in the best poster competition at FOTONİK 2023.</description></item><item><title>PhoBioS COST Action meeting in Gdańsk</title><link>https://biocil.github.io/tr/post/20230718/</link><pubDate>Tue, 18 Jul 2023 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20230718/</guid><description>Fatih Toy attended the management committee meeting of COST Action CA21159 PhoBioS in Gdańsk, Poland.</description></item><item><title>In-situ measurement of anisotropic Young's modulus in fused deposition modeling printed cantilevers</title><link>https://biocil.github.io/tr/publication/2023_jmems_tekin/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2023_jmems_tekin/</guid><description>In this study, we investigate the effect of fused deposition modeling printing direction on the effective Young&amp;rsquo;s modulus value of cantilevers.</description></item><item><title>TÜBA GEBİP annual evaluation meeting</title><link>https://biocil.github.io/tr/post/20221111/</link><pubDate>Fri, 11 Nov 2022 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20221111/</guid><description>Fatih Toy attended the Turkish Academy of Sciences’ annual GEBİP evaluation meeting.</description></item><item><title>PhoBioS: Understanding interaction light – biological surfaces, possibility for new electronic materials and devices</title><link>https://biocil.github.io/tr/funding/ca21159/</link><pubDate>Wed, 19 Oct 2022 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/funding/ca21159/</guid><description/></item><item><title>An integrated top-stage incubator and lens-free holographic imaging system for culture monitoring applications</title><link>https://biocil.github.io/tr/publication/2022_spiepe_ozbilgin/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2022_spiepe_ozbilgin/</guid><description>Here, an integrated portable system is presented that can maintain cell cultures at desired temperature in a 3D printed enclosure while imaging them in lens free inline holographic microscopy modality. Such a system is well suited for tissue culturing and monitoring at limited resources settings.</description></item><item><title>Maskless lithography with holographic feedback for the fabrication of optical elements</title><link>https://biocil.github.io/tr/publication/2022_spiepe_gurcan_b/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2022_spiepe_gurcan_b/</guid><description>In this work we took an alternative route to these problems by combining maskless lithography with digital holography. Addition of digital holography enables the use of feedback by measuring the quantitative phase of specimen near real time and in situ nondestructively. After each near UV exposure, phase retardation map of exposed photopolymer is measured with digital holography part of the system. Any deviation from target phase is corrected by changing the pattern displayed on the mask.</description></item><item><title>Total internal reflection holographic microscopy for cellular imaging</title><link>https://biocil.github.io/tr/publication/2022_spiepe_gurcan_a/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2022_spiepe_gurcan_a/</guid><description>A label free quantitative phase imaging method is realized in this project to enable imaging of an interface between different media. This system is based on an off-axis holographic microscope and uses a high numerical aperture (NA) microscope objective to achieve total internal reflection (TIR).</description></item><item><title>Digital holographic microscopy system with integrated incubator</title><link>https://biocil.github.io/tr/student_projects/incubator/</link><pubDate>Sun, 15 May 2022 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/student_projects/incubator/</guid><description/></item><item><title>High resolution prism spectrometer comprising a diffuser film</title><link>https://biocil.github.io/tr/publication/us11231322/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/us11231322/</guid><description>A prism spectrometer having higher resolution and wider spectral width through the use of a speckle generating diffuser.</description></item><item><title>Low-Cost top stage incubator for live cell imaging applications</title><link>https://biocil.github.io/tr/publication/2021_tiptekno_ozbilgin/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2021_tiptekno_ozbilgin/</guid><description>A low cost alternative to off-the-shelf top stage incubators is realized by using 3D printing technology. A closed system is designed for keeping the inner temperature at the desired value and an ITO coated glass plate is employed as a heater. The temperature inside the incubator is stabilized by using PID (Proportional-Integral-Derivative) algorithm that is controlled via Arduino Uno microcontroller.</description></item><item><title>Projection vein finder</title><link>https://biocil.github.io/tr/student_projects/vein/</link><pubDate>Sat, 15 May 2021 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/student_projects/vein/</guid><description/></item><item><title>Outstanding Young Scientist Award (GEBİP)</title><link>https://biocil.github.io/tr/funding/tuba-gebip/</link><pubDate>Fri, 15 Jan 2021 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/funding/tuba-gebip/</guid><description>&lt;p&gt;The award came with three years of research funding (2021–2024).&lt;/p&gt;</description></item><item><title>Quantitative phase macroscopic system for label-free imaging of tissue sections</title><link>https://biocil.github.io/tr/publication/2021_electrica_toy/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2021_electrica_toy/</guid><description>Here, the system follows an off-axis digital holographic imaging configuration for the acquisition of quantitative phase at single shot. The system compromises from the resolution and magnification of a traditional microscope for the size of visual field, ease of use, and relative cost due to the exclusion of sample stages. A software level stitching further enlarges the effective field of view.</description></item><item><title>High-resolution total internal reflection holographic microscopy for the investigation of cellular interfaces</title><link>https://biocil.github.io/tr/funding/120f099/</link><pubDate>Tue, 15 Sep 2020 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/funding/120f099/</guid><description/></item><item><title>Scattering metal waveguide based speckle-enhanced prism spectrometry</title><link>https://biocil.github.io/tr/publication/2020_jlt_cetindag/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2020_jlt_cetindag/</guid><description>We present an optical efficiency improved speckle spectrometer where a scattering metal wave-guide is utilized along with a conventional prism spectrometer.</description></item><item><title>Wedge prism assisted quantitative phase imaging on standard microscopes</title><link>https://biocil.github.io/tr/publication/2019_oc_toy/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2019_oc_toy/</guid><description>Here, a wedge prism based simple approach is introduced to acquire quantitative phase images on a standard microscope.</description></item><item><title>Speckle-enhanced prism spectrometer</title><link>https://biocil.github.io/tr/publication/2019_omn_cetindag/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2019_omn_cetindag/</guid><description>We present an improved prism spectrometer with high wavelength range and spectral resolution.</description></item><item><title>The World of 3D Cells Is Now Open for EPFL Students to Explore (English Content)</title><link>https://biocil.github.io/tr/post/20190618/</link><pubDate>Tue, 18 Jun 2019 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20190618/</guid><description>&lt;p&gt;Since spring 2019, EPFL’s students have had a gateway to a new world. That was when EPFL’s Discovery Learning Labs (DLL) acquired a 3D Cell Explorer, made by EPFL spin-off Nanolive, for educational purposes. This microscope, which was designed on the EPFL campus, provides high-resolution images of cellular organelles, allowing students to observe them in their natural environment and watch them develop in real time.&lt;/p&gt;</description></item><item><title>Epifluorescence microscopy on a student microscope</title><link>https://biocil.github.io/tr/student_projects/student_mic/</link><pubDate>Wed, 15 May 2019 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/student_projects/student_mic/</guid><description/></item><item><title>A speckle-enhanced prism spectrometer with high dynamic range</title><link>https://biocil.github.io/tr/publication/2018_ptl_cetindag/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2018_ptl_cetindag/</guid><description>With the proposed spectrometer, implemented using a CCD camera, we demonstrate up to 17-pm resolution at 855-nm central wavelength and 756.5-nm wavelength range revealing a dynamic range of ~44 500.</description></item><item><title>Quantitative phase imaging upgrade on a standard microscope</title><link>https://biocil.github.io/tr/publication/2018_nanotr_toy/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2018_nanotr_toy/</guid><description>Here it is proposed to implement an off-axis holography layout that utilizes a single wedge prism.</description></item><item><title>Refractive index tomography of myelinating glial cells</title><link>https://biocil.github.io/tr/publication/2019_qpi_toy/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2019_qpi_toy/</guid><description>Refractive index tomography as an emerging technique enables the 3D morphological investigation of cells with no marker. Here, refractive index tomographic imaging of myelinating glial cells is presented.</description></item><item><title>Webteknodan Hocamız M. Fatih Toy ile Holografik Mikroskoplar (Turkish Content)</title><link>https://biocil.github.io/tr/post/20180807/</link><pubDate>Tue, 07 Aug 2018 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20180807/</guid><description>&lt;p&gt;Tıpta yeni bir dönem başlatan holo-tomografik mikroskobun mucidi ve uzayda biyolojik görüntüleme için Avrupa Uzay Ajansı’nın kullandığı systemin kurucusu.&lt;/p&gt;</description></item><item><title>Yenilikçi Mikroskoplar Kanseri Erken Evrede Teşhis Edecek (Turkish Content)</title><link>https://biocil.github.io/tr/post/20180119/</link><pubDate>Fri, 19 Jan 2018 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20180119/</guid><description>&lt;p&gt;İstanbul Medipol Üniversitesi ‘Yenilikçi Mikroskop Teknolojileri Merkezi’nde geliştirilecek süper-çözünürlüklü ve 3 boyutlu mikroskoplar, erken evre kanserlerin teşhisine destek vermeyi amaçlıyor.&lt;/p&gt;</description></item><item><title>Dr. Toy, “Türkiye’nin 10 Başarılı Genç İnsanı” arasında gösterildi (Turkish Content)</title><link>https://biocil.github.io/tr/post/20171211/</link><pubDate>Mon, 11 Dec 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20171211/</guid><description>&lt;p&gt;Dünyanın en eski ve en yaygın sivil toplum kuruluşlarından biri olan JCI - Junior Chamber International (Uluslararası Genç Liderler ve Girişimciler Derneği), Medipol’den Yrd. Doç. Dr. Fatih Toy’u Fen ve Teknik Gelişme alanında “Türkiye’nin En Başarılı Genç İnsanı” olarak gösterdi.&lt;/p&gt;</description></item><item><title>Ten Outstanding Young Persons of Turkey</title><link>https://biocil.github.io/tr/funding/jci-toyp/</link><pubDate>Mon, 11 Dec 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/funding/jci-toyp/</guid><description>&lt;p&gt;Recognised in the category of scientific and technological development. &lt;a href="https://www.hurriyet.com.tr/yerel-haberler/istanbul/dr-toy-turkiyenin-10-basarili-genc-insani-40674617"&gt;Press coverage (Turkish)&lt;/a&gt;.&lt;/p&gt;</description></item><item><title>Dual-mode and multi-wavelength 3D quantitative phase and fluorescence microscopy</title><link>https://biocil.github.io/tr/funding/116f437/</link><pubDate>Fri, 15 Sep 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/funding/116f437/</guid><description/></item><item><title>”Türkiye’de Bilim mi Var?” Diyenleri Şaşırtacak 10 Mühendislik Harikası ve Mühendisleri (Turkish Content)</title><link>https://biocil.github.io/tr/post/20170721/</link><pubDate>Fri, 21 Jul 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20170721/</guid><description>&lt;p&gt;Uzaydaki yerçekimsiz ortam kas erimesine neden olmaktadır. Yer çekimsiz ortamda kas hücrelerini anlık görüntüleyen sistemler ile ilk defa kas erimesinin nedenleri Avrupa Uzay Ajansı tarafından araştırılıyor. Ve bizi gururlandıran güzel haber: Bu sistem bir Türk bilim adamı Yrd. Doç Dr. M. Fatih Toy tarafından geliştiriliyor ve kendisi tarafından Zero G uçuşlarında test ediliyor.&lt;/p&gt;</description></item><item><title>Center for Novel Microscopy Technologies</title><link>https://biocil.github.io/tr/funding/istka/</link><pubDate>Thu, 15 Dec 2016 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/funding/istka/</guid><description/></item><item><title>MOBIEU: Between Atom and Cell, integrating molecular biophysics approaches for biology and healthcare</title><link>https://biocil.github.io/tr/funding/ca15126/</link><pubDate>Wed, 06 Apr 2016 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/funding/ca15126/</guid><description/></item><item><title>Real-time holographic tracking and control of microrobots</title><link>https://biocil.github.io/tr/publication/2016_ral_hong/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2016_ral_hong/</guid><description>Digital holography is used to track the three-dimensional position of a magnetic microrobot maneuvered in real time by means of an electromagnetic manipulation system.</description></item><item><title>Holographic micro-factory</title><link>https://biocil.github.io/tr/funding/2232/</link><pubDate>Fri, 15 May 2015 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/funding/2232/</guid><description/></item><item><title>Super-resolution phase tomography</title><link>https://biocil.github.io/tr/publication/2013_dh_depeursinge/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2013_dh_depeursinge/</guid><description>Digital Holographic Microscopy (DHM) yields reconstructed complex wavefields. It allows synthesizing the aperture of a virtual microscope up to 2π, offering super-resolution phase images. Live images of micro-organisms and neurons with resolution less than 100 nm are presented.</description></item><item><title>Peering into Living Cells (English Content)</title><link>https://biocil.github.io/tr/post/20130211/</link><pubDate>Mon, 11 Feb 2013 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/post/20130211/</guid><description>&lt;p&gt;Two young EPFL scientists have developed a device that can create 3D images of living cells and track their reaction to various stimuli without the use of contrast dyes or fluorophores.&lt;/p&gt;</description></item><item><title>Marker-free phase nanoscopy</title><link>https://biocil.github.io/tr/publication/2013_nphoton_cotte/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2013_nphoton_cotte/</guid><description>We introduce a microscopic method that determines quantitative optical properties beyond the optical diffraction limit and allows direct imaging of unstained living biological specimens.</description></item><item><title>Accelerated autofocusing of off-axis holograms using critical sampling</title><link>https://biocil.github.io/tr/publication/2012_ol_toy/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2012_ol_toy/</guid><description>In this Letter we propose a fast off-axis hologram autofocusing (AF) approach that is based on the redundant data elimination by the critical resampling of the contained complex field.</description></item><item><title>Dealing with reconstructed complex fields in microscopy: Going to the resolution limit and beyond?</title><link>https://biocil.github.io/tr/publication/2012_fom_depeursinge/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2012_fom_depeursinge/</guid><description>As an illustration of the resolution improvement achieved with the synthetized aperture approach, Fig. 1 shows the resolution improvement obtained on a phase image. In summary, synthetizing the spatial frequencies spectrum in the reciprocal space leads to resolution improvement.</description></item><item><title>Digital holographic microscopy for the cytomorphological imaging of cells under zero gravity</title><link>https://biocil.github.io/tr/publication/2012_3dmultidim_toy/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2012_3dmultidim_toy/</guid><description>Experiments on live myoblast cells are carried out on two different platforms; random positioning machine (RPM), a ground base microgravity simulation platform, and parabolic flight campaign (PFC), a fixed wing plane flight providing short durations of alternating gravity conditions. Results show clear perinuclear phase increase. During seconds scale microgravity exposure, measurable scale morphological modifications are observed with the accumulated effect of repetitive exposures and short breaks.</description></item><item><title>Enhanced robustness digital holographic microscopy for demanding environment of space biology</title><link>https://biocil.github.io/tr/publication/2012_bopex_toy/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2012_bopex_toy/</guid><description>We describe an optimized digital holographic microscopy system (DHM) suitable for high-resolution visualization of living cells under conditions of altered macroscopic mechanical forces such as those that arise from changes in gravitational force.</description></item><item><title>Deconvolved phase imaging for diffraction tomography</title><link>https://biocil.github.io/tr/publication/2011_fio_cotte/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2011_fio_cotte/</guid><description>We present a new technique for coherent imaging based on digital holographic microscopy. For high-resolution tomography, the diffraction effect of the microscope objective is corrected by the system’s complex point spread function.</description></item><item><title>Beyond the lateral resolution limit by phase imaging</title><link>https://biocil.github.io/tr/publication/2011_jbo_cotte/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2011_jbo_cotte/</guid><description>With different illumination phases, enhanced bandpass information content is demonstrated, and its spatial resolution is theoretically shown to be potentially signal-to-noise ratio limited.</description></item><item><title>Realistic 3D coherent transfer function inverse filtering of complex fields</title><link>https://biocil.github.io/tr/publication/2011_bopex_cotte/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2011_bopex_cotte/</guid><description>We present a novel technique for three-dimensional (3D) image processing of complex fields.</description></item><item><title>Fourier optics analysis of grating sensors with tilt errors</title><link>https://biocil.github.io/tr/publication/2011_ol_ferhanoglu/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2011_ol_ferhanoglu/</guid><description>Findings show that diffraction grating readout principle is not limited to translating sensors but also can be used for sensors with tilt or other deflection modes.</description></item><item><title>Applications of complex field deconvolution using digital holographic microscopy</title><link>https://biocil.github.io/tr/publication/2011_fom_cotte/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2011_fom_cotte/</guid><description>We propose a method to improve the spatial resolution of such coherent microscopy systems by filtering of the coherent transfer function (CTF). The 3D complex deconvolution is presented and potential applications shown.</description></item><item><title>Microscopy image resolution improvement by deconvolution of complex fields</title><link>https://biocil.github.io/tr/publication/2010_opex_cotte/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2010_opex_cotte/</guid><description>We demonstrate that complex deconvolution does not require any additional optics in the DHM setup while extending the limit of resolution with coherent illumination by a factor of at least 1.64.</description></item><item><title>Sub-Rayleigh resolution by phase imaging</title><link>https://biocil.github.io/tr/publication/2010_ol_cotte/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2010_ol_cotte/</guid><description>The limit of resolution with coherent illumination is extended by a factor of 1.64x.</description></item><item><title>Real Time 3D Cytomorphological Imaging using Digital Holographic Microscopy and Fluorescence Microscopy for Space Biology</title><link>https://biocil.github.io/tr/publication/2010_dh_toy/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2010_dh_toy/</guid><description>A microscope operating in Digital Holographic Microscopy (DHM) and classical widefield epi-fluorescence microscopy in a time sequential manner is developed to study morphological alterations of mouse myoblast cells under simulated microgravity in real time.</description></item><item><title>Studies on synthetic deconvolution of complex fields with digital holographic microscopy</title><link>https://biocil.github.io/tr/publication/2010_fom_cotte/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2010_fom_cotte/</guid><description>A coherent sub-wavelength resolution in a high-NA diffraction-limited optical system is demonstrated using a transmission DHM setup. By adapting inverse deconvolution post processing to coherent illumination conditions, a complex deconvolution procedure is derived.</description></item><item><title>Digital holographic microscopy real-time monitoring of cytoarchitectural alterations during simulated microgravity</title><link>https://biocil.github.io/tr/publication/2010_jbo_pache/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2010_jbo_pache/</guid><description>The DHM analysis reveals cytoskeletal alterations similar to those previously reported with conventional methods, and in agreement with conventional brightfield fluorescence microscopy a posteriori investigation.</description></item><item><title>Dual-mode digital holographic and fluorescence microscopy for the study of morphological changes in cells under simulated microgravity</title><link>https://biocil.github.io/tr/publication/2010_3dmultidim_toy/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2010_3dmultidim_toy/</guid><description>A dual mode microscope is developed to study morphological evolution of mouse myoblast cells under simulated microgravity in real time.</description></item><item><title>Uncooled infrared thermo-mechanical detector array: Design, fabrication and testing</title><link>https://biocil.github.io/tr/publication/2009_sa_toy/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2009_sa_toy/</guid><description>Thermo-mechanical detector arrays in the 160 x 120 array format are designed, fabricated, and tested. Detectors are composed of SiNx and TiN as absorbing layer, Al to form bimaterial legs, and integrated diffraction grating interferometer underneath each detector.</description></item><item><title>Parylene-based uncooled thermomechanical array</title><link>https://biocil.github.io/tr/publication/2009_spiedef_ferhanoglu/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2009_spiedef_ferhanoglu/</guid><description>Parylene was used as the structural material due to its high thermal isolation and mismatch properties. Calculations reveal that the NETD performance of a thermo-mechanical array using Parylene can be significantly better than SiNx based designs and offer a theoretical NETD value &amp;lt;10mK assuming an optical readout with a high dynamic range detector array.</description></item><item><title>MOEMS thermal imaging camera</title><link>https://biocil.github.io/tr/publication/2008_prime_toy/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2008_prime_toy/</guid><description>A novel thermo-mechanical infrared (IR) imaging array with integrated diffraction gratings for optical readout was fabricated and tested.</description></item><item><title>Two-wavelength grating interferometry for MEMS sensors</title><link>https://biocil.github.io/tr/publication/2007_ptl_ferhanoglu/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2007_ptl_ferhanoglu/</guid><description>A two-wavelength readout method is developed that maintains high sensitivity while increasing the detection range, which is demonstrated using a MEMS spectrometer with integrated diffraction grating.</description></item><item><title>Thermal-mechanical Detector Array with Integrated Diffraction Grating</title><link>https://biocil.github.io/tr/publication/2007_leos_ferhanoglu/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2007_leos_ferhanoglu/</guid><description>An uncooled thermal detector array with low NETD is designed and fabricated using MEMS bimaterial structures. A diffraction grating is embedded on the pixel membrane for sensing sub-nm mechanical deflections.</description></item><item><title>Two-wavelength Grating Interferometry for Extended Range MEMS Metrology</title><link>https://biocil.github.io/tr/publication/2007_omn_toy/</link><pubDate>Sun, 01 Jan 2017 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/publication/2007_omn_toy/</guid><description>A two-wavelength readout method is developed that maintains high sensitivity while increasing the detection range from 105 nm to 1.7 um assuming sensitivity is maintained at &amp;gt;50% of the maximum sensitivity</description></item><item><title>Ekip</title><link>https://biocil.github.io/tr/people/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/people/</guid><description/></item><item><title>İletişim</title><link>https://biocil.github.io/tr/contact/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/contact/</guid><description>&lt;p&gt;Laboratuvar, İstanbul Medipol Üniversitesi Biyomedikal Mühendisliği Bölümü’nün bir parçasıdır ve Boğaz’ın Anadolu yakasında, Beykoz’daki Kavacık yerleşkesinde yer alır.&lt;/p&gt;&#10;&lt;p&gt;İş birlikçilerimiz için numune görüntülemekten, misafir öğrenci ve araştırmacıları ağırlamaktan ve ortak projeler ile başvurular üzerine konuşmaktan memnuniyet duyarız.&lt;/p&gt;</description></item><item><title>Laboratuvara katılın</title><link>https://biocil.github.io/tr/join/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://biocil.github.io/tr/join/</guid><description>Biyomedikal mühendisliği, elektrik mühendisliği, fizik ve bilgisayar biliminden doktora ve yüksek lisans öğrencileri alıyoruz. Masada optik düzenekler kuracak ve bunların verisini ölçümlere dönüştüren kodu yazacaksınız.</description></item></channel></rss>