https://biocil.github.io/tr/publication/Recent content in Yayınlar on Phi-XHugotr-TRWed, 29 Jul 2026 00:00:00 +0000https://biocil.github.io/tr/publication/2026_scirep_oguz/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2026_scirep_oguz/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.https://biocil.github.io/tr/publication/2026_optcon_sahloul/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2026_optcon_sahloul/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.https://biocil.github.io/tr/publication/2026_bopex_hussein/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2026_bopex_hussein/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.https://biocil.github.io/tr/publication/wo2024208601/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/wo2024208601/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.https://biocil.github.io/tr/publication/2024_frbm_altun/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2024_frbm_altun/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.https://biocil.github.io/tr/publication/wo2023172228/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/wo2023172228/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.https://biocil.github.io/tr/publication/2023_jmems_tekin/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2023_jmems_tekin/In this study, we investigate the effect of fused deposition modeling printing direction on the effective Young’s modulus value of cantilevers.https://biocil.github.io/tr/publication/2022_spiepe_ozbilgin/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2022_spiepe_ozbilgin/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.https://biocil.github.io/tr/publication/2022_spiepe_gurcan_b/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2022_spiepe_gurcan_b/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.https://biocil.github.io/tr/publication/2022_spiepe_gurcan_a/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2022_spiepe_gurcan_a/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).https://biocil.github.io/tr/publication/us11231322/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/us11231322/A prism spectrometer having higher resolution and wider spectral width through the use of a speckle generating diffuser.https://biocil.github.io/tr/publication/2021_tiptekno_ozbilgin/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2021_tiptekno_ozbilgin/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.https://biocil.github.io/tr/publication/2021_electrica_toy/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2021_electrica_toy/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.https://biocil.github.io/tr/publication/2020_jlt_cetindag/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2020_jlt_cetindag/We present an optical efficiency improved speckle spectrometer where a scattering metal wave-guide is utilized along with a conventional prism spectrometer.https://biocil.github.io/tr/publication/2019_oc_toy/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2019_oc_toy/Here, a wedge prism based simple approach is introduced to acquire quantitative phase images on a standard microscope.https://biocil.github.io/tr/publication/2019_omn_cetindag/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2019_omn_cetindag/We present an improved prism spectrometer with high wavelength range and spectral resolution.https://biocil.github.io/tr/publication/2018_ptl_cetindag/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2018_ptl_cetindag/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.https://biocil.github.io/tr/publication/2018_nanotr_toy/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2018_nanotr_toy/Here it is proposed to implement an off-axis holography layout that utilizes a single wedge prism.https://biocil.github.io/tr/publication/2019_qpi_toy/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2019_qpi_toy/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.https://biocil.github.io/tr/publication/2016_ral_hong/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2016_ral_hong/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.https://biocil.github.io/tr/publication/2013_dh_depeursinge/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2013_dh_depeursinge/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.https://biocil.github.io/tr/publication/2013_nphoton_cotte/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2013_nphoton_cotte/We introduce a microscopic method that determines quantitative optical properties beyond the optical diffraction limit and allows direct imaging of unstained living biological specimens.https://biocil.github.io/tr/publication/2012_ol_toy/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2012_ol_toy/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.https://biocil.github.io/tr/publication/2012_fom_depeursinge/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2012_fom_depeursinge/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.https://biocil.github.io/tr/publication/2012_3dmultidim_toy/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2012_3dmultidim_toy/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.https://biocil.github.io/tr/publication/2012_bopex_toy/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2012_bopex_toy/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.https://biocil.github.io/tr/publication/2011_fio_cotte/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2011_fio_cotte/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.https://biocil.github.io/tr/publication/2011_jbo_cotte/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2011_jbo_cotte/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.https://biocil.github.io/tr/publication/2011_bopex_cotte/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2011_bopex_cotte/We present a novel technique for three-dimensional (3D) image processing of complex fields.https://biocil.github.io/tr/publication/2011_ol_ferhanoglu/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2011_ol_ferhanoglu/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.https://biocil.github.io/tr/publication/2011_fom_cotte/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2011_fom_cotte/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.https://biocil.github.io/tr/publication/2010_opex_cotte/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2010_opex_cotte/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.https://biocil.github.io/tr/publication/2010_ol_cotte/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2010_ol_cotte/The limit of resolution with coherent illumination is extended by a factor of 1.64x.https://biocil.github.io/tr/publication/2010_dh_toy/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2010_dh_toy/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.https://biocil.github.io/tr/publication/2010_fom_cotte/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2010_fom_cotte/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.https://biocil.github.io/tr/publication/2010_jbo_pache/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2010_jbo_pache/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.https://biocil.github.io/tr/publication/2010_3dmultidim_toy/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2010_3dmultidim_toy/A dual mode microscope is developed to study morphological evolution of mouse myoblast cells under simulated microgravity in real time.https://biocil.github.io/tr/publication/2009_sa_toy/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2009_sa_toy/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.https://biocil.github.io/tr/publication/2009_spiedef_ferhanoglu/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2009_spiedef_ferhanoglu/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 <10mK assuming an optical readout with a high dynamic range detector array.https://biocil.github.io/tr/publication/2008_prime_toy/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2008_prime_toy/A novel thermo-mechanical infrared (IR) imaging array with integrated diffraction gratings for optical readout was fabricated and tested.https://biocil.github.io/tr/publication/2007_ptl_ferhanoglu/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2007_ptl_ferhanoglu/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.https://biocil.github.io/tr/publication/2007_leos_ferhanoglu/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2007_leos_ferhanoglu/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.https://biocil.github.io/tr/publication/2007_omn_toy/Sun, 01 Jan 2017 00:00:00 +0000https://biocil.github.io/tr/publication/2007_omn_toy/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 >50% of the maximum sensitivity