Oguzhan Avci

Smart Interface Materials Integrated with Microfluidics for On-Demand Local Capture and Release of Cells

Stimuli responsive, smart interface materials are integrated with microfluidic technologies creating new functions for a broad range of biological and clinical applications by controlling the material and cell interactions. Local capture and on-demand local release of cells are demonstrated with spatial and temporal control in a microfluidic system.

Interferometric Reflectance Imaging Sensor (IRIS)—A Platform Technology for Multiplexed Diagnostics and Digital Detection

Over the last decade, the growing need in disease diagnostics has stimulated rapid development of new technologies with unprecedented capabilities. Recent emerging infectious diseases and epidemics have revealed the shortcomings of existing diagnostics tools, and the necessity for further improvements. Optical biosensors can lay the foundations for future generation diagnostics by providing means to detect biomarkers in a highly sensitive, specific, quantitative and multiplexed fashion. Here, we review an optical sensing technology, Interferometric Reflectance Imaging Sensor (IRIS), and the relevant features of this multifunctional platform for quantitative, label-free and dynamic detection. We discuss two distinct modalities for IRIS: (i) low-magnification (ensemble biomolecular mass measurements) and (ii) high-magnification (digital detection of individual nanoparticles) along with their applications, including label-free detection of multiplexed protein chips, measurement of single nucleotide polymorphism, quantification of transcription factor DNA binding, and high sensitivity digital sensing and characterization of nanoparticles and viruses.

Physical modeling of interference enhanced imaging and characterization of single nanoparticles.

Interferometric imaging schemes have gained significant interest due to their superior sensitivity over imaging techniques that are solely based on scattered signal. In this study, we outline the theoretical foundations of imaging and characterization of single nanoparticles in an interferometric microscopy scheme, examine key parameters that influence the signal, and benchmark the model against experimental findings.

Pupil function engineering for enhanced nanoparticle visibility in wide-field interferometric microscopy

Wide-field interferometric microscopy techniques have demonstrated their utility in sensing minute changes in the optical path length as well as visualization of sub-diffraction-limited nanoparticles. In this work, we demonstrate enhanced signal levels for nanoparticle detection by pupil function engineering in wide-field common-path interferometric microscopy. We quantify the improvements in nanoparticle signal achieved by novel optical filtering schemes, benchmark them against theory, and provide physical explanations for the signal enhancements. Our refined common-path interferometric microscopy technique provides an overall ten-fold enhancement in the visibility of low-index, non-resonant polystyrene nanospheres (r∼25  nm), resulting in nearly 8% signal-to-background ratio. Our method can be a highly sensitive, low-cost, label-free, high-throughput platform for accurate detection and characterization of weakly scattering low-index nanoparticles with sizes ranging from several hundred down to a few tens of nanometers, covering nearly the entire size spectrum of biological particles.

Robust Visualization and Discrimination of Nanoparticles by Interferometric Imaging

Single-molecule and single-nanoparticle biosensors are a growing frontier in diagnostics. Digital biosensors are those which enumerate all specifically immobilized biomolecules or biological nanoparticles, and thereby achieve limits of detection usually beyond the reach of ensemble measurements. Here, we review modern optical techniques for single nanoparticle detection and describe the single-particle interferometric reflectance imaging sensor (SP-IRIS). We present challenges associated with reliably detecting faint nanoparticles with SP-IRIS, and describe image acquisition processes and software modifications to address them. Specifically, we describe an image acquisition processing method for the discrimination and accurate counting of nanoparticles that greatly reduce both the number of false positives and false negatives. These engineering improvements are critical steps in the translation of SP-IRIS toward applications in medical diagnostics.

Reconstruction in wide-field interferometric microscopy for imaging weakly scattering biological nanoparticles with super-resolution (Conference Presentation)

Wide-field interferometric microscopy is a common-path interferometry technique that allows for label-free and high-throughput detection of weakly scattering sub-diffraction-limited biological nanoparticles. Such nanoparticles appear as diffraction-limited-spots in the image and optically resolving them beyond their ‘digital’ detection still remains a challenge owing to the diffraction barrier as well as the typical signal levels that fall below the noise floor. In this study, we demonstrate the utility of computational optics in the interference enhanced nanoparticle imaging to improve its resolving power to obtain structural information on clinically relevant and often complexed-shaped biological nanoparticles such as viruses and exosomes. We consider a spatially incoherent structured illumination based image reconstruction strategy in wide-field interferometric microscopy to achieve high contrast nanoparticle imaging with super-resolution. Our reconstruction technique makes use of the optical transfer function of the system derived via an analytical model based on angular spectrum representation. We provide experimental demonstrations using an artificial sample to quantify the resolution enhancement as well as a biological sample for concept demonstration. We also benchmark the results against gold standard images obtained using an electron microscope. Our highly-sensitive super-resolution imaging system constitutes a noncomplex optical design, which can be realized with simple modifications to a conventional epi-illumination microscope, offering a cost-effective alternative to the laborious and expensive standard high-resolution microscopy techniques. It has a broad spectrum of applications ranging from clinical diagnostics to biotechnological research.

Nanoparticle classification in wide-field interferometric microscopy by supervised learning from model

Interference-enhanced wide-field nanoparticle imaging is a highly sensitive technique that has found numerous applications in labeled and label-free subdiffraction-limited pathogen detection. It also provides unique opportunities for nanoparticle classification upon detection. More specifically, the nanoparticle defocus images result in a particle-specific response that can be of great utility for nanoparticle classification, particularly based on type and size. In this work, we combine a model-based supervised learning algorithm with a wide-field common-path interferometric microscopy method to achieve accurate nanoparticle classification. We verify our classification schemes experimentally by blindly detecting gold and polystyrene nanospheres, and then classifying them in terms of type and size.

Label-Free and High-Throughput Detection of Biomolecular Interactions Using a Flatbed Scanner Biosensor

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 (∼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 ∼30 pg/mm2, and a scan speed of 5 s (50 s for 10 frames averaged) for a 2 mm × 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.

Digital detection of biomarkers for high-sensitivity diagnostics at low-cost

We have demonstrated Interferometric Reflectance Imaging Sensor (IRIS) with the ability to detect single nanoscale particles. By extending single-particle IRIS to in-liquid dynamic imaging, we demonstrated real-time digital detection of individual viral pathogens as well as single molecules labeled with Au nanoparticles. With this technique we demonstrate real-time simultaneous detection of multiple targets in a single sample, as well as quantitative dynamic detection of individual biomolecular interactions for reaction kinetics measurements. This approach promises to simplify and reduce the cost of rapid diagnostics.

Low cost flatbed scanner label-free biosensor

In this paper, we demonstrate utilization of a commercial flatbed document scanner as a label-free biosensor for highthroughput 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 ~10μm lateral resolution, the presented system offers a super low cost, easy to use alternative to commercially available label-free systems.