S. Sherif

Optical coherence tomography: fundamental principles, instrumental designs and biomedical applications

The advances made in the last two decades in interference technologies, optical instrumentation, catheter technology, optical detectors, speed of data acquisition and processing as well as light sources have facilitated the transformation of optical coherence tomography from an optical method used mainly in research laboratories into a valuable tool applied in various areas of medicine and health sciences. This review paper highlights the place occupied by optical coherence tomography in relation to other imaging methods that are used in medical and life science areas such as ophthalmology, cardiology, dentistry and gastrointestinal endoscopy. Together with the basic principles that lay behind the imaging method itself, this review provides a summary of the functional differences between time-domain, spectral-domain and full-field optical coherence tomography, a presentation of specific methods for processing the data acquired by these systems, an introduction to the noise sources that plague the detected signal and the progress made in optical coherence tomography catheter technology over the last decade.

Improved importance sampling for Monte Carlo simulation of time-domain optical coherence tomography

We developed an importance sampling based method that significantly speeds up the calculation of the diffusive reflectance due to ballistic and to quasi-ballistic components of photons scattered in turbid media: Class I diffusive reflectance. These components of scattered photons make up the signal in optical coherence tomography (OCT) imaging. We show that the use of this method reduces the computation time of this diffusive reflectance in time-domain OCT by up to three orders of magnitude when compared with standard Monte Carlo simulation. Our method does not produce a systematic bias in the statistical result that is typically observed in existing methods to speed up Monte Carlo simulations of light transport in tissue. This fast Monte Carlo calculation of the Class I diffusive reflectance can be used as a tool to further study the physical process governing OCT signals, e.g., obtain the statistics of the depth-scan, including the effects of multiple scattering of light, in OCT. This is an important prerequisite to future research to increase penetration depth and to improve image extraction in OCT.

Monte Carlo simulation of optical coherence tomography for turbid media with arbitrary spatial distributions

Abstract. We developed a Monte Carlo-based simulator of optical coherence tomography (OCT) imaging for turbid media with arbitrary spatial distributions. This simulator allows computation of both Class I diffusive reflectance due to ballistic and quasiballistic scattered photons and Class II diffusive reflectance due to multiple scattered photons. It was implemented using a tetrahedron-based mesh and importance sampling to significantly reduce computational time. Our simulation results were verified by comparing them with results from two previously validated OCT simulators for multilayered media. We present simulation results for OCT imaging of a sphere inside a background slab, which would not have been possible with earlier simulators. We also discuss three important aspects of our simulator: (1) resolution, (2) accuracy, and (3) computation time. Our simulator could be used to study important OCT phenomena and to design OCT systems with improved performance.

Fast calculation of multipath diffusive reflectance in optical coherence tomography

We show how to efficiently calculate the signal in optical coherence tomography (OCT) systems due to the ballistic photons, the quasi-ballistic photons, and the photons that undergo multiple diffusive scattering using Monte Carlo simulations with importance sampling. This method enables the calculation of these three components of the OCT signal with less than one hundredth of the computational time required by the conventional Monte Carlo method. Therefore, it can be used as a design tool to characterize the performance of OCT systems, and can also be used in the development of novel signal processing techniques that can extend the imaging range of OCT systems. We investigate the parameter dependence of our importance sampling method and we validate it by comparison to an existing method.

Assessment of Fusarium and Deoxynivalenol Using Optical Methods

Fusarium is a widely spread fungus that affects small cereal grains mostly during flowering and thrives in warm, moist conditions. Fusarium head blight diminishes the nutritional, physical, and chemical qualities of the grains, which consequently lowers their market value. Mycotoxins are toxic, secondary metabolites produced during the fungal infection process and are not eliminated by industrial processes such as milling, baking, malting, or ethanol production. Above certain levels, mycotoxins can have toxic effects in humans and livestock. Therefore, Fusarium monitoring is extremely important to avoid potential mycotoxin production. Optical techniques are recognized as one of the best ways to assess a batch of samples in a fast and non-destructive way. Previous reviews on Fusarium assessment have provided an overview of all the possible methods for its detection, while others list Fusarium as one among several known plant diseases and provide some applicable methods for safety inspection of food. This paper reviews current techniques for grain quality assessment, particularly a thorough appraisal of the optical methods and classification algorithms applied to identify and determine the infection level of Fusarium spp. Hence, this work highlights the latest literature concerning Fusarium and deoxynivalenol identification and currently used methods to determine levels of infection.

Accelerated simulation of optical coherence tomography of objects with arbitrary spatial distributions

We developed a highly parallel simulator of Optical Coherence Tomography (OCT) of objects with arbitrary spatial distributions. This Monte Carlo method based simulator models the object as a tetrahedron-based mesh, and implements an advanced importance sampling scheme. This new method makes OCT simulations more practical, since the corresponding serial Central Processing Unit (CPU) based implementation requires approximately 360 hours to simulate OCT imaging of a single B-scan. We implemented this new simulator on Graphics Processing Units (GPUs) using the Compute Unified Device Architecture (CUDA) platform and programming model by NVIDIA. We demonstrated that our new simulator requires one order of magnitude less time, compared to its serial implementation, to simulate the same OCT images. Our new parallel OCT simulator could be an important and practical tool to study different OCT phenomena and to design novel OCT systems with superior imaging performance.

High-power 1300 nm FDML swept laser using polygon-based narrowband optical scanning filter

Swept-source optical coherence tomography (SS-OCT) has received much attention in recent years because of its higher sensitivity in high speed imaging. A fast and high powered wavelength-swept laser is important for SS-OCT since its speed and sensitivity directly rely on the sweeping rate and the output power of the swept laser. Much progress has been made on the development of high-speed swept lasers, but their output power has been limited. We present a Fourierdomain mode-locked 1300 nm wavelength-swept laser that uses a polygon-based narrowband optical scanning filter and a high-efficiency semiconductor optical amplifier. The optical filter and laser structure were designed and constructed for an optimized optical power output. Average output powers of 71 mW has been achieved without an external amplifier, while the wavelength is swept continuously from 1247 nm to 1360 nm. A unidirectional wavelength sweeping rate of 7452 nm/ms (65.95 kHz repetition rate) was achieved by using a 72 facet polygon scanner with a rotation rate of 916 revolutions per second. The instantaneous linewidth of this laser is 0.09 nm, which corresponds to a coherence length of 16 mm. This laser is most suitable for optical coherence tomography applications.

Texture based segmentation method to detect atherosclerotic plaque from optical tomography images

Optical coherence tomography (OCT) imaging has been widely employed in assessing cardiovascular disease. Atherosclerosis is one of the major cause cardio vascular diseases. However visual detection of atherosclerotic plaque from OCT images is often limited and further complicated by high frame rates. We developed a texture based segmentation method to automatically detect plaque and non plaque regions from OCT images. To verify our results we compared them to photographs of the vascular tissue with atherosclerotic plaque that we used to generate the OCT images. Our results show a close match with photographs of vascular tissue with atherosclerotic plaque. Our texture based segmentation method for plaque detection could be potentially used in clinical cardiovascular OCT imaging for plaque detection.

Swept-source full-field optical coherence microscopy

Full-Field Optical Coherence Microscopy (FF-OCM) is a microscopic imaging device based on interferometry. It can produce cross-sectional images of bio-tissue or cell samples at a resolution in the order of a micron. Because it can extract an en-face image directly from the sample, it does not need 2D scanning mechanism, which greatly increases the imaging speed compared to fibre-based OCT systems. However, a controlled translation stage is still required in the reference arm of the interferometer to perform the depth scan. Swept-Source OCT (SS-OCT) technology is the second generation of the OCT systems, which not only removes the mechanical scanning, but also increases the signal / noise ratio of the extracted OCT images. In this paper, we describe the design and implementation of a swept-wavelength source based FF-OCM with 60X magnification; 8 um depth resolution; 4 μm depth resolution; 20 mm working distance and 15 frames / second imaging speed.

Scaled nonuniform Fourier transform for image reconstruction in swept source optical coherence tomography

Swept Source optical coherence tomography (SS-OCT) is an important imaging modality for both medical and industrial diagnostic applications. A cross-sectional SS-OCT image is obtained by applying an inverse discrete Fourier transform (DFT) to axial interferograms measured in the frequency domain (k-space). This inverse DFT is typically implemented as a fast Fourier transform (FFT) that requires the data samples to be equidistant in k-space. As the frequency of light produced by a typical wavelength-swept laser is nonlinear in time, the recorded interferogram samples will not be uniformly spaced in k-space. Many image reconstruction methods have been proposed to overcome this problem. Most such methods rely on oversampling the measured interferogram then use either hardware, e.g., Mach-Zhender interferometer as a frequency clock module, or software, e.g., interpolation in k-space, to obtain equally spaced samples that are suitable for the FFT. To overcome the problem of nonuniform sampling in k-space without any need for interferogram oversampling, an earlier method demonstrated the use of the nonuniform discrete Fourier transform (NDFT) for image reconstruction in SS-OCT. In this paper, we present a more accurate method for SS-OCT image reconstruction from nonuniform samples in k-space using a scaled nonuniform Fourier transform. The result is demonstrated using SS-OCT images of Axolotl salamander eggs.