Efficient reduction of speckle noise in Optical Coherence Tomography

Speckle pattern, which is inherent in coherence imaging, influences significantly axial and transversal resolution of Optical Coherence Tomography (OCT) instruments. The well known speckle removal techniques are either sensitive to sample motion, require sophisticated and expensive sample tracking systems, or involve sophisticated numerical procedures. As a result, their applicability to in vivo real-time imaging is limited. In this work, we propose to average multiple A-scans collected in a fully controlled way to reduce the speckle contrast. This procedure involves non-coherent averaging of OCT A-scans acquired from adjacent locations on the sample. The technique exploits scanning protocol with fast beam deflection in the direction perpendicular to lateral dimension of the cross-sectional image. Such scanning protocol reduces the time interval between A-scans to be averaged to the repetition time of the acquisition system. Consequently, the averaging algorithm is immune to bulk motion of an investigated sample, does not require any sophisticated data processing to align cross-sectional images, and allows for precise control of lateral shift of the scanning beam on the object. The technique is tested with standard Spectral OCT system with an extra resonant scanner used for rapid beam deflection in the lateral direction. Ultrahigh speed CMOS camera serves as a detector and acquires 200,000 spectra per second. A dedicated A-scan generation algorithm allows for real-time display of images with reduced speckle contrast at 6 frames/second. This technique is applied to in vivo imaging of anterior and posterior segments of the human eye and human skin

Customizable tubular model for n-furcating blood vessels and its application to 3D reconstruction of the cerebrovascular system

Understanding the 3D cerebral vascular network is one of the pressing issues impacting the diagnostics of various systemic disorders and is helpful in clinical therapeutic strategies. Unfortunately, the existing software in the radiological workstation does not meet the expectations of radiologists who require a computerized system for detailed, quantitative analysis of the human cerebrovascular system in 3D and a standardized geometric description of its components. In this study, we show a method that uses 3D image data from magnetic resonance imaging with contrast to create a geometrical reconstruction of the vessels and a parametric description of the reconstructed segments of the vessels. First, the method isolates the vascular system using controlled morphological growing and performs skeleton extraction and optimization. Then, around the optimized skeleton branches, it creates tubular objects optimized for quality and accuracy of matching with the originally isolated vascular data. Finally, it optimizes the joints on n-furcating vessel segments. As a result, the algorithm gives a complete description of shape, position in space, position relative to other segments, and other anatomical structures of each cerebrovascular system segment. Our method is highly customizable and in principle allows reconstructing vascular structures from any 2D or 3D data. The algorithm solves shortcomings of currently available methods including failures to reconstruct the vessel mesh in the proximity of junctions and is free of mesh collisions in high curvature vessels. It also introduces a number of optimizations in the vessel skeletonization leading to a more smooth and more accurate model of the vessel network. We have tested the method on 20 datasets from the public magnetic resonance angiography image database and show that the method allows for repeatable and robust segmentation of the vessel network and allows to compute vascular lateralization indices. Graphical abstract: [Figure not available: see fulltext.]</p

Blood flow rate estimation in optic disc capillaries and vessels using Doppler optical coherence tomography with 3D fast phase unwrapping

The retinal volumetric flow rate contains useful information not only for ophthalmology but also for the diagnosis of common civilization diseases such as diabetes, Alzheimer's disease, or cerebrovascular diseases. Non-invasive optical methods for quantitative flow assessment, such as Doppler optical coherence tomography (OCT), have certain limitations. One is the phase wrapping that makes simultaneous calculations of the flow in all human retinal vessels impossible due to a very large span of flow velocities. We demonstrate that three-dimensional Doppler OCT combined with three-dimensional four Fourier transform fast phase unwrapping (3D 4FT FPU) allows for the calculation of the volumetric blood flow rate in real-time by the implementation of the algorithms in a graphics processing unit (GPU). The additive character of the flow at the furcations is proven using a microfluidic device with controlled flow rates as well as in the retinal veins bifurcations imaged in the optic disc area of five healthy volunteers. We show values of blood flow rates calculated for retinal capillaries and vessels with diameters in the range of 12-150 µm. The potential of quantitative measurement of retinal blood flow volume includes noninvasive detection of carotid artery stenosis or occlusion, measuring vascular reactivity and evaluation of vessel wall stiffness

Imaging of the stroke-related changes in the vascular system of the mouse brain with the use of extended focus Optical Coherence Microscopy

We used Optical Coherence Microscopy (OCM) to monitor structural and functional changes due to ischemic stroke in small animals brains in vivo. To obtain lateral resolution of 2.2 μm over the range of 600 μm we used extended focus configuration of OCM instrument involving Bessel beam. It provided access to detailed 3D information about the changes in brain vascular system up to the level of capillaries across I and II/III layers of neocortex. We used photothrombotic stroke model involving photoactive application of rose bengal to assure minimal invasiveness of the procedure and precise localization of the clot distribution center. We present the comparative analysis involving structural and angiographic maps of the stroke-affected brain enabling in-depth insight to the process of development of the disorder

Anterior segment imaging with Spectral OCT system using a high-speed CMOS camera

We describe a new ultrahigh speed Spectral OCT instrument making use of a CMOS camera and demonstrate high quality in vivo imaging of the anterior segment of the human eye. The high flexibility of the designed imaging system allows a wide range of imaging protocols. Two- and three-dimensional high quality OCT images of the cornea, the anterior chamber and the crystalline lens are presented. A high acquisition rate, up to 135,000 A-scans/second enables three-dimensional reconstruction of the anterior segment during lenticular accommodation, blinking and pupillary reaction to light stimulus. We demonstrate OCT tomographic real time imaging of the lens dynamics during accommodation and high quality OCT cross-sectional images of the entire anterior segment of the eye from the cornea up to posterior part of the crystalline lens. ©2009 Optical Society of America.This work was supported by EuroHORCs-European Science Foundation EURYI Award EURYI-01/2008-PL (M.W.) and EURYI-05-102-ES (S. M.) as well as by Polish Ministry of Science and Higher Education (research grant for years 2006-2008) and by the project operated within the Foundation for Polish Science Ventures Programme co-financed by the EU European Regional Development Fund (M. G.). The support of the Rector of the Nicolaus Copernicus University (scientific grant 504-F M.W.) is also gratefully acknowledged.Peer Reviewe

Estimation of vibration amplitude in Fourier domain optical coherence tomography interferometric signals from Doppler spectrum

In presented method combination of Fourier and Time domain detection enables to broaden the effective bandwidth for time dependent Doppler Signal that allows for using higher-order Bessel functions to calculate unambiguously the vibration amplitudes

Quantitative lateral and axial flow imaging with optical coherence microscopy and tomography

Optical coherence tomography (OCT) and optical coherence microscopy (OCM) allow the acquisition of quantitative three-dimensional axial flow by estimating the Doppler shift caused by moving scatterers. Measuring the velocity of red blood cells is currently the principal application of these methods. In many biological tissues, blood flow is often perpendicular to the optical axis, creating the need for a quantitative measurement of lateral flow. Previous work has shown that lateral flow can be measured from the Doppler bandwidth, albeit only for simplified optical systems. In this work, we present a generalized model to analyze the influence of relevant OCT/OCM system parameters such as light source spectrum, numerical aperture and beam geometry on the Doppler spectrum. Our analysis results in a general framework relating the mean and variance of the Doppler frequency to the axial and lateral flow velocity components. Based on this model, we present an optimized acquisition protocol and algorithm to reconstruct quantitative measurements of lateral and axial flow from the Doppler spectrum for any given OCT/OCM system. To validate this approach, Doppler spectrum analysis is employed to quantitatively measure flow in a capillary with both extended focus OCM and OCT.info:eu-repo/semantics/publishe

Corneal topography from spectral optical coherence tomography (sOCT)

We present a method to obtain accurate corneal topography from a spectral optical coherence tomography (sOCT) system. The method includes calibration of the device, compensation of the fan (or field) distortion introduced by the scanning architecture, and image processing analysis for volumetric data extraction, segmentation and fitting. We present examples of three-dimensional (3-D) surface topography measurements on spherical and aspheric lenses, as well as on 10 human corneas in vivo. Results of sOCT surface topography (with and without fan-distortion correction) were compared with non-contact profilometry (taken as reference) on a spherical lens, and with non-contact profilometry and state-of-the art commercial corneal topography instruments on aspheric lenses and on subjects. Corneal elevation maps from all instruments were fitted by quadric surfaces (as well as by tenth-order Zernike polynomials) using custom routines. We found that the discrepancy in the estimated radius of curvature from nominal values in artificial corneas decreased from 4.6% (without fan distortion correction) to 1.6% (after fan distortion correction), and the difference in the asphericity decreased from 130% to 5%. In human corneas, the estimated corneal radius of curvature was not statistically significantly different across instruments. However, a Bland-Altman analysis showed consistent differences in the estimated asphericity and corneal shape between sOCT topographies without fan distortion correction and the rest of the measurements.This research was funded by grants FIS2008-02065 and EURYI-05-102-ES (EURHORCs-ESF) to S. M., CSIC JAE- Doc Program to D. S., CSIC JAE-Intro to N. C., and MICINN Programa Técnicos de Apoyo to P. P. M. M Szkulmowski was supported by EuroHORCs-European Science Foundation EURYI Award EURYI-01/2008-PL.Peer Reviewe

In vivo brain imaging with multimodal optical coherence microscopy in a mouse model of thromboembolic photochemical stroke

We used a new multimodal imaging system that combines optical coherence microscopy and brightfield microscopy. Using this in vivo brain monitoring approach and cranial window implantation, we three-dimensionally visualized the vascular network during thrombosis, with high temporal (18 s) and spatial (axial, 2.5 μm; lateral, 2.2 μm) resolution.We used a modified mouse model of photochemical thromboembolic stroke in order to more accurately parallel human stroke. Specifically, we applied green laser illumination to focally occlude a branch of the middle cerebral artery. Despite the recanalization of the superficial arteries at 24 h after stroke, no blood flow was detected in the small vessels within deeper regions. Moreover, after 24 h of stroke progression, scattering signal enhancement was observed within the stroke region. We also evaluated the infarct extent and shape histologically. In summary, we present a novel approach for real-time mouse brain monitoring and ischemic variability analysis. This multimodal imaging method permits the analysis of thrombosis progression and reperfusion. Additionally and importantly, the system could be used to study the effect of poststroke drug treatments on blood flow in small arteries and capillaries of the brain