Over the past decades, optical coherence tomography has emerged as an important imaging technique to study biological processes through its ability to perform three-dimensional imaging at high acquisition rates and non-invasively. Furthermore, OCT has shown a growing interest in brain imaging through its capacity in obtaining functional information such as cellular viability, hematocrit and blood flow velocity.
Although OCT can reach image depths spanning a few millimeters, the effective imaging depth is typically dictated by the depth-of-field of the imaging optics. In traditional OCT systems, this depth-of-field is given by the Rayleigh range and is thus coupled to the lateral resolution. As such, increasing the numerical aperture of the system reduces the imaging depth, ultimately hampering the depth-multiplexing advantage of OCT. Wavefront engineering schemes have been devised to overcome this limitation, providing the OCT systems with an extended-focus. We present here two extended-focus OCT systems (xf-OCT) optimized for cerebral imaging. The first system operates in the visible wavelength range and is designed to image the superficial cortex of mice at high contrast and at high resolution. Its high axial and lateral resolution of 0.8 and 1.4 um respectively, maintained over 200 um enable resolving structures such as myelinated axons, neuronal cells and micro-vessels in vivo. The second system is optimized for deep microvascular cortical imaging and operates in the infrared spectral range. Through its extended-focus and increased penetration, the second system can provide maps of cortical microvasculature over 800 um in depth in the cortex in vivo.
Visible light optical coherence tomography has shown great interest in recent years for spectroscopic and high-resolution retinal and cerebral imaging. Here, we present an extended-focus optical coherence microscopy system operating from the visible to the near-infrared wavelength range for high axial and lateral resolution imaging of cortical structures in vivo. The system exploits an ultrabroad illumination spectrum centered in the visible wavelength range (λc = 650 nm, Δλ ∼ 250 nm) offering a submicron axial resolution (∼0.85 μm in water) and an extended-focus configuration providing a high lateral resolution of ∼1.4 μm maintained over ∼150 μm in depth in water. The system’s axial and lateral resolution are first characterized using phantoms, and its imaging performance is then demonstrated by imaging the vasculature, myelinated axons, and neuronal cells in the first layers of the somatosensory cortex of mice in vivo.
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.
KEYWORDS: Optical coherence tomography, Visualization, Real time imaging, Data processing, Doppler tomography, Data acquisition, Graphics processing units, Cameras, 3D image processing, Doppler effect
In this report the application of graphics processing unit (GPU) programming for real-time 3D Fourier domain Optical Coherence Tomography (FdOCT) imaging with implementation of Doppler algorithms for visualization of the flows in capillary vessels is presented. Generally, the time of the data processing of the FdOCT data on the main processor of the computer (CPU) constitute a main limitation for real-time imaging. Employing additional algorithms, such as Doppler OCT analysis, makes this processing even more time consuming. Lately developed GPUs, which offers a very high computational power, give a solution to this problem. Taking advantages of them for massively parallel data processing, allow for real-time imaging in FdOCT. The presented software for structural and Doppler OCT allow for the whole processing with visualization of 2D data consisting of 2000 A-scans generated from 2048 pixels spectra with frame rate about 120 fps. The 3D imaging in the same mode of the volume data build of 220 × 100 A-scans is performed at a rate of about 8 frames per second. In this paper a software architecture, organization of the threads and optimization applied is shown. For illustration the screen shots recorded during real time imaging of the phantom (homogeneous water solution of Intralipid in glass capillary) and the human eye in-vivo is presented.
The authors present the application of graphics processing unit (GPU) programming for real-time three-dimensional (3-D) Fourier domain optical coherence tomography (FdOCT) imaging with implementation of flow visualization algorithms. One of the limitations of FdOCT is data processing time, which is generally longer than data acquisition time. Utilizing additional algorithms, such as Doppler analysis, further increases computation time. The general purpose computing on GPU (GPGPU) has been used successfully for structural OCT imaging, but real-time 3-D imaging of flows has so far not been presented. We have developed software for structural and Doppler OCT processing capable of visualization of two-dimensional (2-D) data (2000 A-scans, 2048 pixels per spectrum) with an image refresh rate higher than 120 Hz. The 3-D imaging of 100×100 A-scans data is performed at a rate of about 9 volumes per second. We describe the software architecture, organization of threads, and optimization. Screen shots recorded during real-time imaging of a flow phantom and the human eye are presented.
Examination of brain functions in small animal models may help improve the diagnosis and treatment of neurological conditions. Transcranial imaging of small rodents' brains poses a major challenge for optical microscopy. Another challenge is to reduce the measurement time. We describe methods and algorithms for three-dimensional assessment of blood flow in the brains of small animals, through the intact skull, using spectral and time domain optical coherence tomography. By introducing a resonant scanner to the optical setup of the optical coherence tomography (OCT) system, we have developed and applied a high-speed spectral OCT technique that allows us to vary the imaging range of flow and to shorten measurement time. Multi-parameter signal analysis enables us to obtain both qualitative and quantitative information about flow velocity from the same set of data.
KEYWORDS: Signal to noise ratio, Image quality, Optical coherence tomography, Scattering, Signal detection, Retina, In vivo imaging, Data acquisition, Interference (communication), Speckle
Spectral and Time domain OCT (STdOCT) is a data analysis scheme proposed for sensitive Doppler
imaging. In this work we show that it has an additional feature: when compared to those created using
complex or amplitude averaging, tomograms prepared using STdOCT have the highest contrast to noise
ratio and preserve high signal to noise ratio and image dynamic range. Images of uniformly scattering
phantom as well as images of human retina in vivo prepared with three different techniques are shown.
KEYWORDS: Data processing, Optical coherence tomography, Visualization, Data acquisition, Real time imaging, Graphics processing units, Imaging systems, Parallel processing, 3D acquisition, Image processing
In this contribution we describe a specialised data processing system for Spectral Optical Coherence Tomography (SOCT)
biomedical imaging which utilises massively parallel data processing on a low-cost, Graphics Processing Unit (GPU). One
of the most significant limitations of SOCT is the data processing time on the main processor of the computer (CPU),
which is generally longer than the data acquisition. Therefore, real-time imaging with acceptable quality is limited to a
small number of tomogram lines (A-scans). Recent progress in graphics cards technology gives a promising solution of
this problem. The newest graphics processing units allow not only for a very high speed three dimensional (3D)
rendering, but also for a general purpose parallel numerical calculations with efficiency higher than provided by the
CPU. The presented system utilizes CUDATM graphic card and allows for a very effective real time SOCT imaging. The
total imaging speed for 2D data consisting of 1200 A-scans is higher than refresh rate of a 120 Hz monitor. 3D rendering
of the volume data build of 10 000 A-scans is performed with frame rate of about 9 frames per second. These frame rates
include data transfer from a frame grabber to GPU, data processing and 3D rendering to the screen. The software
description includes data flow, parallel processing and organization of threads. For illustration we show real time high
resolution SOCT imaging of human skin and eye.
Recently introduced smart scanning protocols called segmented protocols offer possibility to create Spectral
Optical Coherence Tomography images with strongly reduced speckle contrast. The algorithm is fast, robust and
gives cross-sectional images with preserved high lateral resolution. To obtain efficient speckle reduction only
slight modification to the optical setup is required. Cross-sectional images of anterior and posterior parts of the
human eye with reduced speckle noise are presented.
In this paper we demonstrate applicability of Optical Coherence Tomography (OCT) for three-dimensional analysis of
blood flow in brain of small animals. We proposed scanning protocols that enable receiving both qualitative and
quantitative information about flow. Presented data are obtained with a laboratory high resolution and high speed
Spectral OCT system. Data analysis is performed using joint Spectral and Time domain OCT.
We present an application of the Joint Spectral and Time domain OCT (STdOCT) method for detection of wide range of
flows in the retinal vessels. We utilized spectral/Fourier domain OCT (SOCT) technique for development of scan
protocols for Doppler signal analysis. We performed retinal imaging in normal eyes using ultrahigh speed (200 000 axial
scans/s) SOCT instrument with a CMOS camera. Various raster scan protocols were implemented for investigation of
blood flow in the retina. Data analysis was performed using the method of joint Spectral and Time domain OCT
(STdOCT). Detection of blood flow velocities ranging from several tens of mm/s to a fraction of mm/s was possible with
scanning methods allowing for appropriate selection of time intervals between data taken for Doppler OCT analysis.
Axial blood flow velocity measurement was possible in retinal vessels. Doppler OCT signal can be utilized as a contrast
mechanism for visualization of retinal capillaries.
We present a simple and efficient numerical technique for segmentation retinal and choroidal blood
vasculature with bulk motion correction in functional Doppler Spectral Optical Coherence Tomography
(Doppler SOCT). The technique uses local variance of velocity tomogram which is higher in the areas of
the tomogram with internal flow. The resulting variance map reveals the position of vessels. This can be
used either for vessel segmentation purposes or for masking the vessels on velocity tomograms. The
remaining velocity information is connected only with static structure velocity offset. As only Fourier
transformations are used in calculations the algorithm removes the bulk motion from velocity tomograms
and provides images of segmented vessels with speed of 80 000 lines/s. The algorithm is shown to work
with velocity tomograms obtained by joint Spectral and Time domain OCT (STdOCT).
We show that recently developed joint Spectral and Time Optical Coherence Tomography data analysis
scheme combined with oscillatory change of optical path difference allows for simultaneous complex
ambiguity removal and quantitative flow velocity estimation. Full range structural tomograms as well as
velocity distributions of Intralipid solution in glass capillaries are presented.
We propose a modified method of acquisition and analysis of Spectral Optical Coherence Tomography (SOCT)
data to provide information about flow velocities in three dimensions. Joint Spectral and Time domain Optical
Coherence Tomography (joint STdOCT) enables flow velocity assessment and segmentation of flows. STdOCT
method is based on direct detection of Doppler shift that arises in time during the measurement. New scanning
protocols and analysis tools are proposed to create velocity distribution maps of the retina and to segment and
visualize 3D flows. STdOCT segmentation is more sensitive than methods based on phase measurements and
calculations are more straightforward than other techniques, which require more complex experimental setup and
more sophisticated numerical tools. We also discuss parameters, which improve the flow based segmentation
procedure with special attention paid to the problem of broadening of flow velocity distribution.
In this submission we demonstrate a new application of the joint Spectral and Time domain Optical Coherence
Tomography (STdOCT) technique for segmenting and measuring the retinal blood flow velocity in three
dimensions. The method is based on direct detection of Doppler shift that arises in time during the measurement.
New scanning protocols and analysis tools are proposed to create velocity distribution maps of the retina and to
segment and visualize 3D vasculature of human eye in-vivo. STdOCT segmentation is more sensitive than methods
based on phase measurements and calculations are more straightforward than other techniques, which require more
complex experimental setup and more sophisticated numerical tools. The usage of ultra-fast line scan camera allows
to broaden the axial velocity range up to ±24mm/s, thus all high flows in human retina can be registered.
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