Real time processing of Fourier domain optical coherence tomography with fixed-pattern noise removal by partial median subtraction using a graphics processing unit

Optimized depth-resolved estimation to measure optical attenuation coefficients from optical coherence tomography and its application in cerebral damage determination

The optical attenuation coefficient (OAC) reflects the optical properties of various tissues or tissues of the same type under different physiological conditions. Quantitative measurement of OAC from optical coherence tomography (OCT) signals can provide additional information and can increase the potential for OCT applications. We present an optimized depth-resolved estimation (ODRE) method that derives a precise mapping between the measured OCT signal and the OAC. In contrast to previous depth-resolved estimation (DRE) methods, the optimized method can estimate the OAC in any depth range and ignore whether the light is completely attenuated. Numerical simulations and phantom experiments are used to verify its validity, and this method is applied to detect cerebral damage. In combination with OCT angiography, real-time observation of the change of blood perfusion and the degree of cerebral damage in mice with focal cerebral ischemia provides important information to help us understand the temporal relationship between brain damage and ischemia.

Functional optical coherence tomography of rat olfactory bulb with periodic odor stimulation

In rodent olfactory bulb (OB), optical intrinsic signal imaging (OISI) is commonly used to investigate functional maps to odorant stimulations. However, in such studies, the spatial resolution in depth direction (z-axis) is lost because of the integration of light from different depths. To solve this problem, we propose functional optical coherence tomography (fOCT) with periodic stimulation and continuous recording. In fOCT experiments of in vivo rat OB, propionic acid and m-cresol were used as odor stimulus presentations. Such a periodic stimulation enabled us to detect the specific odor-responses from highly scattering brain tissue. Swept source OCT operating at a wavelength of 1334 nm and a frequency of 20 kHz, was employed with theoretical depth and lateral resolutions of 6.7 μm and 15.4 μm, respectively. We succeeded in visualizing 2D cross sectional fOCT map across the neural layer structure of OCT in vivo. The detected fOCT signals corresponded to a few glomeruli of the medial and lateral parts of dorsal OB. We also obtained 3D fOCT maps, which upon integration across z-axis agreed well with OISI results. We expect such an approach to open a window for investigating and possibly addressing toward inter/intra-layer connections at high resolutions in the future.

Graphics processing unit accelerated intensity-based optical coherence tomography angiography using differential frames with real-time motion correction

We demonstrate intensity-based optical coherence tomography (OCT) angiography using the squared difference of two sequential frames with bulk-tissue-motion (BTM) correction. This motion correction was performed by minimization of the sum of the pixel values using axial- and lateral-pixel-shifted structural OCT images. We extract the BTM-corrected image from a total of 25 calculated OCT angiographic images. Image processing was accelerated by a graphics processing unit (GPU) with many stream processors to optimize the parallel processing procedure. The GPU processing rate was faster than that of a line scan camera (46.9 kHz). Our OCT system provides the means of displaying structural OCT images and BTM-corrected OCT angiographic images in real time.

Dual-band Fourier domain optical coherence tomography with depth-related compensations

Dual-band Fourier domain optical coherence tomography (FD-OCT) provides depth-resolved spectroscopic imaging that enhances tissue contrast and reduces image speckle. However, previous dual-band FD-OCT systems could not correctly give the tissue spectroscopic contrast due to depth-related discrepancy in the imaging method and attenuation in biological tissue samples. We designed a new dual-band full-range FD-OCT imaging system and developed an algorithm to compensate depth-related fall-off and light attenuation. In our imaging system, the images from two wavelength bands were intrinsically overlapped and their intensities were balanced. The processing time of dual-band OCT image reconstruction and depth-related compensations were minimized by using multiple threads that execute in parallel. Using the newly developed system, we studied tissue phantoms and human cancer xenografts and muscle tissues dissected from severely compromised immune deficient mice. Improved spectroscopic contrast and sensitivity were achieved, benefiting from the depth-related compensations.

Medical image processing on the GPU - past, present and future

Graphics processing units (GPUs) are used today in a wide range of applications, mainly because they can dramatically accelerate parallel computing, are affordable and energy efficient. In the field of medical imaging, GPUs are in some cases crucial for enabling practical use of computationally demanding algorithms. This review presents the past and present work on GPU accelerated medical image processing, and is meant to serve as an overview and introduction to existing GPU implementations. The review covers GPU acceleration of basic image processing operations (filtering, interpolation, histogram estimation and distance transforms), the most commonly used algorithms in medical imaging (image registration, image segmentation and image denoising) and algorithms that are specific to individual modalities (CT, PET, SPECT, MRI, fMRI, DTI, ultrasound, optical imaging and microscopy). The review ends by highlighting some future possibilities and challenges.

Real-time speckle variance swept-source optical coherence tomography using a graphics processing unit

Advances in swept source laser technology continues to increase the imaging speed of swept-source optical coherence tomography (SS-OCT) systems. These fast imaging speeds are ideal for microvascular detection schemes, such as speckle variance (SV), where interframe motion can cause severe imaging artifacts and loss of vascular contrast. However, full utilization of the laser scan speed has been hindered by the computationally intensive signal processing required by SS-OCT and SV calculations. Using a commercial graphics processing unit that has been optimized for parallel data processing, we report a complete high-speed SS-OCT platform capable of real-time data acquisition, processing, display, and saving at 108,000 lines per second. Subpixel image registration of structural images was performed in real-time prior to SV calculations in order to reduce decorrelation from stationary structures induced by the bulk tissue motion. The viability of the system was successfully demonstrated in a high bulk tissue motion scenario of human fingernail root imaging where SV images (512 × 512 pixels, n = 4) were displayed at 54 frames per second.

Ultra-fast displaying Spectral Domain Optical Doppler Tomography system using a Graphics Processing Unit

We demonstrate an ultrafast displaying Spectral Domain Optical Doppler Tomography system using Graphics Processing Unit (GPU) computing. The calculation of FFT and the Doppler frequency shift is accelerated by the GPU. Our system can display processed OCT and ODT images simultaneously in real time at 120 fps for 1,024 pixels × 512 lateral A-scans. The computing time for the Doppler information was dependent on the size of the moving average window, but with a window size of 32 pixels the ODT computation time is only 8.3 ms, which is comparable to the data acquisition time. Also the phase noise decreases significantly with the window size. Since the performance of a real-time display for OCT/ODT is very important for clinical applications that need immediate diagnosis for screening or biopsy. Intraoperative surgery can take much benefit from the real-time display flow rate information from the technology. Moreover, the GPU is an attractive tool for clinical and commercial systems for functional OCT features as well.