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Superpixel guided active contour segmentation of retinal layers in OCT volumes OCT卷中视网膜层的超像素引导活动轮廓分割
Fangliang Bai, S. Gibson, M. Marques, A. Podoleanu
Retinal OCT image segmentation is a precursor to subsequent medical diagnosis by a clinician or machine learning algorithm. In the last decade, many algorithms have been proposed to detect retinal layer boundaries and simplify the image representation. Inspired by the recent success of superpixel methods for pre-processing natural images, we present a novel framework for segmentation of retinal layers in OCT volume data. In our framework, the region of interest (e.g. the fovea) is located using an adaptive-curve method. The cell layer boundaries are then robustly detected firstly using 1D superpixels, applied to A-scans, and then fitting active contours in B-scan images. Thereafter the 3D cell layer surfaces are efficiently segmented from the volume data. The framework was tested on healthy eye data and we show that it is capable of segmenting up to 12 layers. The experimental results imply the effectiveness of proposed method and indicate its robustness to low image resolution and intrinsic speckle noise.
视网膜OCT图像分割是临床医生或机器学习算法进行后续医学诊断的前兆。在过去的十年中,人们提出了许多算法来检测视网膜层边界并简化图像表示。受最近超像素方法预处理自然图像成功的启发,我们提出了一种新的框架,用于分割OCT体数据中的视网膜层。在我们的框架中,使用自适应曲线方法定位感兴趣的区域(例如中央凹)。然后,首先使用1D超像素健壮地检测细胞层边界,应用于a扫描,然后拟合b扫描图像中的活动轮廓。然后有效地从体数据中分割出三维单元层表面。该框架在健康的眼睛数据上进行了测试,我们表明它能够分割多达12层。实验结果表明了该方法的有效性,并表明了该方法对低分辨率图像和固有散斑噪声的鲁棒性。
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引用次数: 2
Towards an ultra-thin medical endoscope: multimode fibre as a wide-field image transferring medium 迈向超薄医用内窥镜:多模光纤作为宽视场图像传输介质
M. Ďuriš, A. Bradu, A. Podoleanu, M. Hughes
Multimode optical fibres are attractive for biomedical and industrial applications such as endoscopes because of the small cross section and imaging resolution they can provide in comparison to widely-used fibre bundles. However, the image is randomly scrambled by propagation through a multimode fibre. Even though the scrambling is unpredictable, it is deterministic, and therefore the scrambling can be reversed. To unscramble the image, we treat the multimode fibre as a linear, disordered scattering medium. To calibrate, we scan a focused beam of coherent light over thousands of different beam positions at the distal end and record complex fields at the proximal end of the fibre. This way, the inputoutput response of the system is determined, which then allows computational reconstruction of reflection-mode images. However, there remains the problem of illuminating the tissue via the fibre while avoiding back reflections from the proximal face. To avoid this drawback, we provide here the first preliminary confirmation that an image can be transferred through a 2x2 fibre coupler, with the sample at its distal port interrogated in reflection. Light is injected into one port for illumination and then collected from a second port for imaging.
多模光纤对于内窥镜等生物医学和工业应用具有吸引力,因为与广泛使用的光纤束相比,它们可以提供较小的横截面和成像分辨率。然而,通过多模光纤传播的图像被随机打乱。尽管打乱是不可预测的,但它是确定的,因此打乱是可以逆转的。为了对图像进行解译,我们将多模光纤看作是一种线性的、无序的散射介质。为了校准,我们在远端扫描一束聚焦的相干光在数千个不同的光束位置上,并在光纤近端记录复杂的场。这样,系统的输入输出响应被确定,然后允许计算重建反射模式图像。然而,仍然存在通过纤维照亮组织的问题,同时避免近端面部的反射。为了避免这个缺点,我们在这里提供了第一个初步确认,图像可以通过2x2光纤耦合器传输,样品在其远端端口反射询问。光被注入一个端口用于照明,然后从第二个端口收集用于成像。
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引用次数: 0
Long axial imaging range using conventional swept source lasers in optical coherence tomography via re-circulation loops 在光学相干层析成像中,通过再循环回路使用传统扫源激光器进行长轴向成像
A. Bradu, D. Jackson, A. Podoleanu
Typically, swept source optical coherence tomography (SS-OCT) imaging instruments are capable of a longer axial range than their camera based (CB) counterpart. However, there are still various applications that would take advantage for an extended axial range. In this paper, we propose an interferometer configuration that can be used to extend the axial range of the OCT instruments equipped with conventional swept-source lasers up to a few cm. In this configuration, the two arms of the interferometer are equipped with adjustable optical path length rings. The use of semiconductor optical amplifiers in the two rings allows for compensating optical losses hence, multiple paths depth reflectivity profiles (Ascans) can be combined axially. In this way, extremely long overall axial ranges are possible. The use of the recirculation loops produces an effect equivalent to that of extending the coherence length of the swept source laser. Using this approach, the achievable axial imaging range in SS-OCT can reach values well beyond the limit imposed by the coherence length of the laser, to exceed in principle many centimeters. In the present work, we demonstrate axial ranges exceeding 4 cm using a commercial swept source laser and reaching 6 cm using an “in-house” swept source laser. When used in a conventional set-up alone, both these lasers can provide less than a few mm axial range.
通常,扫描源光学相干层析成像(SS-OCT)成像仪器能够比基于相机(CB)的对偶具有更长的轴向范围。然而,仍然有各种各样的应用,将利用扩大轴向范围。在本文中,我们提出了一种干涉仪配置,可用于将配备传统扫描源激光器的OCT仪器的轴向范围扩展到几厘米。在这种配置中,干涉仪的两个臂配备了可调的光程长度环。在两个环中使用半导体光放大器可以补偿光损耗,因此,可以轴向组合多路径深度反射率剖面(ascan)。通过这种方式,可以实现极长的整体轴向范围。再循环回路的使用产生的效果相当于延长了扫描源激光器的相干长度。使用这种方法,SS-OCT可实现的轴向成像范围可以达到远远超出激光相干长度限制的值,原则上超过许多厘米。在目前的工作中,我们演示了使用商用扫描源激光器的轴向范围超过4厘米,使用“内部”扫描源激光器的轴向范围达到6厘米。当在传统设置单独使用时,这两种激光器可以提供小于几毫米的轴向范围。
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引用次数: 0
Supercontinuum ultra-high resolution line-field OCT; experimental spectrograph comparison and comparison with current clinical OCT systems by the imaging of a human cornea 超连续统超高分辨率线场OCT;对实验摄谱仪进行比较,并与现有临床OCT系统对人角膜的成像进行比较
S. Lawman, V. Romano, P. Madden, S. Mason, Bryan M. Williams, Yalin Zheng, Yaochun Shen
Ultra high axial resolution (UHR) was demonstrated early in the development of optical coherence tomography (OCT), but has not yet reached clinical practice. We present the combination of supercontinuum light source and line field (LF-) OCT as a technical and economical route to get UHR-OCT into clinic and other OCT application areas. We directly compare images of a human donor cornea taken with low and high resolution current generation clinical OCT systems with UHR-LF-OCT. These images highlight the massive information increase of UHR-OCT. Application to pharmaceutical pellets, and the functionality and imaging performance of different imaging spectrograph choices for LF- OCT are also demonstrated.
超高轴向分辨率(UHR)在光学相干断层扫描(OCT)发展的早期就得到了证实,但尚未达到临床应用。我们认为超连续光源与线场OCT相结合是将超磁共振OCT应用于临床和其他OCT应用领域的技术和经济途径。我们直接比较了低分辨率和高分辨率当代临床OCT系统与UHR-LF-OCT所拍摄的人类供体角膜图像。这些图像突出了UHR-OCT的大量信息增加。本文还介绍了LF- OCT在制药微丸中的应用,以及不同成像光谱仪的功能和成像性能。
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引用次数: 3
Use of a supercontinuum white light in evaluating the spectral sensitivity of the pupil light reflex 用超连续白光评价瞳孔光反射的光谱灵敏度
Catherine Chin, L. Leick, A. Podoleanu, G. Lall
We assessed the spectral sensitivity of the pupillary light reflex in mice using a high power super continuum white light (SCWL) source in a dual wavelength configuration. This novel approach was compared to data collected from a more traditional setup using a Xenon arc lamp fitted with monochromatic interference filters. Irradiance response curves were constructed using both systems, with the added benefit of a two-wavelength, equivocal power, output using the SCWL. The variables applied to the light source were intensity, wavelength and stimulus duration through which the physiological output measured was the minimum pupil size attained under such conditions. We show that by implementing the SCWL as our novel stimulus we were able to dramatically increase the physiological usefulness of our pupillometry system.
我们使用双波长配置的高功率超连续白光(SCWL)光源评估了小鼠瞳孔光反射的光谱灵敏度。将这种新方法与使用单色干涉滤光片的氙气弧光灯的传统装置收集的数据进行了比较。使用这两种系统构建辐照度响应曲线,并使用SCWL进行双波长、模糊功率输出的附加好处。应用于光源的变量是强度、波长和刺激持续时间,通过这些变量测量的生理输出是在这些条件下达到的最小瞳孔大小。我们表明,通过实施SCWL作为我们的新刺激,我们能够显著提高我们的瞳孔测量系统的生理用途。
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引用次数: 0
Phase estimation for global defocus correction in optical coherence tomography 光学相干层析成像中全局离焦校正的相位估计
Mikkel Jensen, N. Israelsen, A. Podoleanu, O. Bang
In this work we investigate three techniques for estimation of the non-linear phase present due to defocus in optical coherence tomography, and apply them with the angular spectrum method. The techniques are: Least squares fitting the of unwrapped phase of the angular spectrum, iterative optimization, and sub-aperture correlations. The estimated phase of a single en-face image is used to extrapolate the non-linear phase at all depths, which in the end can be used to correct the entire 3-D tomogram, and any other tomogram from the same system.
在这项工作中,我们研究了光学相干层析成像中由于离焦而存在的非线性相位的三种估计技术,并将它们与角谱方法相结合。这些技术包括:角谱解包裹相位的最小二乘拟合、迭代优化和子孔径关联。单个正面图像的估计相位用于外推所有深度的非线性相位,最终可用于校正整个三维层析图,以及来自同一系统的任何其他层析图。
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引用次数: 0
Stable supercontinuum source based on random lasing 基于随机激光的稳定超连续谱源
R. Ma, Y. Rao, Weili Zhang, Xiong Zeng, Han Wu
Backward supercontinuum generation seeded by random distributed feedback fiber laser is proposed and demonstrated. Fully-distributed random lasing is firstly used as an effective pump laser to generate supercontinuum in the hybrid configuration with TrueWave fiber and dispersion compensated fiber. Supercontinuum in both propagating directions are generated through the collective nonlinear effects. It is found backward supercontinuum possesses much lower dynamical amplitude fluctuation in time domain. Random distributed lasing pumped supercontinuum generation not only enrich both the research scope of supercontinuum and random fiber laser, but also provide a practical way for development of stable broadband sources for OCT applications.
提出了一种基于随机分布反馈光纤激光器的反向超连续谱产生方法并进行了验证。在TrueWave光纤和色散补偿光纤的混合配置下,首次将全分布随机激光作为一种有效的泵浦激光器来产生超连续介质。两个传播方向上的超连续统是由集体非线性效应产生的。发现后向超连续谱在时域上具有更小的动态振幅波动。随机分布激光泵浦超连续谱的产生不仅丰富了超连续谱和随机光纤激光器的研究范围,而且为开发用于OCT应用的稳定宽带光源提供了一条切实可行的途径。
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引用次数: 4
Optimisation of a polygon mirror-based spectral filter for swept source optical coherence tomography (SS-OCT) 扫描源光学相干层析成像(SS-OCT)中基于多边形镜的光谱滤波器的优化
Michael Everson, Virgil-Florin Duma, G. Dobre
Medical imaging using Optical Coherence Tomography (OCT) provides clinicians with 3D, high resolution reconstructions of microscopic structures, in depth. It has been initially developed for ophthalmology, in order to scan the retinas of patients to diagnose illness. The quality of the images depends upon their axial and lateral resolutions and the properties of the light being used. Research using a polygon mirror (PM) as a spectral filter in Swept Source OCT (SS-OCT) has resulted in a variety of different experimental arrangements. Although the application of PM-based SS-OCT sources has been successfully demonstrated, the combination of their components’ fundamental properties and the overall impact they have on imaging performance is rarely reported. A more detailed examination of these properties would lead to a full description of their operation and to the best methods to employ if system performance is to be maximised. This work presents our current findings of on-going research into the optimisation of PM-based SS-OCT systems. A swept source spectral filter, consisting of a collimator, a transmission grating, a two-lens telescope and an off-axis PM with an end reflector mirror has been evaluated experimentally and compared with theoretical predictions. The system’s performance has been compared for two different fibre collimators. Although the beam width on the grating is different for each of the two collimators, the spot size at the PM facet is made the same by selecting appropriate focal lengths. An improvement in the signal roll-off at the interferometer output of ~1.0 dB/mm was obtained when using a 3.4 mm collimator compared to a 1.5 mm collimator.
使用光学相干断层扫描(OCT)的医学成像为临床医生提供了三维、高分辨率的微观结构深度重建。它最初是为眼科开发的,目的是扫描患者的视网膜来诊断疾病。图像的质量取决于它们的轴向和横向分辨率以及所使用的光的特性。在扫描源OCT (SS-OCT)中使用多边形反射镜(PM)作为光谱滤波器的研究导致了各种不同的实验安排。尽管基于pm的SS-OCT源的应用已经成功展示,但其组成部分的基本特性及其对成像性能的总体影响的组合很少被报道。对这些属性进行更详细的检查,将导致对其操作的完整描述,以及如果要最大限度地提高系统性能所采用的最佳方法。这项工作介绍了我们目前正在进行的基于pm的SS-OCT系统优化研究的发现。对由准直器、透射光栅、双透镜望远镜和带端反射镜的离轴PM组成的掠源光谱滤波器进行了实验评价,并与理论预测进行了比较。在两种不同的光纤准直器下,对系统的性能进行了比较。虽然光栅上的光束宽度对于两个准直器中的每一个都是不同的,但通过选择适当的焦距,PM面处的光斑尺寸是相同的。与使用1.5 mm准直器相比,使用3.4 mm准直器可使干涉仪输出端的信号滚降提高到~1.0 dB/mm。
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引用次数: 3
New clinical opportunities for retinal vascular imaging: adaptive optics to OCT angiography 视网膜血管成像的新临床机会:自适应光学到OCT血管造影
R. Rosen, Toco Y P Chui, Rishard Weitz, A. Dubra, J. Carroll, P. Garcia, Alexander Pinhas, Nicole K. Scripsema, Shelley Mo, Steven Agemy, Brian D. Krawitz
As techniques of retinal imaging have evolved, anatomic features that were only assessable in the laboratory have become available in the clinic for patient care. The retinal capillaries were initially described on microscope sections in the pathology laboratory. As optical methods have advanced these features have become part of the routine clinical landscape inspected daily by physicians. This paper briefly traces the evolution of these techniques and shows how they fit into the modern diagnostic armamentarium of ophthalmic retinal care.
随着视网膜成像技术的发展,只能在实验室中评估的解剖特征已经可以在临床中用于患者护理。视网膜毛细血管最初是在病理实验室的显微镜切片上描述的。随着光学方法的进步,这些特征已经成为医生日常检查的常规临床景观的一部分。本文简要地追溯了这些技术的演变,并展示了它们如何适应眼科视网膜护理的现代诊断设备。
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引用次数: 0
Photonic compressive sensing enabled data efficient time stretch optical coherence tomography 光子压缩感知实现了数据高效的时间拉伸光学相干层析成像
Chaitanya K. Mididoddi, Chao Wang
Photonic time stretch (PTS) has enabled real time spectral domain optical coherence tomography (OCT). However, this method generates a torrent of massive data at GHz stream rate, which requires capturing as per Nyquist principle. If the OCT interferogram signal is sparse in Fourier domain, which is always true for samples with limited number of layers, it can be captured at lower (sub-Nyquist) acquisition rate as per compressive sensing method. In this work we report a data compressed PTS-OCT system based on photonic compressive sensing with 66% compression with low acquisition rate of 50MHz and measurement speed of 1.51MHz per depth profile. A new method has also been proposed to improve the system with all-optical random pattern generation, which completely avoids electronic bottleneck in traditional binary pseudorandom binary sequence (PRBS) generators.
光子时间拉伸(PTS)实现了实时光谱域光学相干层析成像(OCT)。然而,这种方法会产生以千兆赫赫兹流速率的大量数据流,这需要根据奈奎斯特原理进行捕获。如果OCT干涉图信号在傅里叶域中是稀疏的(对于层数有限的样本总是如此),那么根据压缩感知方法可以以较低的(亚奈奎斯特)采集速率捕获它。本文报道了一种基于光子压缩感知的数据压缩PTS-OCT系统,其压缩率为66%,低采集率为50MHz,每深度剖面测量速度为1.51MHz。提出了一种改进系统的全光随机模式生成方法,完全避免了传统二进制伪随机二进制序列(PRBS)发生器的电子瓶颈。
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引用次数: 2
期刊
Canterbury Workshop and School in Optical Coherence Tomography and Adaptive Optics
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