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Biometry study of foveal isoplanatic patch variation for adaptive optics retinal imaging. 用于自适应光学视网膜成像的眼窝等平面斑块变化的生物测量学研究。
IF 2.9 2区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-04 eCollection Date: 2024-10-01 DOI: 10.1364/BOE.536645
Xiaojing Huang, Aubrey Hargrave, Julie Bentley, Alfredo Dubra

The change in ocular wavefront aberrations with visual angle determines the isoplanatic patch, defined as the largest field of view over which diffraction-limited retinal imaging can be achieved. Here, we study how the isoplanatic patch at the foveal center varies across 32 schematic eyes, each individualized with optical biometry estimates of corneal and crystalline lens surface topography, assuming a homogeneous refractive index for the crystalline lens. The foveal isoplanatic patches were calculated using real ray tracing through 2, 4, 6 and 8 mm pupil diameters for wavelengths of 400-1200 nm, simulating five adaptive optics (AO) strategies. Three of these strategies, used in flood illumination, point-scanning, and line-scanning ophthalmoscopes, apply the same wavefront correction across the entire field of view, resulting in almost identical isoplanatic patches. Two time-division multiplexing (TDM) strategies are proposed to increase the isoplanatic patch of AO scanning ophthalmoscopes through field-varying wavefront correction. Results revealed substantial variation in isoplanatic patch size across eyes (40-500%), indicating that the field of view in AO ophthalmoscopes should be adjusted for each eye. The median isoplanatic patch size decreases with increasing pupil diameter, coarsely following a power law. No statistically significant correlations were found between isoplanatic patch size and axial length. The foveal isoplanatic patch increases linearly with wavelength, primarily due to its wavelength-dependent definition (wavefront root-mean-squared, RMS <λ/14), rather than aberration chromatism. Additionally, ray tracing reveals that in strongly ametropic eyes, induced aberrations can result in wavefront RMS errors as large as λ/3 for an 8-mm pupil, with implications for wavefront sensing, open-loop ophthalmic AO, spectacle prescription and refractive surgery.

眼球波前像差随视角的变化决定了等光斑,等光斑被定义为可实现衍射极限视网膜成像的最大视场。在此,我们研究了眼窝中心的等平面斑块在 32 只示意眼睛中的变化情况,每只眼睛都有角膜和晶状体表面形貌的光学生物测量估计值,并假设晶状体的折射率是均匀的。在波长为 400-1200 纳米的情况下,通过 2、4、6 和 8 毫米瞳孔直径的真实光线追踪,模拟五种自适应光学(AO)策略,计算出眼窝等平面斑块。其中用于泛光照明、点扫描和线扫描眼底镜的三种策略在整个视场中应用相同的波前校正,从而产生几乎完全相同的等光斑。本文提出了两种时分复用(TDM)策略,通过场变波前校正来增加自动光学扫描眼底镜的等平面补丁。结果表明,不同眼睛的等平面光斑大小差异很大(40%-500%),这表明应针对每只眼睛调整 AO 眼科视场。随着瞳孔直径的增大,中位等平补丁大小也随之减小,大致呈幂律变化。在统计学上,等平面斑块大小与轴长之间没有发现明显的相关性。眼窝等平面斑块随波长线性增加,这主要是由于其定义与波长有关(波前均方根,RMS
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引用次数: 0
Aberration compensation in Doppler holography of the human eye fundus by subaperture signal correlation. 通过子光圈信号相关性对人眼眼底多普勒全息成像中的像差进行补偿。
IF 2.9 2区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-04 eCollection Date: 2024-10-01 DOI: 10.1364/BOE.528568
Zofia Bratasz, Olivier Martinache, Julia Sverdlin, Damien Gatinel, Michael Atlan

The process of obtaining images of capillary vessels in the human eye's fundus using Doppler holography encounters difficulties due to ocular aberrations. To enhance the accuracy of these images, it is advantageous to apply an adaptive aberration correction technique. This study focuses on numerical Shack-Hartmann, which employs sub-pupil correlation as the wavefront sensing method. Application of this technique to Doppler holography encounters unique challenges due to the holographic detection properties. A detailed comparative analysis of the regularization technique against direct gradient integration in the estimation of aberrations is made. Two different reference images for the measurement of image shifts across subapertures are considered. The comparison reveals that direct gradient integration exhibits greater effectiveness in correcting asymmetrical aberrations.

在使用多普勒全息技术获取人眼眼底毛细血管图像的过程中,会遇到眼球像差带来的困难。为了提高这些图像的精确度,应用自适应像差校正技术是非常有利的。本研究的重点是数值 Shack-Hartmann,它采用瞳孔下相关性作为波前感应方法。由于全息检测的特性,将这种技术应用于多普勒全息技术会遇到独特的挑战。在估计像差时,对正则化技术与直接梯度积分进行了详细的比较分析。考虑了两种不同的参考图像,用于测量跨子孔径的图像偏移。比较结果表明,直接梯度积分在校正不对称像差方面表现出更大的有效性。
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引用次数: 0
Experimental characterization of an isoplanatic patch in mouse cortex using adaptive optics. 利用自适应光学技术对小鼠皮层中的等平面斑块进行实验鉴定。
IF 2.9 2区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-04 eCollection Date: 2024-10-01 DOI: 10.1364/BOE.527313
Jean Commère, Marie Glanc, Laurent Bourdieu, Raphaël Galicher, Éric Gendron, Gérard Rousset

Optical microscopy techniques have become essential tools for studying normal and pathological biological systems. However, in many situations, image quality deteriorates rapidly in the field of view due to optical aberrations and scattering induced by thick tissues. To compensate for these aberrations and restore the microscope's image quality, adaptive optics (AO) techniques have been proposed for the past 15 years. A key parameter for the AO implementation lies in the limited isoplanatic dimension over which the image quality remains uniform. Here, we propose a method for measuring this dimension and deducing the anisoplanatism and intensity transmission of the samples. We apply this approach to fixed slices of mouse cortices as a function of their thickness. We find a typical mid-maximum width of 20 µm for the isoplanatic spot, which is independent of sample thickness.

光学显微镜技术已成为研究正常和病理生物系统的重要工具。然而,在许多情况下,由于厚组织引起的光学像差和散射,视场中的图像质量会迅速下降。为了补偿这些像差并恢复显微镜的图像质量,自适应光学(AO)技术在过去的 15 年中不断被提出。实施自适应光学技术的一个关键参数在于图像质量保持一致的有限等平面尺寸。在此,我们提出了一种测量该维度并推导出样品的异面性和强度传输的方法。我们将这种方法应用于小鼠皮层的固定切片,并将其作为厚度的函数。我们发现等平面光斑的典型中间最大宽度为 20 µm,与样本厚度无关。
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引用次数: 0
ninjaNIRS: an open hardware solution for wearable whole-head high-density functional near-infrared spectroscopy. ninjaNIRS:用于可穿戴式全头高密度功能性近红外光谱分析的开放式硬件解决方案。
IF 2.9 2区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-04 eCollection Date: 2024-10-01 DOI: 10.1364/BOE.531501
W Joseph O'Brien, Laura Carlton, Johnathan Muhvich, Sreekanth Kura, Antonio Ortega-Martinez, Jay Dubb, Sudan Duwadi, Eric Hazen, Meryem A Yücel, Alexander von Lühmann, David A Boas, Bernhard B Zimmermann

Functional near-infrared spectroscopy (fNIRS) technology has been steadily advancing since the first measurements of human brain activity over 30 years ago. Initially, efforts were focused on increasing the channel count of fNIRS systems and then to moving from sparse to high density arrays of sources and detectors, enhancing spatial resolution through overlapping measurements. Over the last ten years, there have been rapid developments in wearable fNIRS systems that place the light sources and detectors on the head as opposed to the original approach of using fiber optics to deliver the light between the hardware and the head. The miniaturization of the electronics and increased computational power continues to permit impressive advances in wearable fNIRS systems. Here we detail our design for a wearable fNIRS system that covers the whole head of an adult human with a high-density array of 56 sources and up to 192 detectors. We provide characterization of the system showing that its performance is among the best in published systems. Additionally, we provide demonstrative images of brain activation during a ball squeezing task. We have released the hardware design to the public, with the hope that the community will build upon our foundational work and drive further advancements.

自 30 多年前首次测量人脑活动以来,功能性近红外光谱(fNIRS)技术一直在稳步发展。最初,人们致力于增加 fNIRS 系统的通道数,然后将源和探测器从稀疏阵列转向高密度阵列,通过重叠测量提高空间分辨率。在过去的十年中,可穿戴式 fNIRS 系统发展迅速,该系统将光源和探测器置于头部,而不是使用光纤在硬件和头部之间传输光线的原始方法。电子设备的微型化和计算能力的提高,使可穿戴 fNIRS 系统继续取得令人瞩目的进步。在此,我们详细介绍了我们设计的可穿戴 fNIRS 系统,该系统可覆盖成人的整个头部,具有 56 个光源和多达 192 个探测器的高密度阵列。我们对该系统进行了鉴定,结果表明其性能在已发布的系统中名列前茅。此外,我们还提供了挤球任务中大脑激活的演示图像。我们已向公众发布了硬件设计,希望社会各界能在我们的基础工作上再接再厉,推动系统的进一步发展。
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引用次数: 0
FLUID: a fluorescence-friendly lipid-compatible ultrafast clearing method. FLUID:一种荧光友好型脂质兼容超快清除方法。
IF 2.9 2区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-03 eCollection Date: 2024-10-01 DOI: 10.1364/BOE.533072
Zizheng Wang, Xiao Xiao, Ziwen Zhou, Yunyin Chen, Tianqi Xia, Xiangyi Sheng, Yiping Han, Wei Gong, Ke Si

Many clearing methods achieve high transparency by removing lipid components from tissues, which damages microstructure and limits their application in lipid research. As for methods which preserve lipid, it is difficult to balance transparency, fluorescence preservation and clearing speed. In this study, we propose a rapid water-based clearing method that is fluorescence-friendly and preserves lipid components. FLUID allows for preservation of endogenous fluorescence over 60 days. It shows negligible tissue distortion and is compatible with various types of fluorescent labeling and tissue staining methods. High quality imaging of human brain tissue and compatibility with pathological staining demonstrated the potential of our method for three-dimensional (3D) biopsy and clinical pathological diagnosis.

许多清除方法是通过清除组织中的脂质成分来实现高透明度的,这就破坏了微观结构,限制了其在脂质研究中的应用。至于保留脂质的方法,则很难在透明度、荧光保留和清除速度之间取得平衡。在这项研究中,我们提出了一种快速的水基清除方法,它既能保持荧光,又能保留脂质成分。FLUID 可使内源性荧光保存 60 天以上。它的组织变形可忽略不计,并与各种类型的荧光标记和组织染色方法兼容。人类脑组织的高质量成像以及与病理染色的兼容性证明了我们的方法在三维(3D)活检和临床病理诊断方面的潜力。
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引用次数: 0
Enhanced microvascular imaging through deep learning-driven OCTA reconstruction with squeeze-and-excitation block integration. 通过深度学习驱动的 OCTA 重建与挤压和激发块整合,增强微血管成像。
IF 2.9 2区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-03 eCollection Date: 2024-10-01 DOI: 10.1364/BOE.525928
Mohammad Rashidi, Georgy Kalenkov, Daniel J Green, Robert A McLaughlin

Skin microvasculature is essential for cardiovascular health and thermoregulation in humans, yet its imaging and analysis pose significant challenges. Established methods, such as speckle decorrelation applied to optical coherence tomography (OCT) B-scans for OCT-angiography (OCTA), often require a high number of B-scans, leading to long acquisition times that are prone to motion artifacts. In our study, we propose a novel approach integrating a deep learning algorithm within our OCTA processing. By integrating a convolutional neural network with a squeeze-and-excitation block, we address these challenges in microvascular imaging. Our method enhances accuracy and reduces measurement time by efficiently utilizing local information. The Squeeze-and-Excitation block further improves stability and accuracy by dynamically recalibrating features, highlighting the advantages of deep learning in this domain.

皮肤微血管对人类的心血管健康和体温调节至关重要,但其成像和分析却面临巨大挑战。既有的方法,如应用于光学相干断层扫描(OCT)B扫描的斑点相关技术(speckle decorrelation),往往需要大量的B扫描,导致采集时间过长,容易产生运动伪影。在我们的研究中,我们提出了一种在 OCTA 处理中集成深度学习算法的新方法。通过将卷积神经网络与挤压激发块集成,我们解决了微血管成像中的这些难题。我们的方法通过有效利用局部信息,提高了准确性并缩短了测量时间。挤压激励块通过动态重新校准特征,进一步提高了稳定性和准确性,突出了深度学习在这一领域的优势。
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引用次数: 0
Real-time data processing in colorimetry camera-based single-molecule localization microscopy via CPU-GPU-FPGA heterogeneous computation. 通过 CPU-GPU-FPGA 异构计算,在基于比色法相机的单分子定位显微镜中进行实时数据处理。
IF 3.4 2区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-28 DOI: 10.1364/boe.534941
Jiaxun Lin,Kun Wang,Zhen-Li Huang
Because conventional low-light cameras used in single-molecule localization microscopy (SMLM) do not have the ability to distinguish colors, it is often necessary to employ a dedicated optical system and/or a complicated image analysis procedure to realize multi-color SMLM. Recently, researchers explored the potential of a new kind of low-light camera called colorimetry camera as an alternative detector in multi-color SMLM, and achieved two-color SMLM under a simple optical system, with a comparable cross-talk to the best reported values. However, extracting images from all color channels is a necessary but lengthy process in colorimetry camera-based SMLM (called CC-STORM), because this process requires the sequential traversal of a massive number of pixels. By taking advantage of the parallelism and pipeline characteristics of FPGA, in this paper, we report an updated multi-color SMLM method called HCC-STORM, which integrated the data processing tasks in CC-STORM into a home-built CPU-GPU-FPGA heterogeneous computing platform. We show that, without scarifying the original performance of CC-STORM, the execution speed of HCC-STORM was increased by approximately three times. Actually, in HCC-STORM, the total data processing time for each raw image with 1024 × 1024 pixels was 26.9 ms. This improvement enabled real-time data processing for a field of view of 1024 × 1024 pixels and an exposure time of 30 ms (a typical exposure time in CC-STORM). Furthermore, to reduce the difficulty of deploying algorithms into the heterogeneous computing platform, we also report the necessary interfaces for four commonly used high-level programming languages, including C/C++, Python, Java, and Matlab. This study not only pushes forward the mature of CC-STORM, but also presents a powerful computing platform for tasks with heavy computation load.
由于单分子定位显微镜(SMLM)中使用的传统低照度相机不具备分辨颜色的能力,因此通常需要使用专用光学系统和/或复杂的图像分析程序来实现多色 SMLM。最近,研究人员探索了一种新的低照度照相机--测色照相机--作为多色 SMLM 的替代检测器的潜力,并在简单光学系统下实现了双色 SMLM,其串扰与已报道的最佳值相当。然而,在基于比色法相机的 SMLM(称为 CC-STORM)中,提取所有颜色通道的图像是一个必要但漫长的过程,因为这一过程需要顺序遍历大量像素。本文利用 FPGA 的并行性和流水线特性,将 CC-STORM 中的数据处理任务集成到自建的 CPU-GPU-FPGA 异构计算平台中,报告了一种名为 HCC-STORM 的最新多色 SMLM 方法。我们的研究表明,在不影响 CC-STORM 原始性能的情况下,HCC-STORM 的执行速度提高了约三倍。实际上,在 HCC-STORM 中,每幅 1024 × 1024 像素的原始图像的总数据处理时间为 26.9 毫秒。这一改进使 1024 × 1024 像素视场和 30 毫秒曝光时间(CC-STORM 的典型曝光时间)的数据处理成为可能。此外,为了降低将算法部署到异构计算平台的难度,我们还报告了四种常用高级编程语言的必要接口,包括 C/C++、Python、Java 和 Matlab。这项研究不仅推动了 CC-STORM 的成熟,还为计算负荷较重的任务提供了一个强大的计算平台。
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引用次数: 0
High-resolution in vivo 4D-OCT fish-eye imaging using 3D-UNet with multi-level residue decoder. 使用带有多级残差解码器的 3D-UNet 进行高分辨率活体 4D-OCT 鱼眼成像。
IF 3.4 2区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-28 DOI: 10.1364/boe.532258
Ruizhi Zuo,Shuwen Wei,Yaning Wang,Kristina Irsch,Jin U Kang
Optical coherence tomography (OCT) allows high-resolution volumetric imaging of biological tissues in vivo. However, 3D-image acquisition often suffers from motion artifacts due to slow frame rates and involuntary and physiological movements of living tissue. To solve these issues, we implement a real-time 4D-OCT system capable of reconstructing near-distortion-free volumetric images based on a deep learning-based reconstruction algorithm. The system initially collects undersampled volumetric images at a high speed and then upsamples the images in real-time by a convolutional neural network (CNN) that generates high-frequency features using a deep learning algorithm. We compare and analyze both dual-2D- and 3D-UNet-based networks for the OCT 3D high-resolution image reconstruction. We refine the network architecture by incorporating multi-level information to accelerate convergence and improve accuracy. The network is optimized by utilizing the 16-bit floating-point precision for network parameters to conserve GPU memory and enhance efficiency. The result shows that the refined and optimized 3D-network is capable of retrieving the tissue structure more precisely and enable real-time 4D-OCT imaging at a rate greater than 10 Hz with a root mean square error (RMSE) of ∼0.03.
光学相干断层扫描(OCT)可对活体生物组织进行高分辨率容积成像。然而,由于帧频较慢以及活体组织的非自主和生理运动,三维图像采集经常会出现运动伪影。为了解决这些问题,我们实施了一种实时 4D-OCT 系统,该系统能够基于基于深度学习的重建算法重建近乎无失真容积图像。该系统最初以高速收集未采样的容积图像,然后通过卷积神经网络(CNN)对图像进行实时上采样,并利用深度学习算法生成高频特征。我们比较并分析了基于双 2D 网络和 3DUNet 网络的 OCT 3D 高分辨率图像重建。我们通过整合多层次信息来完善网络架构,从而加快收敛速度并提高准确性。网络参数采用 16 位浮点精度,以节省 GPU 内存并提高效率。结果表明,经过改进和优化的三维网络能够更精确地检索组织结构,并能以大于 10 Hz 的速率进行实时 4D-OCT 成像,均方根误差(RMSE)为 ∼0.03。
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引用次数: 0
Automated analysis of scattering-based light sheet microscopy images of anal squamous intraepithelial lesions. 基于散射的肛门鳞状上皮内病变光片显微镜图像的自动分析。
IF 3.4 2区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-28 DOI: 10.1364/boe.531700
Yongjun Kim,Jingwei Zhao,Brooke Liang,Momoka Sugimura,Kenneth Marcelino,Rafael Romero,Ameer Nessaee,Carmella Ocaya,Koeun Lim,Denise Roe,Michelle J Khan,Eric J Yang,Dongkyun Kang
We developed an algorithm for automatically analyzing scattering-based light sheet microscopy (sLSM) images of anal squamous intraepithelial lesions. We developed a method for automatically segmenting sLSM images for nuclei and calculating seven features: nuclear intensity, intensity slope as a function of depth, nuclear-to-nuclear distance, nuclear-to-cytoplasm ratio, cell density, nuclear area, and proportion of pixels corresponding to nuclei. 187 images from 80 anal biopsies were used for feature analysis and classifier development. The automated nuclear segmentation method provided reliable performance with the precision of 0.97 and recall of 0.91 when compared with the manual segmentation. Among the seven features, six showed statistically significant differences between high-grade squamous intraepithelial lesion (HSIL) and non-HSIL (non-dysplastic or low-grade squamous intraepithelial lesion, LSIL). A classifier using linear support vector machine (SVM) achieved promising performance in diagnosing HSIL versus non-HSIL: sensitivity of 90%, specificity of 70%, and area under the curve (AUC) of 0.89 for per-image diagnosis, and sensitivity of 90%, specificity of 80%, and AUC of 0.92 for per-biopsy diagnosis.
我们开发了一种算法,用于自动分析肛门鳞状上皮内病变的散射光片显微镜(sLSM)图像。我们开发了一种方法,用于自动分割 sLSM 图像中的细胞核并计算以下七种特征:核强度、强度斜率与深度的函数关系、核与核之间的距离、核与细胞质的比率、细胞密度、核面积以及与细胞核相对应的像素比例。来自 80 个肛门活检组织的 187 张图像被用于特征分析和分类器开发。与人工分割相比,自动核分割方法具有可靠的性能,精确度为 0.97,召回率为 0.91。在七个特征中,有六个特征显示高级别鳞状上皮内病变(HSIL)与非高级别鳞状上皮内病变(非增生性或低级别鳞状上皮内病变,LSIL)之间存在统计学意义上的显著差异。使用线性支持向量机(SVM)的分类器在诊断 HSIL 与非 HSIL 方面取得了可喜的成绩:每张图像诊断的灵敏度为 90%,特异性为 70%,曲线下面积(AUC)为 0.89;每次活检诊断的灵敏度为 90%,特异性为 80%,曲线下面积(AUC)为 0.92。
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引用次数: 0
Modified Beer-Lambert algorithm to measure pulsatile blood flow, critical closing pressure, and intracranial hypertension. 用于测量搏动性血流、临界关闭压和颅内高压的改良比尔-朗伯算法。
IF 3.4 2区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-27 DOI: 10.1364/boe.529150
Wesley B Baker,Rodrigo M Forti,Pascal Heye,Kristina Heye,Jennifer M Lynch,Arjun G Yodh,Daniel J Licht,Brian R White,Misun Hwang,Tiffany S Ko,Todd J Kilbaugh
We introduce a frequency-domain modified Beer-Lambert algorithm for diffuse correlation spectroscopy to non-invasively measure flow pulsatility and thus critical closing pressure (CrCP). Using the same optical measurements, CrCP was obtained with the new algorithm and with traditional nonlinear diffusion fitting. Results were compared to invasive determination of intracranial pressure (ICP) in piglets (n = 18). The new algorithm better predicted ICP elevations; the area under curve (AUC) from logistic regression analysis was 0.85 for ICP ≥ 20 mmHg. The corresponding AUC for traditional analysis was 0.60. Improved diagnostic performance likely results from better filtering of extra-cerebral tissue contamination and measurement noise.
我们为弥散相关光谱学引入了一种频域修正比尔-朗伯算法,用于无创测量流动脉动性,从而测量临界关闭压力(CrCP)。使用相同的光学测量方法,用新算法和传统的非线性扩散拟合方法获得了临界关闭压(CrCP)。结果与有创测定仔猪(n = 18)颅内压(ICP)的结果进行了比较。新算法能更好地预测 ICP 升高;ICP ≥ 20 mmHg 时,逻辑回归分析的曲线下面积 (AUC) 为 0.85。而传统分析的相应 AUC 为 0.60。诊断性能的提高可能是由于更好地过滤了脑外组织污染和测量噪音。
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引用次数: 0
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Biomedical optics express
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