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SKYQUANT 3D: Quantifying Vascular Anatomy With an Open-Source Workflow for Comprehensive Analysis of Volumetric Optoacoustic Angiography Data SKYQUANT 3D:利用开源工作流程量化血管解剖,全面分析容积光声血管造影数据。
IF 2 3区 物理与天体物理 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-09 DOI: 10.1002/jbio.202400143
Artemii Korobov, Zlata Besedovskaia, Elizaveta Petrova, Alexey Kurnikov, Anna Glyavina, Anna Orlova, Svetlana Nemirova, Irina Druzhkova, Marina Sirotkina, Evgeny Shirshin, Dmitry Gorin, Lei Xi, Daniel Razansky, Pavel Subochev

Efficient visualization of the vascular system is of key importance in biomedical research into tumor angiogenesis, cerebrovascular alterations, and other angiopathies. Optoacoustic (OA) angiography offers a promising solution combining molecular optical contrast with high resolution and deep penetration of ultrasound. However, its hybrid nature implies complex data collection and processing workflows, with significant variability in methodologies across developers and users. To streamline interoperability, we introduce SKYQUANT 3D, a Python-based set of instructions for the Thermo Fisher Scientific Amira/Avizo 3D Visualization & Analysis Software. Our workflow simplifies the batch processing of volumetric optoacoustic angiography images, extracting meaningful quantitative information while also providing statistical analysis and graphical representation of the results. Quantification performance of SKYQUANT 3D is demonstrated using functional preclinical and clinical in vivo 3D OA angiographic tests involving ambient temperature variations and repositioning of the imaged limb.

血管系统的高效可视化对于肿瘤血管生成、脑血管改变和其他血管疾病的生物医学研究至关重要。光声(OA)血管造影术提供了一种前景广阔的解决方案,它将分子光学对比与超声的高分辨率和深穿透相结合。然而,它的混合性质意味着复杂的数据收集和处理工作流程,不同的开发人员和用户在方法上存在很大差异。为了简化互操作性,我们推出了 SKYQUANT 3D,这是一套基于 Python 的赛默飞世尔科技 Amira/Avizo 3D 可视化与分析软件指令。我们的工作流程简化了对容积光声血管造影图像的批量处理,在提取有意义的定量信息的同时,还提供了统计分析和结果图表。SKYQUANT 3D的定量性能通过临床前和临床活体三维OA血管造影功能测试(涉及环境温度变化和成像肢体的重新定位)进行了验证。
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引用次数: 0
Spatially Resolved Fibre-Optic Probe for Cervical Precancer Detection Using Fluorescence Spectroscopy and PCA-ANN-Based Classification Algorithm: An In Vitro Study 利用荧光光谱学和基于 PCA-ANN 分类算法的空间分辨光纤探针检测宫颈癌前病变:体外研究
IF 2 3区 物理与天体物理 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-08 DOI: 10.1002/jbio.202400284
Shivam Shukla, Bhaswati Singha Deo,  Nemichand, Pankaj Singh, Prabodh Kumar Pandey, Asima Pradhan

Cervical cancer can be detected at an early stage through the changes occurring in biochemical and morphological properties of epithelium layer. Fluorescence spectroscopy has the ability to identify these subtle changes non-invasively and in real time with good accuracy in comparison with conventional techniques. In this paper, we report the usage of a custom designed spatially resolved fibre-optic probe (SRFOP), which consists of 77 fibres in two concentric rings, for the detection of cervical cancer using fluorescence spectroscopy technique. The aim of this study is to classify different grades of cervical precancer on the basis of their fluorescence spectra followed by a robust classification algorithm. Fluorescence spectra of 28 cervical tissue samples of different categories have been recorded using six detector fibres of FOP at different spatial locations with the source fibre (SF). A 405 nm laser diode source has been utilised to excite the samples and a USB 4000 Ocean Optics spectrometer to collect the output spectra in the wavelength range 400–700 nm. Principal component analysis (PCA) was applied to the collected spectra to reduce the dimensionality of the data while preserving the most significant features for classification. The first 10 principal components, which captured the majority of the variance in the spectra, were selected as input features for the classification model. Classification was then performed using an artificial neural network (ANN) with a specific architecture, including an input layer, hidden layers, and a softmax activation function in the output layer. Experimental and classification results both demonstrate that proximal fibres (PFs) perform better than distal fibres (DFs) in capturing the discriminatory features present in the epithelium layer of cervical tissue samples as PF collect most of the signal from the epithelium layer. The combined approach of spatially resolved fluorescence spectroscopy and PCA-ANN classification techniques is able to discriminate different grades of cervical precancer and normal with an average sensitivity, specificity and accuracy of 93.33%, 96.67% and 95.57%, respectively.

宫颈癌可通过上皮细胞层的生化和形态特性的变化在早期发现。与传统技术相比,荧光光谱技术能够非侵入性地实时识别这些微妙的变化,并具有良好的准确性。在本文中,我们报告了定制设计的空间分辨光纤探头(SRFOP)的使用情况,该探头由 77 根光纤组成两个同心环,利用荧光光谱技术检测宫颈癌。这项研究的目的是根据荧光光谱对不同等级的宫颈癌前病变进行分类,然后采用一种稳健的分类算法。使用 FOP 的六根检测光纤,在不同的空间位置记录了 28 个不同类别宫颈组织样本的荧光光谱。405 nm 激光二极管源用于激发样品,USB 4000 Ocean Optics 光谱仪用于收集波长范围为 400-700 nm 的输出光谱。对收集到的光谱进行了主成分分析(PCA),以降低数据的维度,同时保留最重要的分类特征。前 10 个主成分捕获了光谱中的大部分差异,被选为分类模型的输入特征。然后使用具有特定结构的人工神经网络(ANN)进行分类,该结构包括输入层、隐藏层和输出层中的软最大激活函数。实验和分类结果都表明,近端纤维(PF)在捕捉宫颈组织样本上皮细胞层的鉴别特征方面比远端纤维(DF)更胜一筹,因为近端纤维收集了上皮细胞层的大部分信号。空间分辨荧光光谱和 PCA-ANN 分类技术的组合方法能够区分不同等级的宫颈癌前病变和正常病变,其平均灵敏度、特异性和准确性分别为 93.33%、96.67% 和 95.57%。
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引用次数: 0
Sparse-View Photoacoustic Reconstruction Method for Diabetic Retinopathy Using Feature Fusion Network 使用特征融合网络的糖尿病视网膜病变稀疏视图光声重建方法
IF 2 3区 物理与天体物理 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-08 DOI: 10.1002/jbio.202400287
Xiaohan Chang, Lingbo Cai, Jianlei Wang, Hongyang Dong, Jing Han, Chun Wang

Diabetic retinopathy is one of the most prevalent microvascular complications of diabetes mellitus, and photoacoustic imaging is an effective method for imaging diabetic retinal vessels. Photoacoustic imaging is an emerging noninvasive imaging method based on the photoacoustic effect, which offers advantages of contrast, resolution, and depth imaging. Appropriate photoacoustic reconstruction methods are essential for obtaining high-quality photoacoustic images. In this study, a multi-input self-attention multiscale feature fusion network (SAMF-Net) is proposed for photoacoustic reconstruction. The algorithm accepts two inputs, namely the original photoacoustic signal and the traditional reconstructed image. Furthermore, a global feature extraction module based on the self-attention mechanism is employed to focus on the global information. The results demonstrate that the proposed method exhibits superior reconstruction capability under different sparse detection views. The method has instructive value for photoacoustic image reconstruction and has the potential for further application in the diagnosis of diabetic retinopathy.

糖尿病视网膜病变是糖尿病最常见的微血管并发症之一,光声成像是糖尿病视网膜血管成像的有效方法。光声成像是一种基于光声效应的新兴无创成像方法,具有对比度、分辨率和深度成像等优点。要获得高质量的光声图像,适当的光声重建方法至关重要。本研究提出了一种用于光声重建的多输入自注意多尺度特征融合网络(SAMF-Net)。该算法接受两个输入,即原始光声信号和传统的重建图像。此外,该算法还采用了基于自注意机制的全局特征提取模块,以关注全局信息。结果表明,所提出的方法在不同的稀疏检测视图下都表现出卓越的重建能力。该方法对光声学图像重建具有指导意义,有望进一步应用于糖尿病视网膜病变的诊断。
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引用次数: 0
Dictionary Learning Method Based on K-Sparse Approximation and Orthogonal Procrustes Analysis for Reconstruction in Bioluminescence Tomography 基于 K-解析逼近和正交 Procrustes 分析的字典学习法用于生物发光断层摄影术的重建
IF 2 3区 物理与天体物理 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-07 DOI: 10.1002/jbio.202400308
Linzhi Su, Limin Chen, Wenlong Tang, Huimin Gao, Yi Chen, Chengyi Gao, Huangjian Yi, Xin Cao

Bioluminescence tomography (BLT) is one kind of noninvasive optical molecular imaging technology, widely used to study molecular activities and disease progression inside live animals. By combining the optical propagation model and inversion algorithm, BLT enables three-dimensional imaging and quantitative analysis of light sources within organisms. However, challenges like light scattering and absorption in tissues, and the complexity of biological structures, significantly impact the accuracy of BLT reconstructions. Here, we propose a dictionary learning method based on K-sparse approximation and Orthogonal Procrustes analysis (KSAOPA). KSAOPA uses an iterative alternating optimization strategy, enhancing solution sparsity with k-coefficients Lipschitzian mappings for sparsity(K-LIMAPS) in the sparse coding stage, and reducing errors with Orthogonal Procrustes analysis in the dictionary update stage, leading to stable and precise reconstructions. We assessed the method performance through simulations and in vivo experiments, which showed that KSAOPA excels in localization accuracy, morphological recovery, and in vivo applicability compared to other methods.

生物发光层析技术(BLT)是一种无创光学分子成像技术,广泛应用于研究活体动物体内的分子活动和疾病进展。通过结合光传播模型和反演算法,BLT 可以对生物体内的光源进行三维成像和定量分析。然而,光在组织中的散射和吸收以及生物结构的复杂性等挑战极大地影响了 BLT 重建的准确性。在此,我们提出了一种基于 K-稀疏逼近和正交 Procrustes 分析(KSAOPA)的字典学习方法。KSAOPA 采用迭代交替优化策略,在稀疏编码阶段使用 K 系数 Lipschitzian 映射稀疏性(K-LIMAPS)增强解稀疏性,在字典更新阶段使用正交 Procrustes 分析减少误差,从而实现稳定精确的重建。我们通过模拟和活体实验评估了该方法的性能,结果表明,与其他方法相比,KSAOPA 在定位精度、形态恢复和活体适用性方面都非常出色。
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引用次数: 0
Unveiling Thymoma Typing Through Hyperspectral Imaging and Deep Learning 通过高光谱成像和深度学习揭示胸腺瘤类型。
IF 2 3区 物理与天体物理 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-03 DOI: 10.1002/jbio.202400325
Qize Lv, Ke Liang, ChongXuan Tian, YanHai Zhang, YunZe Li, JinLin Deng, WeiMing Yue, Wei Li

Thymoma, a rare tumor from thymic epithelial cells, presents diagnostic challenges because of the subjective nature of traditional methods, leading to high false-negative rates and long diagnosis times. This study introduces a thymoma classification technique that integrates hyperspectral imaging with deep learning. We initially capture pathological slice images of thymoma using a hyperspectral camera and delineate regions of interest to extract spectral data. This data undergoes reflectance calibration and noise reduction. Subsequently, we transform the spectral data into two-dimensional images via the Gramian Angular Field (GAF) method. A variant residual network is then utilized to extract features and classify these images. Our results demonstrate that this model significantly enhances classification accuracy and efficiency, achieving an average accuracy of 95%. The method proves highly effective in automated thymoma diagnosis, optimizing data utilization, and feature representation learning.

胸腺瘤是一种来自胸腺上皮细胞的罕见肿瘤,由于传统方法的主观性,导致假阴性率高和诊断时间长,给诊断带来了挑战。本研究介绍了一种将高光谱成像与深度学习相结合的胸腺瘤分类技术。我们首先使用高光谱相机捕捉胸腺瘤的病理切片图像,并划定感兴趣区域以提取光谱数据。这些数据经过反射率校准和降噪处理。随后,我们通过格拉米安角场(GAF)方法将光谱数据转换为二维图像。然后利用变异残差网络提取特征并对这些图像进行分类。我们的研究结果表明,该模型大大提高了分类的准确性和效率,平均准确率达到 95%。事实证明,该方法在胸腺瘤自动诊断、优化数据利用和特征表征学习方面非常有效。
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引用次数: 0
Feasibility of Monitoring Tissue Properties During Microcirculation Disorder Using a Compact Fiber-Based Probe With Sapphire Tip 使用带蓝宝石尖端的紧凑型光纤探头监测微循环紊乱期间组织特性的可行性。
IF 2 3区 物理与天体物理 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-02 DOI: 10.1002/jbio.202400368
Alina A. Platonova, Polina V. Aleksandrova, Anna I. Alekseeva, Sophya P. Kudryavtseva, Arsen K. Zotov, Kirill I. Zaytsev, Kirill B. Dolganov, Igor V. Reshetov, Vladimir N. Kurlov, Irina N. Dolganova

One of the urgent tasks of modern medicine is to detect microcirculation disorder during surgery to avoid possible consequences like tissue hypoxia, ischemia, and necrosis. To address this issue, in this article, we propose a compact probe with sapphire tip and optical sensing based on the principle of spatially resolved diffuse reflectance analysis. It allows for intraoperative measurement of tissue effective attenuation coefficient and its alteration during the changes of tissue condition, caused by microcirculation disorder. The results of experimental studies using (1) a tissue-mimicking phantom based on lipid emulsion and hemoglobin and (2) a model of hindlimb ischemia performed in a rat demonstrated the ability to detect rapid changes of tissue attenuation confirming the feasibility of the probe to sense the stressful exposure. Due to a compact design of the probe, it could be useful for rather wide surgical operations and diagnostic purposes as an auxiliary instrument.

现代医学的当务之急之一是在手术过程中检测微循环障碍,以避免可能出现的后果,如组织缺氧、缺血和坏死。为了解决这个问题,我们在本文中提出了一种基于空间分辨漫反射分析原理的蓝宝石尖端和光学传感的紧凑型探头。它可以在术中测量组织的有效衰减系数及其在微循环障碍引起的组织状况变化过程中的变化情况。使用(1)基于脂质乳液和血红蛋白的组织模拟模型和(2)大鼠后肢缺血模型进行的实验研究结果表明,该探针能够检测组织衰减的快速变化,证实了探针感知压力暴露的可行性。由于该探针设计小巧,可作为一种辅助仪器用于相当广泛的外科手术和诊断目的。
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引用次数: 0
Microcirculatory Dysfunction in Patients With Diabetes Mellitus Detected by a Distributed System of Wearable Laser Doppler Flowmetry Analysers 通过可穿戴激光多普勒血流测量仪分布式系统检测糖尿病患者的微循环功能障碍。
IF 2 3区 物理与天体物理 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-01 DOI: 10.1002/jbio.202400297
Elena Zharkikh, Yulia Loktionova, Andrey Dunaev

The paper is devoted to the study of perfusion and amplitude-frequency spectra of laser Doppler flowmetry (LDF) signals in patients with diabetes mellitus (DM) in different skin areas of the upper and lower extremities using a distributed system of wearable LDF analysers. LDF measurements were performed in the areas of the fingers, toes, wrists and shins. The mean perfusion values, the amplitudes of blood flow oscillations in endothelial, neurogenic, myogenic, respiratory and cardiac frequency ranges, and the values of nutritive blood flow were analysed. The results revealed a decrease in tissue perfusion and nutritive blood flow in the lower extremities and an increase in these parameters in the upper extremities in patients with DM. A decrease in the amplitudes of endothelial and neurogenic oscillations was observed. The obtained results confirm the possibility of using wearable LDF analysers to detect differences in the blood flow regulation in normal and pathological conditions.

本文利用分布式可穿戴激光多普勒血流分析仪系统,对糖尿病(DM)患者上下肢不同皮肤区域的血流灌注和激光多普勒血流测量仪(LDF)信号的幅频频谱进行了研究。对手指、脚趾、手腕和小腿部位进行了 LDF 测量。对平均灌注值、内皮、神经、肌源、呼吸和心脏频率范围内的血流振荡幅度以及营养血流值进行了分析。结果显示,DM 患者下肢的组织灌注量和营养血流量减少,而上肢的组织灌注量和营养血流量增加。同时还观察到内皮振荡和神经源振荡的振幅减小。这些结果证实了使用可穿戴 LDF 分析仪检测正常和病理情况下血流调节差异的可能性。
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引用次数: 0
Characterizing Biomechanics of Limbal Niche Using Vibrational Optical Coherence Elastography 利用振动光学相干弹性成像技术确定瓣膜壁龛的生物力学特征
IF 2 3区 物理与天体物理 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-27 DOI: 10.1002/jbio.202400172
Ryan Dimmock, Yilong Zhang, Gibran F. Butt, Saaeha Rauz, Zhihong Huang, Ying Yang

The limbal niche is an adult source of epithelial stem cells which regenerate the cornea epithelium. The architecture and biomechanical properties of the limbus have previously been demonstrated to change due to aging and disease. This study aims to non-destructively and simultaneously quantify these limbal niche properties, along with their age-related changes. A lab-built vibrational optical coherence elastography (OCE) device consisting of a phase-sensitive optical coherence tomography (OCT) with a vibrational stimulator has been used to collect structural images and the depth-resolved elasticity of human corneoscleral tissues (aged 4–96 years old). The limbal palisades of Vogt (POV) were delineated well in OCT images which were validated by histology. The POVs have been spatially mapped with simultaneous elasticity measurements in cross-sections, showing tissue stiffness distributions across the undulations. A significant influence of age on the dimensions of the POVs was explored. The elastic modulus within the limbal niches for the ≥65-year-old group was significantly higher than that of the <65-year-old group.

角膜缘龛是上皮干细胞的成人来源,可再生角膜上皮。以前的研究表明,角膜缘的结构和生物力学特性会因衰老和疾病而发生变化。本研究旨在非破坏性地同时量化这些角膜缘龛特性及其与年龄相关的变化。实验室自制的振动光学相干弹性成像(OCE)设备由相位敏感光学相干断层扫描(OCT)和振动刺激器组成,用于收集人类角巩膜组织(4-96 岁)的结构图像和深度分辨弹性。OCT 图像很好地勾勒出了 Vogt 角巩膜瓣(POV)的轮廓,并通过组织学进行了验证。通过横截面的弹性同步测量,对 POV 进行了空间映射,显示了起伏处的组织硬度分布。研究发现,年龄对 POVs 的尺寸有重大影响。年龄≥65 岁组的睑缘龛内弹性模量明显高于年龄≥65 岁组的睑缘龛内弹性模量。
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引用次数: 0
Blood Plasma Film Multifractal Scanning in COVID-19 Consequences Diagnostics COVID-19 后果诊断中的血浆膜多分形扫描。
IF 2 3区 物理与天体物理 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-26 DOI: 10.1002/jbio.202400356
Alexander Ushenko, Natalia Pavlyukovich, Oksana Khukhlina, Olexander Pavlyukovich, Iryna Soltys, Alexander Dubolazov, Yurii Ushenko, Ivan Gordey, Jun Zheng, Zhebo Chen, Lin Bin

A 3D phase scanning method was applied to study blood plasma facies, generating layered polarization maps of the object field. The most sensitive parameters to changes in birefringence distribution were identified. Multifractal analysis using wavelet transforms and fractal dimension spectra provided specific insights into the scale self-similarity of the polarization maps. The multifractal spectra of ellipticity distributions were algorithmically derived, revealing that the third- and fourth-order statistical moments were most sensitive to changes in the supramolecular networks of the facies. These findings were successfully applied to differentiate post-COVID-19 effects with high accuracy.

应用三维相位扫描方法研究血浆面,生成对象场的分层偏振图。确定了对双折射分布变化最敏感的参数。利用小波变换和分形维度光谱进行的多分形分析为了解偏振图的尺度自相似性提供了具体线索。通过算法得出了椭圆度分布的多分形光谱,发现三阶和四阶统计矩对面层超分子网络的变化最为敏感。这些发现被成功地应用于高精度区分后 COVID-19 效应。
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引用次数: 0
Quantitative Characterization of Zebrafish Caudal Fin Regeneration Based on Mueller Matrix OCT In Vivo 基于 Mueller Matrix OCT 的斑马鱼尾鳍再生活体定量特征描述
IF 2 3区 物理与天体物理 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-25 DOI: 10.1002/jbio.202400376
Zaifan Wang, Ke Li, Hui Chen, Zhifang Li, Wangbiao Li, Hui Lin, Liqin Zheng, Xiaoman Zhang, Shulian Wu

Zebrafish serves as a valuable model for studying tissue regeneration due to their comprehensive regenerative abilities, particularly in bone tissue. In this study, a Mueller matrix optical coherence tomography (OCT) system was applied to monitor the regenerative processes of zebrafish caudal fins in vivo. The analysis focused on evaluating the thickness of the caudal fin tip and the distribution of internal bone tissue during the regenerative process. Subsequently, the effect of ectoine solution on the regeneration process was observed and discussed. Our findings revealed that the caudal fin blastema did not exhibit phase-induced polarization characteristics in the Mueller matrix OCT images. Statistical analyses indicated that the caudal fins did not fully regenerate to their original state within 21 days. Furthermore, the results suggested that ectoine solution could enhance tissue regeneration. This approach provides a method for quantifying zebrafish caudal fin regeneration and advances observation techniques for biomedical and clinical applications.

斑马鱼具有全面的再生能力,尤其是骨组织再生能力,因此是研究组织再生的重要模型。本研究应用穆勒矩阵光学相干断层扫描(OCT)系统监测斑马鱼尾鳍的体内再生过程。分析的重点是评估再生过程中尾鳍尖端的厚度和内部骨组织的分布。随后,还观察并讨论了伊可丁溶液对再生过程的影响。我们的研究结果表明,尾鳍囊肿在穆勒矩阵 OCT 图像中没有表现出相位诱导偏振特征。统计分析表明,尾鳍在 21 天内并未完全再生至原始状态。此外,研究结果表明,埃克托因溶液可促进组织再生。这种方法提供了一种量化斑马鱼尾鳍再生的方法,推动了生物医学和临床应用观察技术的发展。
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引用次数: 0
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Journal of Biophotonics
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