Biomedical optics express最新文献

Adaptive Raman spectral unmixing method based on Voigt peak compensation for quantitative analysis of cellular biochemical components. 基于Voigt峰补偿的细胞生化成分定量分析自适应拉曼光谱解混方法。

IF 2.9 2区医学

Biomedical optics express Pub Date : 2025-02-28 eCollection Date: 2025-03-01 DOI: 10.1364/BOE.553461

Xiang Chen, Ping Tang, Jianhui Wan, Weina Zhang, Liyun Zhong

{"title":"Adaptive Raman spectral unmixing method based on Voigt peak compensation for quantitative analysis of cellular biochemical components.","authors":"Xiang Chen, Ping Tang, Jianhui Wan, Weina Zhang, Liyun Zhong","doi":"10.1364/BOE.553461","DOIUrl":"10.1364/BOE.553461","url":null,"abstract":"Raman spectroscopy, with its unique \"molecular fingerprint\" characteristics, is an essential tool for label-free, non-invasive biochemical analysis of cells. It provides precise information on cellular biochemical components, such as proteins, lipids, and nucleic acids by analyzing molecular vibrational modes. However, overlapping Raman spectral signals make spectral unmixing crucial for accurate quantification. Traditional unmixing methods face challenges: unsupervised algorithms yield poorly interpretable results, while supervised methods like BCA rely heavily on accurate reference spectra and are sensitive to environmental changes (e.g., pH, temperature, excitation wavelength), causing spectral distortion and reducing quantitative reliability. This study addresses these challenges by introducing a parameterized Voigt function into the linear spectral mixing model for element spectrum compensation, using iterative least-squares optimization for adaptive unmixing and quantitative analysis. Simulations show that the Voigt-compensated unmixing algorithm improves spectral fitting accuracy and robustness. Applied to Raman spectra from Hela cell apoptosis and iPSCs differentiation, the algorithm accurately tracks biochemical molecular changes, proving its applicability in cellular Raman spectral analysis and a precise, reliable, and versatile tool for quantitative biochemical analysis.","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":"16 3","pages":"1284-1298"},"PeriodicalIF":2.9,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919365/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploiting the detector distance information in image scanning microscopy by phasor-based SPLIT-ISM. 利用基于相量的SPLIT-ISM提取图像扫描显微镜中探测器距离信息。

IF 2.9 2区医学

Biomedical optics express Pub Date : 2025-02-27 eCollection Date: 2025-03-01 DOI: 10.1364/BOE.551255

Elisabetta Di Franco, Giulia Tedeschi, Lorenzo Scipioni, Enrico Gratton, Michelle Digman, Marco Castello, Alberto Diaspro, Giuseppe Vicidomini, Paolo Bianchini, Luca Lanzanò

{"title":"Exploiting the detector distance information in image scanning microscopy by phasor-based SPLIT-ISM.","authors":"Elisabetta Di Franco, Giulia Tedeschi, Lorenzo Scipioni, Enrico Gratton, Michelle Digman, Marco Castello, Alberto Diaspro, Giuseppe Vicidomini, Paolo Bianchini, Luca Lanzanò","doi":"10.1364/BOE.551255","DOIUrl":"10.1364/BOE.551255","url":null,"abstract":"Confocal microscopy is an important bio-imaging technique that increases the resolution using a spatial pinhole to block out-of-focus light. In theory, the maximum resolution and optical sectioning are obtained when the detection pinhole is fully closed, but this is prevented by the dramatic decrease in the signal reaching the detector. In image scanning microscopy (ISM) this limitation is overcome by the use of an array of point detectors rather than a single detector. This, combined with pixel reassignment, increases the resolution of <math><msqrt><mn>2</mn></msqrt> </math> over widefield imaging, with relatively little modification to the existing hardware of a laser-scanning microscope. Separation of photons by lifetime tuning (SPLIT) is a super-resolution technique, based on the phasor analysis of the fluorescent signal into an additional channel of the microscope. Here, we use SPLIT to analyze the information encoded within the array detectors distance for improving the resolution of ISM (SPLIT-ISM). We find that the lateral resolution can be increased of an additional 1.3 × with respect to the pixel-reassigned image with a concomitant increase in optical sectioning. We applied the SPLIT-ISM technique on biological images acquired by two currently available ISM systems: the Genoa Instruments PRISM and the Zeiss Airyscan. We evaluate the improvement provided by SPLIT-ISM through the QuICS algorithm, a quantitative tool based on image correlation spectroscopy. QuICS allows extracting three parameters related to the resolution, and contrast SNR of the image. We find that SPLIT-ISM provides an increase in spatial resolution for both the Genoa Instrument PRISM and the Zeiss Airyscan microscopes.","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":"16 3","pages":"1270-1283"},"PeriodicalIF":2.9,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919353/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Semi-supervised assisted multi-task learning for oral optical coherence tomography image segmentation and denoising. 口腔光学相干断层成像图像分割与去噪的半监督辅助多任务学习。

IF 2.9 2区医学

Biomedical optics express Pub Date : 2025-02-26 eCollection Date: 2025-03-01 DOI: 10.1364/BOE.545377

Jinpeng Liao, Tianyu Zhang, Simon Shepherd, Michaelina Macluskey, Chunhui Li, Zhihong Huang

{"title":"Semi-supervised assisted multi-task learning for oral optical coherence tomography image segmentation and denoising.","authors":"Jinpeng Liao, Tianyu Zhang, Simon Shepherd, Michaelina Macluskey, Chunhui Li, Zhihong Huang","doi":"10.1364/BOE.545377","DOIUrl":"10.1364/BOE.545377","url":null,"abstract":"Optical coherence tomography (OCT) is promising to become an essential imaging tool for non-invasive oral mucosal tissue assessment, but it faces challenges like speckle noise and motion artifacts. In addition, it is difficult to distinguish different layers of oral mucosal tissues from gray level OCT images due to the similarity of optical properties between different layers. We introduce the Efficient Segmentation-Denoising Model (ESDM), a multi-task deep learning framework designed to enhance OCT imaging by reducing scan time from ∼8s to ∼2s and improving oral epithelium layer segmentation. ESDM integrates the local feature extraction capabilities of the convolution layer and the long-term information processing advantages of the transformer, achieving better denoising and segmentation performance compared to existing models. Our evaluation shows that ESDM outperforms state-of-the-art models with a PSNR of 26.272, SSIM of 0.737, mDice of 0.972, and mIoU of 0.948. Ablation studies confirm the effectiveness of our design, such as the feature fusion methods, which enhance performance with minimal model complexity increase. ESDM also presents high accuracy in quantifying oral epithelium thickness, achieving mean absolute errors as low as 5 µm compared to manual measurements. This research shows that ESDM can notably improve OCT imaging and reduce the cost of accurate oral epithermal segmentation, improving diagnostic capabilities in clinical settings.","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":"16 3","pages":"1197-1215"},"PeriodicalIF":2.9,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919357/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Investigating the impact of different time delays between OCT signal and k-clock signal on the structural and vascular imaging in SS-OCT. 探讨不同时间延迟的OCT信号和k-clock信号对SS-OCT结构和血管成像的影响。

IF 2.9 2区医学

Biomedical optics express Pub Date : 2025-02-26 eCollection Date: 2025-03-01 DOI: 10.1364/BOE.553982

Miaohua Chen, Zhaodong Lu, Peijun Tang, Gongpu Lan, Yanping Huang, Jia Qin, Lin An, Haixia Qiu, Jingjiang Xu

{"title":"Investigating the impact of different time delays between OCT signal and k-clock signal on the structural and vascular imaging in SS-OCT.","authors":"Miaohua Chen, Zhaodong Lu, Peijun Tang, Gongpu Lan, Yanping Huang, Jia Qin, Lin An, Haixia Qiu, Jingjiang Xu","doi":"10.1364/BOE.553982","DOIUrl":"10.1364/BOE.553982","url":null,"abstract":"High-quality swept-source optical coherence tomography (SS-OCT) imaging systems require precise synchronization between the OCT signal and the k-clock signal. However, in practical applications, an uncertain time delay between these signals can cause inaccurate k-space sampling, leading to degraded imaging resolution. This study first simulates the axial resolution degradation curve caused by varying time delays and experimentally validates the results. Additionally, the effects of different time delays on both OCT structural and blood flow images are systematically investigated through experiments. To address this issue, a numerical calibration method is implemented to compensate for the nonlinear phase component. This approach involves acquiring two reflection signals at different depths, unwrapping the phase, performing high-order polynomial fitting, and removing nonlinear phase components induced by time delay, which effectively corrects the resolution degradation. Experiments conducted on semi-transparent white tape, blood flow phantom, and human nailfold demonstrate that the proposed correction algorithm significantly improves the axial resolution of both structural and blood flow images. The findings indicate that our investigation and the developed calibration method are instrumental in reconstructing high-resolution SS-OCT images, which are essential for accurate diagnosis and effective treatment monitoring in clinical applications.","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":"16 3","pages":"1225-1239"},"PeriodicalIF":2.9,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919362/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Controlling ocular longitudinal chromatic aberration using a spatial light modulator. 利用空间光调制器控制眼纵色差。

IF 2.9 2区医学

Biomedical optics express Pub Date : 2025-02-26 eCollection Date: 2025-03-01 DOI: 10.1364/BOE.545842

Dibyendu Pusti, Debajyoti Debnath, Seungpil Bang, Geunyoung Yoon

引用次数: 0

Fast blood flow index reconstruction of diffuse correlation spectroscopy using a back-propagation-free data-driven algorithm. 基于无反向传播数据驱动算法的漫射相关光谱快速血流指数重建。

IF 2.9 2区医学

Biomedical optics express Pub Date : 2025-02-26 eCollection Date: 2025-03-01 DOI: 10.1364/BOE.549363

Zhenya Zang, Mingliang Pan, Yuanzhe Zhang, David Day Uei Li

{"title":"Fast blood flow index reconstruction of diffuse correlation spectroscopy using a back-propagation-free data-driven algorithm.","authors":"Zhenya Zang, Mingliang Pan, Yuanzhe Zhang, David Day Uei Li","doi":"10.1364/BOE.549363","DOIUrl":"10.1364/BOE.549363","url":null,"abstract":"This study introduces a fast and accurate online training method for blood flow index (BFI) and relative BFI (rBFI) reconstruction in diffuse correlation spectroscopy (DCS). We implement rigorous mathematical models to simulate the auto-correlation functions (g 2) for semi-infinite homogeneous and three-layer human brain models. We implemented a fast online training algorithm known as random vector functional link (RVFL) to reconstruct BFI from noisy g 2. We extensively evaluated RVFL regarding both speed and accuracy for training and inference. Moreover, we compared RVFL with extreme learning machine (ELM) architecture, a conventional convolutional neural network (CNN), and three fitting algorithms. Results from semi-infinite and three-layer models indicate that RVFL achieves higher accuracy than the other algorithms, as evidenced by comprehensive metrics. While RVFL offers comparable accuracy to CNNs, it boosts training speeds that are 3900-fold faster and inference speeds that are 19.8-fold faster, enhancing its generalizability across different experimental settings. We also used g 2 from one- and three-layer Monte Carlo (MC)-based in-silico simulations, as well as from analytical models, to compare the accuracy and consistency of the results obtained from RVFL and ELM. Furthermore, we discuss how RVFL is more suitable for embedded hardware due to its lower computational complexity than ELM and CNN for training and inference.","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":"16 3","pages":"1254-1269"},"PeriodicalIF":2.9,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919341/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Active remote focus stabilization in oblique plane microscopy. 主动远程聚焦稳定在斜面显微镜。

IF 2.9 2区医学

Biomedical optics express Pub Date : 2025-02-26 eCollection Date: 2025-03-01 DOI: 10.1364/BOE.553545

Trung Duc Nguyen, Amir Rahmani, Aleks Ponjavic, Alfred Millett-Sikking, Reto Fiolka

引用次数: 0

Improving the performance of multifocal diffractive lens designs by adding a peripheral piston. 通过增加外围活塞来改善多焦衍射透镜设计的性能。

IF 2.9 2区医学

Biomedical optics express Pub Date : 2025-02-25 eCollection Date: 2025-03-01 DOI: 10.1364/BOE.549909

Sabyasachi Goswami, Tianlun Zou, Sara Aissati, Gustavo Gandara-Montano, Len Zheleznyak, Susana Marcos

引用次数: 0

Establishing the feasibility and reliability of broadband absorption spectroscopy for measuring cerebral water content in adults. 建立宽带吸收光谱法测定成人脑水含量的可行性和可靠性。

IF 2.9 2区医学

Biomedical optics express Pub Date : 2025-02-25 eCollection Date: 2025-03-01 DOI: 10.1364/BOE.551192

Vidisha Goyal, Michael D Arrington, Rodrigo M Forti, LaBeausha H Harris, Shasha Bai, Feras Akbik, Owen B Samuels, Prem A Kandiah, Ofer Sadan, Erin M Buckley

引用次数: 0

Adaptive lensless microscopic imaging with unknown phase modulation. 未知相位调制的自适应无透镜显微成像。

IF 2.9 2区医学

Biomedical optics express Pub Date : 2025-02-25 eCollection Date: 2025-03-01 DOI: 10.1364/BOE.555679

Xiangyu Chen, Hao Sha, Chunyu Chen, Yuan Jiang, Wenzhen Zou, Yongbing Zhang

{"title":"Adaptive lensless microscopic imaging with unknown phase modulation.","authors":"Xiangyu Chen, Hao Sha, Chunyu Chen, Yuan Jiang, Wenzhen Zou, Yongbing Zhang","doi":"10.1364/BOE.555679","DOIUrl":"10.1364/BOE.555679","url":null,"abstract":"Lensless imaging is a popular research field because of its small size, wide field-of-view, and low aberration in recent years. However, some traditional lensless imaging methods suffer from slow convergence, mechanical errors, and conjugate solution interference, which limit their further application and development. In this work, we proposed a lensless imaging method based on a spatial light modulator (SLM) with unknown phase modulation values. In our imaging system, the SLM is utilized to modulate the wavefront of the object. When the phase modulation values of the SLM are inaccurate or unknown, conventional algorithms such as amplitude-phase retrieval (APR) or the extended ptychographic iterative engine (ePIE) fail to reconstruct the complex amplitude information of the object. To address this challenge, we introduce a novel approach that combines ptychographic scanning along a spiral path with the ePIE algorithm, enabling accurate reconstruction of the original image. We further analyze the effect of modulation function and the characteristics of the coherent light source on the quality of the reconstructed image. The experiments show that the proposed method is superior to traditional methods in terms of recovering speed and accuracy, with the recovering resolution up to 14 μm in the reconstruction of the USAF phase plate image.","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":"16 3","pages":"1160-1171"},"PeriodicalIF":2.9,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0