Biomedical optics express最新文献_第2页

Microfluidics-based automatic immunofluorescence staining for single-molecule localization microscopy. 基于微流控技术的单分子定位显微镜自动免疫荧光染色。

IF 2.9 2区医学

Biomedical optics express Pub Date : 2024-11-21 eCollection Date: 2024-12-01 DOI: 10.1364/BOE.540434

Jun Dong, Weibing Kuang, Bing Shi, Zhen-Li Huang

{"title":"Microfluidics-based automatic immunofluorescence staining for single-molecule localization microscopy.","authors":"Jun Dong, Weibing Kuang, Bing Shi, Zhen-Li Huang","doi":"10.1364/BOE.540434","DOIUrl":"10.1364/BOE.540434","url":null,"abstract":"Full automation of single-molecule localization microscopy (SMLM) is crucial for large-scale and high-throughput cellular imaging. It is well-known that SMLM typically consists of three major steps: immunofluorescence (IF) staining, optical imaging, and image processing. Currently, automation in optical imaging and image processing is almost complete; however, the automation of IF staining has been slow to advance, probably due to its complicated experimental operations. Here we present a low-cost automated method for IF staining, called super-resolution immunofluorescence staining by microfluidics (SRIF-fluidics). This method is suitable for both adherent and suspension cells and supports single-color and multi-color IF staining for SMLM. Our results show that SRIF-fluidics reduces antibody consumption by about 75% and shortens the sample preparation time from 5.6 hours (manual operation) to 2.5 ∼ 4.4 hours, depending on the sample types. Importantly, this method provides a satisfactory consistency of imaging results without sacrificing sample labeling quality. We believe that the method proposed in this paper is a necessary supplement to achieving fully automated SMLM and facilitating high-throughput SMLM in the near future.","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":"15 12","pages":"6893-6904"},"PeriodicalIF":2.9,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11640577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142827321","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

Identifying retinal pigment epithelium cells in adaptive optics-optical coherence tomography images with partial annotations and superhuman accuracy.

IF 2.9 2区医学

Biomedical optics express Pub Date : 2024-11-21 eCollection Date: 2024-12-01 DOI: 10.1364/BOE.538473

Somayyeh Soltanian-Zadeh, Katherine Kovalick, Samira Aghayee, Donald T Miller, Zhuolin Liu, Daniel X Hammer, Sina Farsiu

引用次数: 0

Semi-supervised 3D retinal fluid segmentation via correlation mutual learning with global reasoning attention. 通过全局推理注意的相关相互学习进行半监督三维视网膜液分割。

IF 2.9 2区医学

Biomedical optics express Pub Date : 2024-11-21 eCollection Date: 2024-12-01 DOI: 10.1364/BOE.541655

Kaizhi Cao, Yi Liu, Xinhao Zeng, Xiaoyang Qin, Renxiong Wu, Ling Wan, Bolin Deng, Jie Zhong, Guangming Ni, Yong Liu

{"title":"Semi-supervised 3D retinal fluid segmentation via correlation mutual learning with global reasoning attention.","authors":"Kaizhi Cao, Yi Liu, Xinhao Zeng, Xiaoyang Qin, Renxiong Wu, Ling Wan, Bolin Deng, Jie Zhong, Guangming Ni, Yong Liu","doi":"10.1364/BOE.541655","DOIUrl":"10.1364/BOE.541655","url":null,"abstract":"Accurate 3D segmentation of fluid lesions in optical coherence tomography (OCT) is crucial for the early diagnosis of diabetic macular edema (DME). However, higher-dimensional spatial complexity and limited annotated data present significant challenges for effective 3D lesion segmentation. To address these issues, we propose a novel semi-supervised strategy using a correlation mutual learning framework for segmenting 3D DME lesions from 3D OCT images. Our method integrates three key innovations: (1) a shared encoder with three parallel, slightly different decoders, exhibiting cognitive biases and calculating statistical discrepancies among the decoders to represent uncertainty in unlabeled challenging regions. (2) a global reasoning attention module integrated into the encoder's output to transfer label prior knowledge to unlabeled data; and (3) a correlation mutual learning scheme, enforcing mutual consistency between one decoder's probability map and the soft pseudo labels generated by the other decoders. Extensive experiments demonstrate that our approach outperforms state-of-the-art (SOTA) methods, highlighting the potential of our framework for tackling the complex task of 3D retinal lesion segmentation.","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":"15 12","pages":"6905-6921"},"PeriodicalIF":2.9,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11640579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142827326","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

Quantitative investigations on light emission profiles for interstitial laser treatment.

IF 2.9 2区医学

Biomedical optics express Pub Date : 2024-11-20 eCollection Date: 2024-12-01 DOI: 10.1364/BOE.540470

Minh Duc Ta, Yeongeun Kim, Hwarang Shin, Van Gia Truong, Hyun Wook Kang

{"title":"Quantitative investigations on light emission profiles for interstitial laser treatment.","authors":"Minh Duc Ta, Yeongeun Kim, Hwarang Shin, Van Gia Truong, Hyun Wook Kang","doi":"10.1364/BOE.540470","DOIUrl":"10.1364/BOE.540470","url":null,"abstract":"Interstitial laser treatment (ILT) using a diffusing applicator (DA) has been employed to treat tumors. However, the treatment efficacy and safety of the emission profiles from DAs have been poorly explored. This study investigated the effect of the emission profiles from DAs on prostate tumor treatment. Dual-peak and proximal-/distal-end peak profiles using 980 nm laser at 5 W for 60 s were tested to compare the extent of thermal coagulation in soft tissue numerically and experimentally. The numerical simulation predicted the temperature development in the tissue. Ex vivo porcine liver and in vivo rat models were used to compare the performance of the profiles. The dual-peak profile yielded a coagulation extent that was almost equivalent to that of the flat-top profile (in simulation) and 1.3 times larger than those of the other profiles in both ex vivo and in vivo. The dual-peak profile predictably entailed uniform coagulation within the irradiated region. Further in vivo studies using different tumor sizes will be evaluated to warrant the efficacy and safety of the dual-peak profile for the ILT of prostate tumors.","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":"15 12","pages":"6877-6892"},"PeriodicalIF":2.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11640558/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142827325","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

Full-view volumetric photoacoustic imaging using a hemispheric transducer array combined with an acoustic reflector.

IF 2.9 2区医学

Biomedical optics express Pub Date : 2024-11-19 eCollection Date: 2024-12-01 DOI: 10.1364/BOE.540392

Mingli Sun, Xuanhao Wang, Yuqi Wang, Yuqian Meng, Da Gao, Chiye Li, Ruimin Chen, Kaikai Huang, Junhui Shi

{"title":"Full-view volumetric photoacoustic imaging using a hemispheric transducer array combined with an acoustic reflector.","authors":"Mingli Sun, Xuanhao Wang, Yuqi Wang, Yuqian Meng, Da Gao, Chiye Li, Ruimin Chen, Kaikai Huang, Junhui Shi","doi":"10.1364/BOE.540392","DOIUrl":"10.1364/BOE.540392","url":null,"abstract":"Photoacoustic computed tomography (PACT) has evoked extensive interest for applications in preclinical and clinical research. However, the current systems suffer from the limited view provided by detection setups, thus impeding the sufficient acquisition of intricate tissue structures. Here, we propose an approach to enable fast 3D full-view imaging. A hemispherical ultrasonic transducer array combined with a planar acoustic reflector serves as the ultrasonic detection device in the PACT system. The planar acoustic reflector can create a mirrored virtual transducer array, and the detection view range can be enlarged to cover approximately 3.7 <math><mi>π</mi></math> steradians in our detection setup. To verify the effectiveness of our proposed configuration, we present the imaging results of a hair phantom, an in vivo zebrafish larva, and a leaf skeleton phantom. Furthermore, the real-time dynamic imaging capacity of this system is demonstrated by observing the movement of zebrafish within 2 s. This strategy holds great potential for both preclinical and clinical research by providing more detailed and comprehensive images of biological tissues.","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":"15 12","pages":"6864-6876"},"PeriodicalIF":2.9,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11640568/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142827284","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

Mask-guided network for finger vein feature extraction and biometric identification. 用于手指静脉特征提取和生物识别的掩膜引导网络。

IF 2.9 2区医学

Biomedical optics express Pub Date : 2024-11-15 eCollection Date: 2024-12-01 DOI: 10.1364/BOE.535390

Haohan Bai, Yubo Tan, Yong-Jie Li

{"title":"Mask-guided network for finger vein feature extraction and biometric identification.","authors":"Haohan Bai, Yubo Tan, Yong-Jie Li","doi":"10.1364/BOE.535390","DOIUrl":"10.1364/BOE.535390","url":null,"abstract":"The problems of complex background, low quality of finger vein images, and poor discriminative features have been the bottleneck of feature extraction and finger vein recognition. To this end, we propose a feature extraction algorithm based on the open-set testing protocol. In order to eliminate the interference of irrelevant areas, this paper proposes the idea of segmentation-assisted classification, that is, using the rough mask of the finger vein to constrain the feature learning process so that the network can focus on the vein area and learn greater weight for the vein. Specifically, the feature maps of the shallow layers of the network are first sent to the feature pyramid module to fuse the primary features of different scales, which are then sent to the spatial attention module to obtain the spatial weight map of the image. Based on the results of several classical vein skeleton extraction algorithms, a weighting method is used to obtain a more accurate mask to constrain the learning of the spatial weight map. Finally, a hybrid loss function combining triplet loss and cross-entropy loss is used to reduce the distance between feature vectors of the same categories and increase the distance between feature vectors of different categories in the Euclidean space, thereby improving feature discriminability. Good recognition results were achieved on the three public data sets of SDUMLA, MMCBNU, and FVUSM, and the values of equal error rate (EER) on them are as low as 2.50%, 0.20%, and 0.14%, respectively.","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":"15 12","pages":"6845-6863"},"PeriodicalIF":2.9,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11640582/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142827319","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

Imaging of prostate micro-architecture using three-dimensional wide-field optical coherence tomography.

IF 2.9 2区医学

Biomedical optics express Pub Date : 2024-11-14 eCollection Date: 2024-12-01 DOI: 10.1364/BOE.537783

Marta K Skrok, Szymon Tamborski, Matt S Hepburn, Qi Fang, Mateusz Maniewski, Marek Zdrenka, Maciej Szkulmowski, Adam Kowalewski, Łukasz Szylberg, Brendan F Kennedy

{"title":"Imaging of prostate micro-architecture using three-dimensional wide-field optical coherence tomography.","authors":"Marta K Skrok, Szymon Tamborski, Matt S Hepburn, Qi Fang, Mateusz Maniewski, Marek Zdrenka, Maciej Szkulmowski, Adam Kowalewski, Łukasz Szylberg, Brendan F Kennedy","doi":"10.1364/BOE.537783","DOIUrl":"10.1364/BOE.537783","url":null,"abstract":"Prostate cancer is a global health issue that requires new diagnostic methods to provide accurate and precise visualization of prostate tissue on the micro-scale. Such methods have the potential to improve nerve-sparing surgery and to provide image guidance during prostate biopsy. In this feasibility study, we assess the potential of en face three-dimensional wide-field optical coherence tomography (OCT), covering a volumetric imaging field-of-view up to 46 × 46 × 1 mm3, to visualize micro-architecture in 18 freshly excised human prostate specimens. In each case, validation of contrast in OCT images is provided by co-registered wide-field histology images. Using this co-registration, we demonstrate that OCT can distinguish between healthy and cancerous glands at different stages, as well as visualize micro-architecture in the prostate, such as epineurium and perineurium in nerves and the tunica intima and tunica media in blood vessels.","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":"15 12","pages":"6816-6833"},"PeriodicalIF":2.9,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11640564/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142827286","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

Diffractive hyperchromatic objective for chromatic confocal microscopy.

IF 2.9 2区医学

Biomedical optics express Pub Date : 2024-11-14 eCollection Date: 2024-12-01 DOI: 10.1364/BOE.543322

Jiabin Chen, Shaobai Li, Wenjun Kang, Shuyuan Guan, Zhihan Hong, Rongguang Liang

引用次数: 0

Fast and customizable image formation model for optical coherence tomography. 快速、可定制的光学相干断层扫描图像形成模型。

IF 2.9 2区医学

Biomedical optics express Pub Date : 2024-11-13 eCollection Date: 2024-12-01 DOI: 10.1364/BOE.534263

Andrea Mazzolani, Callum Macdonald, Peter R T Munro

{"title":"Fast and customizable image formation model for optical coherence tomography.","authors":"Andrea Mazzolani, Callum Macdonald, Peter R T Munro","doi":"10.1364/BOE.534263","DOIUrl":"10.1364/BOE.534263","url":null,"abstract":"Optical coherence tomography (OCT) is a technique that performs high-resolution, three-dimensional, imaging of semi-transparent scattering biological tissues. Models of OCT image formation are needed for applications such as aiding image interpretation and validating OCT signal processing techniques. Existing image formation models generally trade off between model realism and computation time. In particular, the most realistic models tend to be highly computationally demanding, which becomes a limiting factor when simulating C-scan generation. Here we present an OCT image formation model based on the first-order Born approximation that is significantly faster than existing models, whilst maintaining a high degree of realism. This model is made more powerful because it is amenable to simulation of phase sensitive OCT, thus making it applicable to scenarios where sample displacement is of interest, such as optical coherence elastography (OCE) or Doppler OCT. The low computational cost of the model also makes it suitable for creating large OCT data sets needed for training deep learning OCT signal processing models. We present details of our novel image formation model and demonstrate its accuracy and computational efficiency.","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":"15 12","pages":"6783-6798"},"PeriodicalIF":2.9,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11640576/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142827282","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

Embedded CPU-GPU pupil tracking.

IF 2.9 2区医学

Biomedical optics express Pub Date : 2024-11-13 eCollection Date: 2024-12-01 DOI: 10.1364/BOE.541421

Bartlomiej Kowalski, Xiaojing Huang, Alfredo Dubra

{"title":"Embedded CPU-GPU pupil tracking.","authors":"Bartlomiej Kowalski, Xiaojing Huang, Alfredo Dubra","doi":"10.1364/BOE.541421","DOIUrl":"10.1364/BOE.541421","url":null,"abstract":"We explore camera-based pupil tracking using high-level programming in computing platforms with end-user discrete and integrated central processing units (CPUs) and graphics processing units (GPUs), seeking low calculation latencies previously achieved with specialized hardware and programming (Kowalski et al., [Biomed. Opt. Express12, 6496 (2021)10.1364/BOE.433766]. Various desktop and embedded computers were tested, some with two operating systems, using the traditional sequential pupil tracking paradigm, in which the processing of the camera image only starts after it is fully downloaded to the computer. The pupil tracking was demonstrated using two Scheimpflug optical setups, telecentric in both image and object spaces, with different optical magnifications and nominal diffraction-limited performance over an ∼18 mm full field of view illuminated with 940 nm light. Eye images from subjects with different iris and skin pigmentation captured at this wavelength suggest that the proposed pupil tracking does not suffer from ethnic bias. The optical axis of the setups is tilted at 45° to facilitate integration with other instruments without the need for beam splitting. Tracking with ∼0.9-4.4 µm precision and safe light levels was demonstrated using two complementary metal-oxide-semiconductor cameras with global shutter, operating at 438 and 1,045 fps with an ∼500 × 420 pixel region of interest (ROI), and at 633 and 1,897 fps with ∼315 × 280 pixel ROI. For these image sizes, the desktop computers achieved calculation times as low as 0.5 ms, while low-cost embedded computers delivered calculation times in the 0.8-1.3 ms range.","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":"15 12","pages":"6799-6815"},"PeriodicalIF":2.9,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11640584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142827280","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