Biomedical optics express最新文献

{"title":"Spectral library and method for sparse unmixing of hyperspectral images in fluorescence guided resection of brain tumors","authors":"David Black, Benoit Liquet, Antonio Di Ieva, Walter Stummer, Eric Suero Molina","doi":"10.1364/boe.528535","DOIUrl":"https://doi.org/10.1364/boe.528535","url":null,"abstract":"Through spectral unmixing, hyperspectral imaging (HSI) in fluorescence-guided brain tumor surgery has enabled the detection and classification of tumor regions invisible to the human eye. Prior unmixing work has focused on determining a minimal set of viable fluorophore spectra known to be present in the brain and effectively reconstructing human data without overfitting. With these endmembers, non-negative least squares regression (NNLS) was commonly used to compute the abundances. However, HSI images are heterogeneous, so one small set of endmember spectra may not fit all pixels well. Additionally, NNLS is the maximum likelihood estimator only if the measurement is normally distributed, and it does not enforce sparsity, which leads to overfitting and unphysical results. In this paper, we analyzed 555666 HSI fluorescence spectra from 891 ex vivo measurements of patients with various brain tumors to show that a Poisson distribution indeed models the measured data 82% better than a Gaussian in terms of the Kullback-Leibler divergence, and that the endmember abundance vectors are sparse. With this knowledge, we introduce (1) a library of 9 endmember spectra, including PpIX (620 nm and 634 nm photostates), NADH, FAD, flavins, lipofuscin, melanin, elastin, and collagen, (2) a sparse, non-negative Poisson regression algorithm to perform physics-informed unmixing with this library without overfitting, and (3) a highly realistic spectral measurement simulation with known endmember abundances. The new unmixing method was then tested on the human and simulated data and compared to four other candidate methods. It outperforms previous methods with 25% lower error in the computed abundances on the simulated data than NNLS, lower reconstruction error on human data, better sparsity, and 31 times faster runtime than state-of-the-art Poisson regression. This method and library of endmember spectra can enable more accurate spectral unmixing to aid the surgeon better during brain tumor resection.","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141868632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-Speed, Long-Range and Wide-Field OCT for in vivo 3D Imaging of Oral Cavity Achieved by 600 kHz Swept Source Laser","authors":"Yaping Shi, Jian Liu, Ruikang K Wang","doi":"10.1364/boe.528287","DOIUrl":"https://doi.org/10.1364/boe.528287","url":null,"abstract":"","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141357840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GAN-based quantitative oblique back-illumination microscopy enables computationally efficient epi-mode refractive index tomography","authors":"Zhenmin Li, Paloma Casteleiro Costa, Zhe Guang, Caroline Filan, Francisco E. Robles","doi":"10.1364/boe.528968","DOIUrl":"https://doi.org/10.1364/boe.528968","url":null,"abstract":"","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141355501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simultaneous removal of noise and correction of motion warping in neuron calcium imaging using a pipeline structure of self-supervised deep learning models","authors":"Hongdong Zhang, Zhiqiang Xu, Ningbo Chen, Fei Ma, Wei Zheng, Chengbo Liu, Jing Meng","doi":"10.1364/boe.527919","DOIUrl":"https://doi.org/10.1364/boe.527919","url":null,"abstract":"","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141358154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep autoencoder as an interpretable tool for Raman spectroscopy investigation of chemical and extracellular vesicle mixtures.","authors":"Mohammadrahim Kazemzadeh, Miguel Martinez-Calderon, Robert Otupiri, Anastasiia Artuyants, MoiMoi Lowe, Xia Ning, Eduardo Reategui, Zachary D Schultz, Weiliang Xu, Cherie Blenkiron, Lawrence W Chamley, Neil G R Broderick, Colin L Hisey","doi":"10.1364/BOE.522376","DOIUrl":"10.1364/BOE.522376","url":null,"abstract":"<p><p>Surface-enhanced Raman spectroscopy (SERS) is a powerful tool that provides valuable insight into the molecular contents of chemical and biological samples. However, interpreting Raman spectra from complex or dynamic datasets remains challenging, particularly for highly heterogeneous biological samples like extracellular vesicles (EVs). To overcome this, we developed a tunable and interpretable deep autoencoder for the analysis of several challenging Raman spectroscopy applications, including synthetic datasets, chemical mixtures, a chemical milling reaction, and mixtures of EVs. We compared the results with classical methods (PCA and UMAP) to demonstrate the superior performance of the proposed technique. Our method can handle small datasets, provide a high degree of generalization such that it can fill unknown gaps within spectral datasets, and even quantify relative ratios of cell line-derived EVs to fetal bovine serum-derived EVs within mixtures. This simple yet robust approach will greatly improve the analysis capabilities for many other Raman spectroscopy applications.</p>","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11249694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632543","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}

{"title":"Erratum: Effect of transdermal drug delivery patches on the stratum corneum: in vivo inspection with a handheld terahertz probe: publisher's note.","authors":"Arturo I Hernandez-Serrano, Xuefei Ding, Goncalo Costa, Gabit Nurumbetov, David M Haddleton, Emma Pickwell-Macpherson","doi":"10.1364/BOE.531811","DOIUrl":"10.1364/BOE.531811","url":null,"abstract":"<p><p>[This corrects the article on p. 3064 in vol. 15, PMID: 38855675.].</p>","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11249697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632544","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}

{"title":"Fabrication of a low-cost benchtop optical imager for quantum dot microarray-based stress biomarker detection.","authors":"Anusha Kishore, Arun Mathew Varughese, Bernhard Roth, Carsten Zeilinger","doi":"10.1364/BOE.527338","DOIUrl":"10.1364/BOE.527338","url":null,"abstract":"<p><p>We report on a simplified optical imager to detect the presence of a stress biomarker protein, namely the Heat shock protein 90 (Hsp90). The imager consists of two elements the optical unit and the sensor, which is a custom-made biochip. Measurement is based on the masking of the streptavidin conjugated quantum dot's (Sav-QDs) fluorescence when Hsp90 attaches to it via biotinylated antibodies (Ab). The masking effect was directly proportional to the Hsp90 concentration. The cost-efficient benchtop imager developed comprises a CMOS sensor, standard optical lenses, and a narrow bandpass filter for optically eliminating background fluorescence. This approach is promising for the realization of cheap, robust, and reliable point-of-care detection systems for various biomarker analyses.</p>","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11249684/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632545","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}

{"title":"Towards a sensing model using a random laser combined with diffuse reflectance spectroscopy","authors":"Dongqin Ni, Florian Klämpfl, Michael Schmidt, Martin Hohmann","doi":"10.1364/boe.525693","DOIUrl":"https://doi.org/10.1364/boe.525693","url":null,"abstract":"The previous research proves that the random laser emission reflects not only the scattering properties but also the absorption properties. The random laser is therefore considered a potential tool for optical properties sensing. Although the qualitative sensing using the random laser is extensively investigated, a quantitative measurement of optical properties is still rare. In this study, a generalized mathematical quantitative model using random laser combined with diffuse reflectance spectroscopy is proposed for optical sensing in turbid media. This model describes the gain effect of the active medium and the optical properties effect of the passive medium separately. Rhodamine 6G is used as the active medium. Intralipid and ink are employed to demonstrate the effect of the scattering and absorption, respectively. The peak wavelength shift of the random laser is proved to be an ideal sensing parameter for this sensing model. It is also revealed that the scaling parameters in the sensing model are interrelated and can be simplified to one. With this combined model, the direct sensing of optical properties in diverse turbid media is promising.","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141873078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Real-time breath gas analysis of methane using a multipass cell based near-infrared gas sensor","authors":"Rong Kong, jie Huang, peng liu, Xin Zhou","doi":"10.1364/boe.528923","DOIUrl":"https://doi.org/10.1364/boe.528923","url":null,"abstract":"","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141267671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantifying tissue temperature changes induced by infrared neural stimulation: numerical simulation and MR thermometry.","authors":"Yinghua Xi, Kenneth E Schriver, Anna Wang Roe, Xiaotong Zhang","doi":"10.1364/BOE.530854","DOIUrl":"10.1364/BOE.530854","url":null,"abstract":"<p><p>Infrared neural stimulation (INS) delivered via short pulse trains is an innovative tool that has potential for us use for studying brain function and circuitry, brain machine interface, and clinical use. The prevailing mechanism for INS involves the conversion of light energy into thermal transients, leading to neuronal membrane depolarization. Due to the potential risks of thermal damage, it is crucial to ensure that the resulting local temperature increases are within non-damaging limits for brain tissues. Previous studies have estimated damage thresholds using histological methods and have modeled thermal effects based on peripheral nerves. However, additional quantitative measurements and modeling studies are needed for the central nervous system. Here, we performed 7 T MRI thermometry on <i>ex vivo</i> rat brains following the delivery of infrared pulse trains at five different intensities from 0.1-1.0 J/cm² (each pulse train 1,875 nm, 25 us/pulse, 200 Hz, 0.5 s duration, delivered through 200 µm fiber). Additionally, we utilized the General BioHeat Transfer Model (GBHTM) to simulate local temperature changes in perfused brain tissues while delivering these laser energies to tissue (with optical parameters of human skin) via three different sizes of optical fibers at five energy intensities. The simulation results clearly demonstrate that a 0.5 second INS pulse train induces an increase followed by an immediate drop in temperature at stimulation offset. The delivery of multiple pulse trains with 2.5 s interstimulus interval (ISI) leads to rising temperatures that plateau. Both thermometry and modeling results show that, using parameters that are commonly used in biological applications (200 µm diameter fiber, 0.1-1.0 J/cm²), the final temperature increase at the end of the 60 sec stimuli duration does not exceed 1°C with stimulation values of 0.1-0.5 J/cm² and does not exceed 2°C with stimulation values of up to 1.0 J/cm². Thus, the maximum temperature rise is consistent with the thermal damage threshold reported in previous studies. This study provides a quantitative evaluation of the temperature changes induced by INS, suggesting that existing practices pose minimal major safety concerns for biological tissues.</p>","PeriodicalId":8969,"journal":{"name":"Biomedical optics express","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11249695/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632566","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}