Optical biopsy identification and grading of gliomas using label-free visible resonance Raman spectroscopy.

Glioma is one of the most refractory types of brain tumor. Accurate tumor boundary identification and complete resection of the tumor are essential for glioma removal during brain surgery. We present a method based on visible resonance Raman (VRR) spectroscopy to identify glioma margins and grades. A set of diagnostic spectral biomarkers features are presented based on tissue composition changes revealed by VRR. The Raman spectra include molecular vibrational fingerprints of carotenoids, tryptophan, amide I/II/III, proteins, and lipids. These basic in situ spectral biomarkers are used to identify the tissue from the interface between brain cancer and normal tissue and to evaluate glioma grades. The VRR spectra are also analyzed using principal component analysis for dimension reduction and feature detection and support vector machine for classification. The cross-validated sensitivity, specificity, and accuracy are found to be 100%, 96.3%, and 99.6% to distinguish glioma tissues from normal brain tissues, respectively. The area under the receiver operating characteristic curve for the classification is about 1.0. The accuracies to distinguish normal, low grade (grades I and II), and high grade (grades III and IV) gliomas are found to be 96.3%, 53.7%, and 84.1% for the three groups, respectively, along with a total accuracy of 75.1%. A set of criteria for differentiating normal human brain tissues from normal control tissues is proposed and used to identify brain cancer margins, yielding a diagnostic sensitivity of 100% and specificity of 71%. Our study demonstrates the potential of VRR as a label-free optical molecular histopathology method used for in situ boundary line judgment for brain surgery in the margins

Inverse and forward modeling tools for biophotonic data

Biophotonic data require specific treatments due to the difficulty of directly extracting information from them. Therefore, artificial intelligence tools including machine learning and deep learning brought into play. These tools can be grouped into inverse modeling, preprocessing and data modeling categories. In each of these three categories, one research question was investigated. First, the aim was to develop a method that can acquire the Raman-like spectra from coherent anti-Stokes Raman scattering (CARS) spectra without apriori knowledge. In general, CARS spectra suffer from the non-resonant background (NRB) contribution, and existing methods were commonly implemented to remove it. However, these methods were not able to completely remove the NRB and need additional preprocessing afterward. Therefore, deep learning via the long-short-term memory network was applied and outperformed these existing methods. Then, a denoising technique via deep learning was developed for reconstructing high-quality (HQ) multimodal images (MM) from low-quality (LQ) ones. Since the measurement of HQ MM images is time-consuming, which is impractical for clinical applications, we developed a network, namely incSRCNN, to directly predict HQ images using only LQ ones. This network shows better performance when compared with standard methods. Finally, we intended to improve the accuracy of the classification model in particular when LQ Raman data or Raman data with varying quality are obtained. Therefore, a novel method based on functional data analysis was implemented, which converts the Raman data into functions and then applies functional dimension reduction followed by a classification method. The results showed better performance for the functional approach in comparison with the classical method

The Boston University Photonics Center annual report 2016-2017

This repository item contains an annual report that summarizes activities of the Boston University Photonics Center in the 2016-2017 academic year. The report provides quantitative and descriptive information regarding photonics programs in education, interdisciplinary research, business innovation, and technology development. The Boston University Photonics Center (BUPC) is an interdisciplinary hub for education, research, scholarship, innovation, and technology development associated with practical uses of light.This has undoubtedly been the Photonics Center’s best year since I became Director 10 years ago. In the following pages, you will see highlights of the Center’s activities in the past year, including more than 100 notable scholarly publications in the leading journals in our field, and the attraction of more than 22 million dollars in new research grants/contracts. Last year I had the honor to lead an international search for the first recipient of the Moustakas Endowed Professorship in Optics and Photonics, in collaboration with ECE Department Chair Clem Karl. This professorship honors the Center’s most impactful scholar and one of the Center’s founding visionaries, Professor Theodore Moustakas. We are delighted to haveawarded this professorship to Professor Ji-Xin Cheng, who joined our faculty this year.The past year also marked the launch of Boston University’s Neurophotonics Center, which will be allied closely with the Photonics Center. Leading that Center will be a distinguished new faculty member, Professor David Boas. David and I are together leading a new Neurophotonics NSF Research Traineeship Program that will provide $3M to promote graduate traineeships in this emerging new field. We had a busy summer hosting NSF Sites for Research Experiences for Undergraduates, Research Experiences for Teachers, and the BU Student Satellite Program. As a community, we emphasized the theme of “Optics of Cancer Imaging” at our annual symposium, hosted by Darren Roblyer. We entered a five-year second phase of NSF funding in our Industry/University Collaborative Research Center on Biophotonic Sensors and Systems, which has become the centerpiece of our translational biophotonics program. That I/UCRC continues to focus on advancing the health care and medical device industries

The Boston University Photonics Center annual report 2014-2015

This repository item contains an annual report that summarizes activities of the Boston University Photonics Center in the 2014-2015 academic year. The report provides quantitative and descriptive information regarding photonics programs in education, interdisciplinary research, business innovation, and technology development. The Boston University Photonics Center (BUPC) is an interdisciplinary hub for education, research, scholarship, innovation, and technology development associated with practical uses of light.This has been a good year for the Photonics Center. In the following pages, you will see that the center’s faculty received prodigious honors and awards, generated more than 100 notable scholarly publications in the leading journals in our field, and attracted $18.6M in new research grants/contracts. Faculty and staff also expanded their efforts in education and training, and were awarded two new National Science Foundation– sponsored sites for Research Experiences for Undergraduates and for Teachers. As a community, we hosted a compelling series of distinguished invited speakers, and emphasized the theme of Advanced Materials by Design for the 21st Century at our annual symposium. We continued to support the National Photonics Initiative, and are a part of a New York–based consortium that won the competition for a new photonics- themed node in the National Network of Manufacturing Institutes. Highlights of our research achievements for the year include an ambitious new DoD-sponsored grant for Multi-Scale Multi-Disciplinary Modeling of Electronic Materials led by Professor Enrico Bellotti, continued support of our NIH-sponsored Center for Innovation in Point of Care Technologies for the Future of Cancer Care led by Professor Catherine Klapperich, a new award for Personalized Chemotherapy Through Rapid Monitoring with Wearable Optics led by Assistant Professor Darren Roblyer, and a new award from DARPA to conduct research on Calligraphy to Build Tunable Optical Metamaterials led by Professor Dave Bishop. We were also honored to receive an award from the Massachusetts Life Sciences Center to develop a biophotonics laboratory in our Business Innovation Center

The Boston University Photonics Center annual report 2014-2015

This repository item contains an annual report that summarizes activities of the Boston University Photonics Center in the 2014-2015 academic year. The report provides quantitative and descriptive information regarding photonics programs in education, interdisciplinary research, business innovation, and technology development. The Boston University Photonics Center (BUPC) is an interdisciplinary hub for education, research, scholarship, innovation, and technology development associated with practical uses of light.This has been a good year for the Photonics Center. In the following pages, you will see that the center’s faculty received prodigious honors and awards, generated more than 100 notable scholarly publications in the leading journals in our field, and attracted $18.6M in new research grants/contracts. Faculty and staff also expanded their efforts in education and training, and were awarded two new National Science Foundation– sponsored sites for Research Experiences for Undergraduates and for Teachers. As a community, we hosted a compelling series of distinguished invited speakers, and emphasized the theme of Advanced Materials by Design for the 21st Century at our annual symposium. We continued to support the National Photonics Initiative, and are a part of a New York–based consortium that won the competition for a new photonics- themed node in the National Network of Manufacturing Institutes. Highlights of our research achievements for the year include an ambitious new DoD-sponsored grant for Multi-Scale Multi-Disciplinary Modeling of Electronic Materials led by Professor Enrico Bellotti, continued support of our NIH-sponsored Center for Innovation in Point of Care Technologies for the Future of Cancer Care led by Professor Catherine Klapperich, a new award for Personalized Chemotherapy Through Rapid Monitoring with Wearable Optics led by Assistant Professor Darren Roblyer, and a new award from DARPA to conduct research on Calligraphy to Build Tunable Optical Metamaterials led by Professor Dave Bishop. We were also honored to receive an award from the Massachusetts Life Sciences Center to develop a biophotonics laboratory in our Business Innovation Center

Looking for a perfect match: multimodal combinations of Raman spectroscopy for biomedical applications

Raman spectroscopy has shown very promising results in medical diagnostics by providing label-free and highly specific molecular information of pathological tissue ex vivo and in vivo. Nevertheless, the high specificity of Raman spectroscopy comes at a price, i.e., low acquisition rate, no direct access to depth information, and limited sampling areas. However, a similar case regarding advantages and disadvantages can also be made for other highly regarded optical modalities, such as optical coherence tomography, autofluorescence imaging and fluorescence spectroscopy, fluorescence lifetime microscopy, second-harmonic generation, and others. While in these modalities the acquisition speed is significantly higher, they have no or only limited molecular specificity and are only sensitive to a small group of molecules. It can be safely stated that a single modality provides only a limited view on a specific aspect of a biological specimen and cannot assess the entire complexity of a sample. To solve this issue, multimodal optical systems, which combine different optical modalities tailored to a particular need, become more and more common in translational research and will be indispensable diagnostic tools in clinical pathology in the near future. These systems can assess different and partially complementary aspects of a sample and provide a distinct set of independent biomarkers. Here, we want to give an overview on the development of multimodal systems that use RS in combination with other optical modalities to improve the diagnostic performance

Application of Unsupervised Multivariate Analysis Methods to Raman Spectroscopic Assessment of Human Dental Enamel

Funding Information: Acknowledgments: This work has been financially supported by Fundação para a Ciência e a Tecnolo-gia through the LIBPhys funding UID/FIS/ 04559/2021 and I. Otel PhD grant PD/BDE/143107/2018. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.This work explores the suitability of data treatment methodologies for Raman spectra of teeth using multivariate analysis methods. Raman spectra were measured in our laboratory and obtained from control enamel samples and samples with a protective treatment before and after an erosive attack. Three different approaches for data treatment were undertaken in order to evaluate the aptitude of distinguishing between groups: A—Principal Component Analysis of the numerical parameters derived from deconvoluted spectra; B—PCA of average Raman spectra after baseline correction; and C—PCA of average raw Raman spectra. Additionally, Hierarchical Cluster Analysis were applied to Raman spectra of enamel measured with different laser wavelengths (638 nm or 785 nm) to evaluate the most suitable choice of illumination. According to the different approaches, PC1 scores obtained between control and treatment group were A—50.5%, B—97.1% and C—83.0% before the erosive attack and A—55.2%, B—93.2% and C—87.8% after an erosive attack. The obtained results showed that performing PCA analysis of raw or baseline corrected Raman spectra of enamel was not as efficient in the evaluation of samples with different treatments. Moreover, acquiring Raman spectra with a 785 nm laser increases precision in the data treatment methodologies.publishersversionpublishe

Histopathological image analysis : a review

Over the past decade, dramatic increases in computational power and improvement in image analysis algorithms have allowed the development of powerful computer-assisted analytical approaches to radiological data. With the recent advent of whole slide digital scanners, tissue histopathology slides can now be digitized and stored in digital image form. Consequently, digitized tissue histopathology has now become amenable to the application of computerized image analysis and machine learning techniques. Analogous to the role of computer-assisted diagnosis (CAD) algorithms in medical imaging to complement the opinion of a radiologist, CAD algorithms have begun to be developed for disease detection, diagnosis, and prognosis prediction to complement the opinion of the pathologist. In this paper, we review the recent state of the art CAD technology for digitized histopathology. This paper also briefly describes the development and application of novel image analysis technology for a few specific histopathology related problems being pursued in the United States and Europe