Jonne J. Goedhart, Thijs P. Kuipers, Vassilis M. Papadakis
Raman hyperspectral imaging (RHSI) is a valuable tool for gaining crucial information about the chemical composition of materials. However, obtaining clear Raman signals is not always a trivial task. Raw Raman signals can be susceptible to photoluminescence interference and noise. Hence, the preprocessing of RHSI is a required step for an effective and reliable chemical analysis. The main challenge is splitting the measured RHSI into separate Raman photoluminescence signals. Since no golden-standard exists, it is non-trivial to validate the correctness of the separated signals. While current state-of-the-art preprocessing methods are effective, they require expert knowledge and involve unintuitive hyperparameters. Current approaches also lack generalizability, requiring extensive hyperparameter tuning on a case-by-case basis, while even then results are not always as expected. To this end, this work proposes a novel iterative RHSI preprocessing pipeline for splitting raw Raman signals and noise removal based on linear spline and radial basis function regression (IlsaRBF). The proposed method involves hyperparameters based on the physical properties of Raman spectroscopy, making them intuitive to use. This leads to more robust and stable hyperparameters, reducing the necessity for extensive hyperparameter tuning. A thorough evaluation shows that the proposed method outperforms the current state-of-the-art. Additionally, a cosmic ray identification and removal algorithm (CRIR) and dynamic PCA for noise reduction are introduced. A standalone tool containing our proposed methods is provided, making RHSI preprocessing available to a broader audience, aiding further research and advancements in the field of Raman spectroscopy.
{"title":"Raman and photoluminescence signal separation in Raman hyperspectral imagery including noise reduction","authors":"Jonne J. Goedhart, Thijs P. Kuipers, Vassilis M. Papadakis","doi":"10.1002/jrs.6651","DOIUrl":"10.1002/jrs.6651","url":null,"abstract":"<p>Raman hyperspectral imaging (RHSI) is a valuable tool for gaining crucial information about the chemical composition of materials. However, obtaining clear Raman signals is not always a trivial task. Raw Raman signals can be susceptible to photoluminescence interference and noise. Hence, the preprocessing of RHSI is a required step for an effective and reliable chemical analysis. The main challenge is splitting the measured RHSI into separate Raman photoluminescence signals. Since no <i>golden-standard</i> exists, it is non-trivial to validate the correctness of the separated signals. While current state-of-the-art preprocessing methods are effective, they require expert knowledge and involve unintuitive hyperparameters. Current approaches also lack generalizability, requiring extensive hyperparameter tuning on a case-by-case basis, while even then results are not always as expected. To this end, this work proposes a novel iterative RHSI preprocessing pipeline for splitting raw Raman signals and noise removal based on linear spline and radial basis function regression (IlsaRBF). The proposed method involves hyperparameters based on the physical properties of Raman spectroscopy, making them intuitive to use. This leads to more robust and stable hyperparameters, reducing the necessity for extensive hyperparameter tuning. A thorough evaluation shows that the proposed method outperforms the current state-of-the-art. Additionally, a cosmic ray identification and removal algorithm (CRIR) and dynamic PCA for noise reduction are introduced. A standalone tool containing our proposed methods is provided, making RHSI preprocessing available to a broader audience, aiding further research and advancements in the field of Raman spectroscopy.</p>","PeriodicalId":16926,"journal":{"name":"Journal of Raman Spectroscopy","volume":"55 5","pages":"598-614"},"PeriodicalIF":2.5,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jrs.6651","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139559645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nikita V. Chukanov, Ramiza K. Rastsvetaeva, Natalia V. Zubkova, Marina F. Vigasina, Igor V. Pekov, Andrey A. Zolotarev, Julia A. Mikhailova, Sergey M. Aksenov
Microporous materials containing hydrated silanol groups Si–OH as well as hydrated proton complexes, H2n+1On+, including hydronium (n = 1), Zundel (n = 2), and Eigen (n = 4) cations, are of practical importance as potential ion exchangers and ion conductors. In this paper, we provide data on crystal-chemical features, hydrogen bonding and Raman spectra of alkaline microporous titano-, niobo-, zircono-, and aluminosilicate minerals belonging to the labuntsovite, lovozerite, eudialyte, and sodalite groups in which a part of sodium was substituted by hydrated proton complexes under low-temperature hydrothermal or supergene conditions. Most minerals studied in this work do not have synthetic analogues and are considered as possible natural prototypes of microporous materials with technologically important properties. The obtained experimental data and their comparison with the results of ab initio theoretical calculations published elsewhere show that Raman spectroscopy is an effective tool for the precise identification of hydrated proton complexes with extremely strong hydrogen bonds and estimation of corresponding O···O distances in the range of 2.37–2.68 Å. The presence of hydrated proton complexes in microporous silicates is a clear and sensitive geological indicator showing that a rock underwent the low-temperature alteration.
含有水合硅醇基团 Si-OH 以及水合质子络合物 H2n+1On+(包括氢鎓阳离子(n = 1)、尊德尔阳离子(n = 2)和艾根阳离子(n = 4))的微孔材料作为潜在的离子交换剂和离子导体具有重要的实用价值。本文提供了碱性微孔钛、铌、锆和铝硅酸盐矿物的晶体化学特征、氢键和拉曼光谱数据,这些矿物属于拉邦特索维石、洛泽斯特、乌迪尔特和钠长石组,其中的部分钠在低温热液或超成岩条件下被水合质子络合物取代。这项工作中研究的大多数矿物都没有人工合成的类似物,因此被认为是具有重要技术特性的微孔材料的可能天然原型。获得的实验数据及其与其他地方发表的 ab initio 理论计算结果的比较表明,拉曼光谱是一种有效的工具,可以精确识别氢键极强的水合质子络合物,并估算出 2.37-2.68 Å 范围内相应的 O-O 距离。微孔硅酸盐中水合质子复合物的存在是一个明确而敏感的地质指标,表明岩石经历了低温蚀变。
{"title":"Spectroscopic characterization of extra-framework hydrated proton complexes with the extremely strong hydrogen bonds in microporous silicate minerals","authors":"Nikita V. Chukanov, Ramiza K. Rastsvetaeva, Natalia V. Zubkova, Marina F. Vigasina, Igor V. Pekov, Andrey A. Zolotarev, Julia A. Mikhailova, Sergey M. Aksenov","doi":"10.1002/jrs.6656","DOIUrl":"10.1002/jrs.6656","url":null,"abstract":"<p>Microporous materials containing hydrated silanol groups Si–OH as well as hydrated proton complexes, H<sub>2<i>n</i>+1</sub>O<sub><i>n</i></sub><sup>+</sup>, including hydronium (<i>n</i> = 1), Zundel (<i>n</i> = 2), and Eigen (<i>n</i> = 4) cations, are of practical importance as potential ion exchangers and ion conductors. In this paper, we provide data on crystal-chemical features, hydrogen bonding and Raman spectra of alkaline microporous titano-, niobo-, zircono-, and aluminosilicate minerals belonging to the labuntsovite, lovozerite, eudialyte, and sodalite groups in which a part of sodium was substituted by hydrated proton complexes under low-temperature hydrothermal or supergene conditions. Most minerals studied in this work do not have synthetic analogues and are considered as possible natural prototypes of microporous materials with technologically important properties. The obtained experimental data and their comparison with the results of ab initio theoretical calculations published elsewhere show that Raman spectroscopy is an effective tool for the precise identification of hydrated proton complexes with extremely strong hydrogen bonds and estimation of corresponding O···O distances in the range of 2.37–2.68 Å. The presence of hydrated proton complexes in microporous silicates is a clear and sensitive geological indicator showing that a rock underwent the low-temperature alteration.</p>","PeriodicalId":16926,"journal":{"name":"Journal of Raman Spectroscopy","volume":"55 5","pages":"581-597"},"PeriodicalIF":2.5,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139559622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alexander Czaja, Samer Awad, Olga E. Eremina, Augusta Fernando, Cristina Zavaleta
Surface-enhanced Raman scattering nanoparticles (SERS NPs) offer powerful optical contrast features for imaging assays. Their gold core enhances the inelastic scattering cross section, allowing highly sensitive and rapid detection, and their characteristic sets of narrow spectral bands give them unsurpassed multiplexing capabilities. Multiplexed hyperspectral images are commonly unmixed using a compensation matrix of reference spectra to produce quantitative image channels illustrating the distribution of each material. It is these unmixed channels that are fit for interpretation from assays utilizing SERS NP contrast agents. Some factors that may impact SERS NP quantitative and dynamic range capabilities may include endogenous background heterogeneity, the ability of unmixing algorithms to account for signal variances, and linear system conditioning imposed by contrast agent signals. We report on hyperspectral Raman imaging of mixtures of SERS NPs from an expanded library of contrast agents. We study increasing plexity and varying degrees of system conditioning as inputs to a diverse set of classical, non-negatively constrained, and regularized regression algorithms to investigate which signal features and unmixing methods deliver the most promising quantitation performance with the least error. Raman imaging of SERS NP mixtures is performed on controlled substrates and representative biological specimens, and experimental results are compared against ground truth data. We evaluate spectral fitting fidelity, quantitation, and specificity correlations with system conditioning. Spectral unmixing with a regularized hybrid of least squares regression with principal component analysis (HLP) algorithm approximated spectra with 3.5× better fitting fidelity and 3× better quantitation robustness with tissue background compared with simpler unmixing routines.
{"title":"Assessment of unmixing approaches for the quantitation of SERS nanoparticles in highly multiplexed spectral images","authors":"Alexander Czaja, Samer Awad, Olga E. Eremina, Augusta Fernando, Cristina Zavaleta","doi":"10.1002/jrs.6653","DOIUrl":"10.1002/jrs.6653","url":null,"abstract":"<p>Surface-enhanced Raman scattering nanoparticles (SERS NPs) offer powerful optical contrast features for imaging assays. Their gold core enhances the inelastic scattering cross section, allowing highly sensitive and rapid detection, and their characteristic sets of narrow spectral bands give them unsurpassed multiplexing capabilities. Multiplexed hyperspectral images are commonly unmixed using a compensation matrix of reference spectra to produce quantitative image channels illustrating the distribution of each material. It is these unmixed channels that are fit for interpretation from assays utilizing SERS NP contrast agents. Some factors that may impact SERS NP quantitative and dynamic range capabilities may include endogenous background heterogeneity, the ability of unmixing algorithms to account for signal variances, and linear system conditioning imposed by contrast agent signals. We report on hyperspectral Raman imaging of mixtures of SERS NPs from an expanded library of contrast agents. We study increasing plexity and varying degrees of system conditioning as inputs to a diverse set of classical, non-negatively constrained, and regularized regression algorithms to investigate which signal features and unmixing methods deliver the most promising quantitation performance with the least error. Raman imaging of SERS NP mixtures is performed on controlled substrates and representative biological specimens, and experimental results are compared against ground truth data. We evaluate spectral fitting fidelity, quantitation, and specificity correlations with system conditioning. Spectral unmixing with a regularized hybrid of least squares regression with principal component analysis (HLP) algorithm approximated spectra with 3.5× better fitting fidelity and 3× better quantitation robustness with tissue background compared with simpler unmixing routines.</p>","PeriodicalId":16926,"journal":{"name":"Journal of Raman Spectroscopy","volume":"55 5","pages":"566-580"},"PeriodicalIF":2.5,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139559643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Helicobacter pylori and Epstein–Barr Virus (EBV) are Group 1 carcinogens that can enhance gastric cancer progression. Bioactive substances extracted from plants can be effective therapeutic agents in cancer treatment. For example, Withania somnifera extract-WSE reduces the Gankyrin oncoprotein, which is upregulated in the presence of H. pylori and EBV. The various biochemical and metabolic changes upon 24 hrs post-infection followed by W. somnifera extract (WSE) treatment on gastric epithelial cells (AGS) can be studied using spectroscopic techniques. In the biomedical sciences, Raman and NMR spectroscopy have been extensively employed to interpret cellular alterations contributing to the onset of infection and the severity of gastric cancer. More specifically, alterations in cellular biochemical homeostasis are linked to the moieties of cholesterol, collagen, choline, carbohydrate, lipids, tyrosine, and phenylalanine. Further, we have found significantly elevated FWHM for carbohydrates, tumor associated protein, collagen, cholesterol, and cholesterol ester in the co-infection model. We also looked into the potential correlation between these molecules using molecular network analysis and found several related factors that can be modulated through biomolecular levels. These molecules are crucial in several physiological functions, including cell division, cell proliferation, apoptosis, necrosis, cell migration, and lipid transport. Our study paves the pathway to study H. pylori and EBV co-infection in human gastric epithelial cells and the therapeutic interventions of WSE in this scenario and highlights specific biomolecular alterations, which can be focused for further mechanistic investigations.
{"title":"Spectroscopic assessment of biomolecular changes in Helicobacter pylori and Epstein–Barr virus co-infected gastric epithelial cells","authors":"Dharmendra Kashyap, Manushree Tanwar, Chanchal Rani, Pranit Hemant Bagde, Siddharth Singh, Nidhi Varshney, Vaishali Saini, Amit Mishra, Rajesh Kumar, Hem Chandra Jha","doi":"10.1002/jrs.6652","DOIUrl":"10.1002/jrs.6652","url":null,"abstract":"<p><i>Helicobacter pylori</i> and Epstein–Barr Virus (EBV) are Group 1 carcinogens that can enhance gastric cancer progression. Bioactive substances extracted from plants can be effective therapeutic agents in cancer treatment. For example, <i>Withania somnifera</i> extract-WSE reduces the Gankyrin oncoprotein, which is upregulated in the presence of <i>H. pylori</i> and EBV. The various biochemical and metabolic changes upon 24 hrs post-infection followed by <i>W. somnifera</i> extract (WSE) treatment on gastric epithelial cells (AGS) can be studied using spectroscopic techniques. In the biomedical sciences, Raman and NMR spectroscopy have been extensively employed to interpret cellular alterations contributing to the onset of infection and the severity of gastric cancer. More specifically, alterations in cellular biochemical homeostasis are linked to the moieties of cholesterol, collagen, choline, carbohydrate, lipids, tyrosine, and phenylalanine. Further, we have found significantly elevated FWHM for carbohydrates, tumor associated protein, collagen, cholesterol, and cholesterol ester in the co-infection model. We also looked into the potential correlation between these molecules using molecular network analysis and found several related factors that can be modulated through biomolecular levels. These molecules are crucial in several physiological functions, including cell division, cell proliferation, apoptosis, necrosis, cell migration, and lipid transport. Our study paves the pathway to study <i>H. pylori</i> and EBV co-infection in human gastric epithelial cells and the therapeutic interventions of WSE in this scenario and highlights specific biomolecular alterations, which can be focused for further mechanistic investigations.</p>","PeriodicalId":16926,"journal":{"name":"Journal of Raman Spectroscopy","volume":"55 5","pages":"549-565"},"PeriodicalIF":2.5,"publicationDate":"2024-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139516046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Monika Halat, Katarzyna Pajor, Rafal Baranski, Malgorzata Baranska
Although the potential of Raman Optical Activity (ROA) spectroscopy in the field of organic and inorganic materials research has been well demonstrated, its practical application is still limited. This work shows historical background, current state of the art and challenges of ROA spectroscopy facing scientists today. Expectations and development prospects for the coming years are also discussed. Efforts have already been made to improve but also to properly interpret the ROA signal when the ROA technique is combined with other spectroscopies (i.e., ROA/Electronic Circular Dichroism and ROA/Circularly Polarized Luminescence). The paper shows how to intensify the ROA effect to shorten the spectrum accumulation time, control possible artefacts and support the analysis of ROA spectra with actual and new theoretical approaches. However, the challenge is to increase the interest in this technique among the academic community, develop reliable protocols and adapt them for practical use. National and international research networks can significantly contribute to the growth of methodologies and standardization in areas in which the ROA has so far been little used. This paper presents a perspective vision for the future progress of ROA alongside other chiroptical methods.
{"title":"(Resonance) Raman optical activity among chiroptical spectroscopies: Quo vadis?","authors":"Monika Halat, Katarzyna Pajor, Rafal Baranski, Malgorzata Baranska","doi":"10.1002/jrs.6650","DOIUrl":"10.1002/jrs.6650","url":null,"abstract":"<p>Although the potential of Raman Optical Activity (ROA) spectroscopy in the field of organic and inorganic materials research has been well demonstrated, its practical application is still limited. This work shows historical background, current state of the art and challenges of ROA spectroscopy facing scientists today. Expectations and development prospects for the coming years are also discussed. Efforts have already been made to improve but also to properly interpret the ROA signal when the ROA technique is combined with other spectroscopies (i.e., ROA/Electronic Circular Dichroism and ROA/Circularly Polarized Luminescence). The paper shows how to intensify the ROA effect to shorten the spectrum accumulation time, control possible artefacts and support the analysis of ROA spectra with actual and new theoretical approaches. However, the challenge is to increase the interest in this technique among the academic community, develop reliable protocols and adapt them for practical use. National and international research networks can significantly contribute to the growth of methodologies and standardization in areas in which the ROA has so far been little used. This paper presents a perspective vision for the future progress of ROA alongside other chiroptical methods.</p>","PeriodicalId":16926,"journal":{"name":"Journal of Raman Spectroscopy","volume":"55 5","pages":"539-548"},"PeriodicalIF":2.5,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139496127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Petr Shvets, Alexander Krylov, Ksenia Maksimova, Goikhman
We summarize the current knowledge on crystal structures, synthesis, applications, and Raman spectroscopy of Wadsley phases of vanadium oxide, including VO2 (B), V6O13, V4O9, V3O7, and V2O5. While these oxides have garnered significant attention for potential energy storage applications and have been studied for decades, there remains inconsistency in data regarding their characteristic Raman spectra. To address this, we synthesized a series of Wadsley phases by physical vapor deposition of amorphous vanadium oxide films and subsequent annealing in a controlled environment. X-ray diffraction studies confirmed the formation of VO2 (B), V6O13, V4O9, and V3O7. We meticulously measured the room-temperature Raman spectra of these phases, offering robust reference data for the easy identification of vanadium oxides in unknown samples. Finally, we studied low-temperature phase transitions in VO2 (B) and V6O13.
{"title":"Raman spectroscopy of Wadsley phases of vanadium oxide","authors":"Petr Shvets, Alexander Krylov, Ksenia Maksimova, Goikhman","doi":"10.1002/jrs.6644","DOIUrl":"10.1002/jrs.6644","url":null,"abstract":"<p>We summarize the current knowledge on crystal structures, synthesis, applications, and Raman spectroscopy of Wadsley phases of vanadium oxide, including VO<sub>2</sub> (B), V<sub>6</sub>O<sub>13</sub>, V<sub>4</sub>O<sub>9</sub>, V<sub>3</sub>O<sub>7</sub>, and V<sub>2</sub>O<sub>5</sub>. While these oxides have garnered significant attention for potential energy storage applications and have been studied for decades, there remains inconsistency in data regarding their characteristic Raman spectra. To address this, we synthesized a series of Wadsley phases by physical vapor deposition of amorphous vanadium oxide films and subsequent annealing in a controlled environment. X-ray diffraction studies confirmed the formation of VO<sub>2</sub> (B), V<sub>6</sub>O<sub>13</sub>, V<sub>4</sub>O<sub>9</sub>, and V<sub>3</sub>O<sub>7</sub>. We meticulously measured the room-temperature Raman spectra of these phases, offering robust reference data for the easy identification of vanadium oxides in unknown samples. Finally, we studied low-temperature phase transitions in VO<sub>2</sub> (B) and V<sub>6</sub>O<sub>13</sub>.</p>","PeriodicalId":16926,"journal":{"name":"Journal of Raman Spectroscopy","volume":"55 4","pages":"445-458"},"PeriodicalIF":2.5,"publicationDate":"2024-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139475798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rasmus Öberg, Lars Landström, Eduardo Gracia-Espino, Andreas Larsson, Magnus Andersson, Per Ola Andersson
Fentanyls are synthetic opioids up to 10,000 times more potent than morphine. Although initially developed for medical applications, fentanyl and its analogues have recently grown synonymous with the ongoing opioid epidemic. To combat the continued spread of these substances, there is a need for rapid and sensitive techniques for chemical detection. Surface-enhanced Raman spectroscopy (SERS) has the potential for trace detection of harmful chemical substances. However, vibrational spectra obtained by SERS often differ between SERS substrates, as well as compared with spectra from normal Raman (NR) spectroscopy. Herein, SERS and NR responses from two fentanyl analogues, carfentanil (CF) and thiofentanil (TF), were measured and analysed with support from density functional theory (DFT) modelling. Using commercially available silver nanopillar SERS substrates, the SERS signatures of samples diluted in acetonitrile between 0.01 and 1000 µg/mL were studied. Relative SERS peak intensities measured in the range of 220–1800 cm−1 vary with concentration, while SERS and NR spectra largely agree for CF at higher concentrations (