Browse
Submit Data
Databases
API
Help

Dataset Information

32 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dynamic Sparse Sampling for Confocal Raman Microscopy.

ABSTRACT: The total number of data points required for image generation in Raman microscopy was greatly reduced using sparse sampling strategies, in which the preceding set of measurements informed the next most information-rich sampling location. Using this approach, chemical images of pharmaceutical materials were obtained with >99% accuracy from 15.8% sampling, representing an ?6-fold reduction in measurement time relative to full field of view rastering with comparable image quality. This supervised learning approach to dynamic sampling (SLADS) has the distinct advantage of being directly compatible with standard confocal Raman instrumentation. Furthermore, SLADS is not limited to Raman imaging, potentially providing time-savings in image reconstruction whenever the single-pixel measurement time is the limiting factor in image generation.

SUBMITTER: Zhang S

PROVIDER: S-EPMC6025898 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Dynamic Sparse Sampling for Confocal Raman Microscopy.

Zhang Shijie S Song Zhengtian Z Godaliyadda G M Dilshan P GMDP Ye Dong Hye DH Chowdhury Azhad U AU Sengupta Atanu A Buzzard Gregery T GT Bouman Charles A CA Simpson Garth J GJ

Analytical chemistry 20180320 7

The total number of data points required for image generation in Raman microscopy was greatly reduced using sparse sampling strategies, in which the preceding set of measurements informed the next most information-rich sampling location. Using this approach, chemical images of pharmaceutical materials were obtained with >99% accuracy from 15.8% sampling, representing an ∼6-fold reduction in measurement time relative to full field of view rastering with comparable image quality. This supervised l ...[more]

PMID: 29521493

Similar Datasets

Confocal Raman microscopy to identify bacteria in oral subgingival biofilm models.

Project description:The study of oral disease progression, in relation to the accumulation of subgingival biofilm in gingivitis and periodontitis is limited, due to either the ability to monitor plaque in vitro. When compared, optical spectroscopic techniques offer advantages over traditional destructive or biofilm staining approaches, making it a suitable alternative for the analysis and continued development of three-dimensional structures. In this work, we have developed a confocal Raman spectroscopy analysis approach towards in vitro subgingival plaque models. The main objective of this study was to develop a method for differentiating multiple oral subgingival bacterial species in planktonic and biofilm conditions, using confocal Raman microscopy. Five common subgingival bacteria (Fusobacterium nucleatum, Streptococcus mutans, Veillonella dispar, Actinomyces naeslundii and Prevotella nigrescens) were used and differentiated using a 2-way orthogonal Partial Least Square with Discriminant Analysis (O2PLS-DA) for the collected spectral data. In addition to planktonic growth, mono-species biofilms cultured using the 'Zürich Model' were also analyzed. The developed method was successfully used to predict planktonic and mono-species biofilm species in a cross validation setup. The results show differences in the presence and absence of chemical bands within the Raman spectra. The O2PLS-DA model was able to successfully predict 100% of all tested planktonic samples and 90% of all mono-species biofilm samples. Using this approach we have shown that Confocal Raman microscopy can analyse and predict the identity of planktonic and mono-species biofilm species, thus enabling its potential as a technique to map oral multi-species biofilm models.

| S-EPMC7213720 | biostudies-literature

Label-Free, Noninvasive Bone Cell Classification by Hyperspectral Confocal Raman Microscopy.

Project description:Characterizing and identifying cells in multicellular in vitro models remain a substantial challenge. Here, we utilize hyperspectral confocal Raman microscopy and principal component analysis coupled with linear discriminant analysis to form a label-free, noninvasive approach for classifying bone cells and osteosarcoma cells. Through the development of a library of hyperspectral Raman images of the K7M2-wt osteosarcoma cell lines, 7F2 osteoblast cell lines, RAW 264.7 macrophage cell line, and osteoclasts induced from RAW 264.7 macrophages, we built a linear discriminant model capable of correctly identifying each of these cell types. The model was cross-validated using a k-fold cross validation scheme. The results show a minimum of 72% accuracy in predicting cell type. We also utilize the model to reconstruct the spectra of K7M2 and 7F2 to determine whether osteosarcoma cancer cells and normal osteoblasts have any prominent differences that can be captured by Raman. We find that the main differences between these two cell types are the prominence of the β-sheet protein secondary structure in K7M2 versus the α-helix protein secondary structure in 7F2. Additionally, differences in the CH2 deformation Raman feature highlight that the membrane lipid structure is different between these cells, which may affect the overall signaling and functional contrasts. Overall, we show that hyperspectral confocal Raman microscopy can serve as an effective tool for label-free, nondestructive cellular classification and that the spectral reconstructions can be used to gain deeper insight into the differences that drive different functional outcomes of different cells.

| S-EPMC10900511 | biostudies-literature

Bulk and Surface-Stabilized Structures of Paracetamol Revisited by Raman Confocal Microscopy.

Project description:We revisit the polymorphism of paracetamol by means of a micro-Raman technique, which has proved to be a powerful tool for structure recognition. Distinct lattice phonon spectra clearly identified the pure phases. Confocality enabled us to detect phase mixing between form II and either I or III on a micrometric scale in the same crystallite. Following the most recent findings on surface-mediated structures, we also investigated spin-coated films grown on glass, gold, and polystyrene substrates, confirming the selectivity of these surfaces for the metastable form III, which shows an unprecedented stability over a time span of several months. A mechanism of its transformation to phase II, via a partially ordered intermediate state, is suggested by polarized Raman measurements.

| S-EPMC6645084 | biostudies-literature

Specific intracellular signature of SARS-CoV-2 infection using confocal Raman microscopy.

Project description:SARS-CoV-2 infection remains spread worldwide and requires a better understanding of virus-host interactions. Here, we analyzed biochemical modifications due to SARS-CoV-2 infection in cells by confocal Raman microscopy. Obtained results were compared with the infection with another RNA virus, the measles virus. Our results have demonstrated a virus-specific Raman molecular signature, reflecting intracellular modification during each infection. Advanced data analysis has been used to distinguish non-infected versus infected cells for two RNA viruses. Further, classification between non-infected and SARS-CoV-2 and measles virus-infected cells yielded an accuracy of 98.9 and 97.2 respectively, with a significant increase of the essential amino-acid tryptophan in SARS-CoV-2-infected cells. These results present proof of concept for the application of Raman spectroscopy to study virus-host interaction and to identify factors that contribute to the efficient SARS-CoV-2 infection and may thus provide novel insights on viral pathogenesis, targets of therapeutic intervention and development of new COVID-19 biomarkers.

| S-EPMC9311350 | biostudies-literature

Gene expession profle of melanoma subtypes selected by reflectance confocal microscopy

Project description:Melanoma is the deadliest type of skin cancer, characterized by high cellular heterogeneity which contributes to therapy resistance and unpredictable disease outcome. Recently, by correlating Reflectance-Confocal-Microscopy (RCM) morphology with histopathological type, we identified four distinct melanoma-subtypes: dendritic-cell (DC), round-cell (RC), dermal-nest (DN), and combined-type (CT) melanomas. Our results demontsrate that each melanoma subtypes has a distinct biological and gene expression profile, related to tumor aggressiveness, confirming that RCM can be a dependable tool for in vivo detecting different types of melanoma and for early diagnostic screening

2021-11-26 | GSE174395 | GEO

Microstructural Analysis of Whey/Soy Protein Isolate Mixed Gels Using Confocal Raman Microscopy.

Project description:This work explores the potential of confocal Raman microscopy to investigate the microstructure of mixed protein gel systems. Heat-set protein gels were prepared using whey protein isolate (WPI), soy protein isolate (SPI), and mixtures thereof, with a total of five different whey-to-soy protein ratios (100, 75, 50, 25, and 0%). These were analysed using confocal Raman microscopy, and different data analysis approaches were used to maximize the amount of structural and compositional information extracted from the spectral datasets generated, including both univariate and multivariate analysis methods. Small spectral differences were found between pure WPI and SPI gels, mainly attributed to conformational differences (amide bands), but SPI exhibited considerably greater auto-fluorescence than WPI. The univariate analysis method allowed for a rapid microstructural analysis, successfully mapping the distribution of protein and water in the gels. The greater fluorescence of the capsule-like structures found in the mixed gels, compared to other regions rich in proteins, suggested that these may be enriched in soy proteins. Further analysis, using a multivariate approach, allowed us to distinguish proteins with different levels of hydration within the gels and to detect non-proteinaceous compounds. Raman microscopy proved to be particularly useful to detect the presence of residual lipids in protein gels.

| S-EPMC8467414 | biostudies-literature

Imaging lutein and zeaxanthin in the human retina with confocal resonance Raman microscopy.

Project description:Lutein and zeaxanthin are xanthophyll carotenoids that are highly concentrated in the human macula, where they protect the eye from oxidative damage and improve visual performance. Distinguishing lutein from zeaxanthin in images of the human retina in vivo or in donor eye tissues has been challenging because no available technology has been able to reliably differentiate between these two carotenoids, which differ only in the position of one C = C bond. Here, we report the differential distributions of lutein and zeaxanthin in human donor retinas mapped with confocal resonance Raman microscopy. Zeaxanthin is highly concentrated in the fovea, extending from the inner to the outer limiting membranes, with especially high concentrations in the outer plexiform layer, while lutein is much more diffuse at relatively lower concentration. Our results imply that zeaxanthin may play a more important role than lutein in human macular health and disease.

| S-EPMC7275724 | biostudies-literature

Low-energy electron microscopy intensity-voltage data - Factorization, sparse sampling and classification.

Project description:Low-energy electron microscopy (LEEM) taken as intensity-voltage (I-V) curves provides hyperspectral images of surfaces, which can be used to identify the surface type, but are difficult to analyse. Here, we demonstrate the use of an algorithm for factorizing the data into spectra and concentrations of characteristic components (FSC3 ) for identifying distinct physical surface phases. Importantly, FSC3 is an unsupervised and fast algorithm. As example data we use experiments on the growth of praseodymium oxide or ruthenium oxide on ruthenium single crystal substrates, both featuring a complex distribution of coexisting surface components, varying in both chemical composition and crystallographic structure. With the factorization result a sparse sampling method is demonstrated, reducing the measurement time by 1-2 orders of magnitude, relevant for dynamic surface studies. The FSC3 concentrations are providing the features for a support vector machine-based supervised classification of the surface types. Here, specific surface regions which have been identified structurally, via their diffraction pattern, as well as chemically by complementary spectro-microscopic techniques, are used as training sets. A reliable classification is demonstrated on both example LEEM I-V data sets.

| S-EPMC10108219 | biostudies-literature

Synthesis of a deuterated probe for the confocal Raman microscopy imaging of squalenoyl nanomedicines.

Project description:The synthesis of ω-di-(trideuteromethyl)-trisnorsqualenic acid has been achieved from natural squalene. The synthesis features the use of a Shapiro reaction of acetone-d 6 trisylhydrazone as a key step to implement the terminal isopropylidene-d 6 moiety. The obtained squalenic acid-d 6 has been coupled to gemcitabine to provide the deuterated analogue of squalenoyl gemcitabine, a powerful anticancer agent endowed with self-assembling properties. The Raman spectra of both deuterated and non-deuterated squalenoyl gemcitabine nanoparticles displayed significant Raman scattering signals. They revealed no differences except from the deuterium peak patterns in the silent spectral region of cells. This paves the way for label-free intracellular trafficking studies of squalenoyl nanomedicines.

| S-EPMC4979966 | biostudies-literature

Mapping Single Walled Carbon Nanotubes in Photosynthetic Algae by Single-Cell Confocal Raman Microscopy.

Project description:Carbon nanotubes (CNTs) are among the most exploited carbon allotropes in the emerging technologies of molecular sensing and bioengineering. However, the advancement of algal nanobiotechnology and nanobionics is hindered by the lack of methods for the straightforward visualization of the CNTs inside the cell. Herein, we present a handy and label-free experimental strategy based on visible Raman microscopy to assess the internalization of single-walled carbon nanotubes (SWCNTs) using the model photosynthetic alga Chlamydomonas reinhardtii as a recipient. The relationship between the properties of SWCNTs and their biological behavior was demonstrated, along with the occurrence of excitation energy transfer from the excited chlorophyll molecules to the SWCNTs. The non-radiative deactivation of the chlorophyll excitation promoted by the SWCNTs enables the recording of Raman signals originating from cellular compounds located near the nanotubes, such as carotenoids, polyphosphates, and starch. Furthermore, the outcome of this study unveils the possibility to exploit SWCNTs as spectroscopic probes in photosynthetic and non-photosynthetic systems where the fluorescence background hinders the acquisition of Raman scattering signals.

| S-EPMC7698160 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data