Infrared Orange: Connecting Hyperspectral Data with Machine Learning

Toplak, Marko; Birarda, Giovanni; Read, Stuart; Sandt, Christophe; Rosendahl, Scott M.; Vaccari, Lisa; Demšar, Janez; Borondics, Ferenc

doi:10.1080/08940886.2017.1338424

Cited by 114 publications

(82 citation statements)

References 4 publications

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“…The version number of software should be recorded. This is particularly important for regularly updated, open source computer code; for example refs [180][181][182][183][184][185]. In-house computer codes should be stored in version controlled source code repositories such as GitHub [186] or Bitbucket [187].…”

Section: Data Sharing-mentioning

confidence: 99%

Clinical applications of infrared and Raman spectroscopy: state of play and future challenges

Baker

Byrne

Chalmers³

et al. 2018

Analyst

189

134

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Vibrational spectroscopies, based on infrared absorption and/or Raman scattering provide a detailed fingerprint of a material, based on the chemical content. Diagnostic and prognostic tools based on these technologies have the potential to revolutionise our clinical systems leading to improved patient outcome, more efficient public services and significant economic savings. However, despite these strong drivers, there are many fundamental scientific and technological challenges which have limited the implementation of this technology in the clinical arena, although recent years have seen significant progress in addressing these challenges. This review examines (i) the state of the art of clinical applications of infrared absorption and Raman spectroscopy, and (ii) the outstanding challenges, and progress towards translation, highlighting specific examples in the areas of in vivo, ex vivo and in vitro applications. In addition, the requirements of instrumentation suitable for use in the clinic, strategies for pre-processing and statistical analysis in clinical spectroscopy and data sharing protocols, will be discussed. Emerging consensus recommendations are presented, and the future perspectives of the field are assessed, particularly in the context of national and international collaborative research initiatives, such as the UK EPSRC Clinical Infrared and Raman Spectroscopy Network, the EU COST Action Raman4Clinics, and the International Society for Clinical Spectroscopy.

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Section: Data Sharing-mentioning

confidence: 99%

Clinical applications of infrared and Raman spectroscopy: state of play and future challenges

Baker

Byrne

Chalmers³

et al. 2018

Analyst

189

134

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“…A data analysis pipeline including hierarchical cluster analysis (HCA) and Principal component analysis (PCA) was exploited for data interpretation. More detail on the data analysis workflow are described in SM3 (Supplementary Materials) [85][86][87]. Here we mention the most characteristic spectral bands exploited for data interpretation: C=O band of hemicellulose and pectin 1775-1700 cm −1 , Amide I of proteins 1680-1565 cm −1 , aromatic rings of lignin 1530-1495 cm −1 , COH deformations and CCO stretching at 1295-1190 cm −1 , C-O-C from polysaccharides 1190-970 cm −1 [88].…”

Section: Infrared Microspectroscopymentioning

confidence: 99%

Mineralogy and Zn Chemical Speciation in a Soil-Plant System from a Metal-Extreme Environment: A Study on Helichrysum microphyllum subsp. tyrrhenicum (Campo Pisano Mine, SW Sardinia, Italy)

et al. 2020

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Environmental contamination due to human activities is a worldwide problem that has led to the development of different remediation techniques, including biotechnological approaches such as phytoextraction and phytostabilization. These techniques take advantage of pioneer plants that naturally develop tolerance mechanisms to survive in extreme environments. A multi-technique and multi-disciplinary approach was applied for the investigation of Helichrysum microphyllum subsp. tyrrhenicum samples, bulk soil, and rhizospheres collected from a metal-extreme environment (Zn-Pb mine of Campo Pisano, SW Sardinia, Italy). Zinc, Pb, and Cd are the most abundant metals, with Zn attaining 3 w/w% in the rhizosphere solid materials, inducing oxidative stress in the roots as revealed by infrared microspectroscopy (IR). X-ray diffraction (XRD), scanning electron microscopy (SEM), and chemical analysis coupled with synchrotron radiation-based (SR) techniques demonstrate that quartz, dolomite, and weddellite biominerals precipitate in roots, stems, and leaves, likely as a response to environmental stress. In the rhizosphere, Zn chemical speciation is mainly related to the Zn ore minerals (smithsonite and hydrozincite) whereas, in plant tissues, Zn is primarily bound to organic compounds such as malate, cysteine, and histidine molecules that act as metal binders and, eventually, detoxification agents for the Zn excess. These findings suggest that H. microphyllum subsp. tyrrhenicum has developed its own adaptation strategy to survive in polluted substrates, making it a potential candidate for phytostabilization aimed at mitigating the dispersion of metals in the surrounding areas.

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“…Spectra normalization was performed using PyMca software. To identify if Mn shows the same coordination depending on different parameters [i.e., species, [Mn] in the seawater of the aquaria, and locations of interest in the sample], a statistical analysis of spectra was performed using the Orange open-source software (Demšar et al, 2013;Toplak et al, 2017). Each spectrum was labeled by the name of species (Ammonia or Bulimina), the culture media conditions (Aq100 or Aq600), and the location of the spectrum in the test structure, as determined from the µXRF maps of Ca and Mn (i.e., "high Mn calcite EXP , " "low Mn calcite PRE , " "high Mn calcite PRE , " and "internal coating").…”

Section: Micro-x-ray Fluorescence and Micro-x-ray Absorption Near-edgmentioning

confidence: 99%

Chemical Heterogeneity of Mg, Mn, Na, S, and Sr in Benthic Foraminiferal Calcite

et al. 2019

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The chemical composition of fossil foraminiferal shells (tests) is widely used as tracers for past ocean chemistry. It is, therefore, important to understand how different (trace) elements are transported and incorporated into these tests from adjacent seawater. The elemental distribution within the walls of foraminiferal tests might be used to differentiate between proposed transport mechanisms. Here, the microdistribution of Mg, Mn, Na, S, and Sr in tests of three species of foraminifera, known to have contrasting test chemistry, is investigated by a combination of electron probe microanalysis (EPMA) and nanoscale secondary ion mass spectrometry (nanoSIMS), micro-X-ray fluorescence (µXRF), and micro-X-ray absorption near-edge structure (µXANES) analyses. The three investigated species are the symbiont-barren Ammonia sp. T6 and Bulimina marginata, which precipitate a low-Mg calcite test, and the symbiont-bearing species Amphistegina lessonii, which produces a test with intermediate Mg content. Because all analyzed tests were formed under controlled and identical laboratory conditions, the observed distributions of elements are not due to environmental variability but are a direct consequence of the processes involved in calcification or, in the case of A. lessonii, possibly symbiont activity. Despite some variability in elemental microdistribution between specimens from a given species, our combined dataset shows species-specific distributions of the elements (e.g., peak heights and/or band-widths) and also a systematic colocation of Mg, Na, S, and Sr for all three species, suggesting a coupled or simultaneous uptake, transport, and incorporation of these elements during chamber addition. The observed trace element patterns generally reflect a laminar calcification model, suggesting that heterogeneity of these elements is intrinsically linked to chamber addition. Although the incorporation of redox-sensitive Mn depends on the Mn concentration of the culture medium, the Mn distribution observed in Ammonia sp. suggests that Mn transport is similarly linked to laminar calcification dynamics. However, for B. marginata, Mn banding was sometimes anticorrelated with Mg banding, suggesting that (bio)availability, uptake, and transport of Mn differ from those for van Dijk et al. Chemical Heterogeneities in Foraminiferal Shells Ammonia sp. Our results from symbiont-bearing A. lessonii suggest that the activity of symbionts (i.e., photosynthesis/respiration) may influence the incorporation of Mn owing to alternation of the chemistry in the microenvironment of the foraminifera, an important consideration in the development of this potential proxy for past oxygenation of the oceans.

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Infrared Orange: Connecting Hyperspectral Data with Machine Learning

Cited by 114 publications

References 4 publications

Clinical applications of infrared and Raman spectroscopy: state of play and future challenges

Clinical applications of infrared and Raman spectroscopy: state of play and future challenges

Mineralogy and Zn Chemical Speciation in a Soil-Plant System from a Metal-Extreme Environment: A Study on Helichrysum microphyllum subsp. tyrrhenicum (Campo Pisano Mine, SW Sardinia, Italy)

Chemical Heterogeneity of Mg, Mn, Na, S, and Sr in Benthic Foraminiferal Calcite

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