Using Fourier transform IR spectroscopy to analyze biological materials
Identifieur interne : 003379 ( Main/Exploration ); précédent : 003378; suivant : 003380Using Fourier transform IR spectroscopy to analyze biological materials
Auteurs : Matthew J. Baker [Royaume-Uni] ; Júlio Trevisan [Royaume-Uni] ; Paul Bassan [Royaume-Uni] ; Rohit Bhargava [États-Unis] ; Holly J. Butler [Royaume-Uni] ; Konrad M. Dorling [Royaume-Uni] ; Peter R. Fielden [Royaume-Uni] ; Simon W. Fogarty [Royaume-Uni] ; Nigel J. Fullwood [Royaume-Uni] ; Kelly A. Heys [Royaume-Uni] ; Caryn Hughes [Royaume-Uni] ; Peter Lasch [Allemagne] ; Pierre L. Martin-Hirsch [Royaume-Uni] ; Blessing Obinaju [Royaume-Uni] ; Ganesh D. Sockalingum [France] ; Josep Sulé-Suso [Royaume-Uni] ; Rebecca J. Strong [Royaume-Uni] ; Michael J. Walsh [États-Unis] ; Bayden R. Wood [Australie] ; Peter Gardner [Royaume-Uni] ; Francis L. Martin [Royaume-Uni]Source :
- Nature protocols [ 1754-2189 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
- anatomopathologie : Côlon.
- instrumentation : Humains, Logiciel, Spectroscopie infrarouge à transformée de Fourier, Techniques de préparation histocytologique.
English descriptors
- KwdEn :
- MESH :
- instrumentation : Spectroscopy, Fourier Transform Infrared.
- methods : Spectroscopy, Fourier Transform Infrared.
- pathology : Colon.
- Histocytological Preparation Techniques, Humans, Software.
Abstract
IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing.
Url:
DOI: 10.1038/nprot.2014.110
PubMed: 24992094
PubMed Central: 4480339
Affiliations:
- Allemagne, Australie, France, Royaume-Uni, États-Unis
- Angleterre, Berlin, Champagne-Ardenne, Grand Est, Grand Manchester, Illinois
- Berlin, Chicago, Manchester, Reims
- Université de Manchester, Université de Reims Champagne-Ardenne, Université de l'Illinois à Chicago
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Le document en format XML
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Fullwood</name><affiliation wicri:level="1"><nlm:aff id="A7">Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation></author><author><name sortKey="Heys, Kelly A" sort="Heys, Kelly A" uniqKey="Heys K" first="Kelly A" last="Heys">Kelly A. 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Martin-Hirsch</name><affiliation wicri:level="1"><nlm:aff id="A2">Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation></author><author><name sortKey="Obinaju, Blessing" sort="Obinaju, Blessing" uniqKey="Obinaju B" first="Blessing" last="Obinaju">Blessing Obinaju</name><affiliation wicri:level="1"><nlm:aff id="A2">Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation></author><author><name sortKey="Sockalingum, Ganesh D" sort="Sockalingum, Ganesh D" uniqKey="Sockalingum G" first="Ganesh D" last="Sockalingum">Ganesh D. Sockalingum</name><affiliation wicri:level="4"><nlm:aff id="A9">Equipe MéDIAN-Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, UnitéMEDyC, CNRS UMR7369, UFR Pharmacie, SFR CAP-Santé FED4231, Reims, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Equipe MéDIAN-Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, UnitéMEDyC, CNRS UMR7369, UFR Pharmacie, SFR CAP-Santé FED4231, Reims</wicri:regionArea><placeName><region type="region">Grand Est</region><region type="old region">Champagne-Ardenne</region><settlement type="city">Reims</settlement><settlement type="city">Reims</settlement></placeName><orgName type="university">Université de Reims Champagne-Ardenne</orgName></affiliation></author><author><name sortKey="Sule Suso, Josep" sort="Sule Suso, Josep" uniqKey="Sule Suso J" first="Josep" last="Sulé-Suso">Josep Sulé-Suso</name><affiliation wicri:level="1"><nlm:aff id="A10">Institute for Science and Technology in Medicine, School of Medicine, Keele University, Stoke-on-Trent, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Institute for Science and Technology in Medicine, School of Medicine, Keele University, Stoke-on-Trent</wicri:regionArea><wicri:noRegion>Stoke-on-Trent</wicri:noRegion></affiliation></author><author><name sortKey="Strong, Rebecca J" sort="Strong, Rebecca J" uniqKey="Strong R" first="Rebecca J" last="Strong">Rebecca J. Strong</name><affiliation wicri:level="1"><nlm:aff id="A2">Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation></author><author><name sortKey="Walsh, Michael J" sort="Walsh, Michael J" uniqKey="Walsh M" first="Michael J" last="Walsh">Michael J. Walsh</name><affiliation wicri:level="4"><nlm:aff id="A11">Department of Pathology, College of Medicine Research Building (COMRB), University of Illinois at Chicago, Chicago, Illinois, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, College of Medicine Research Building (COMRB), University of Illinois at Chicago, Chicago, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region><settlement type="city">Chicago</settlement></placeName><orgName type="university">Université de l'Illinois à Chicago</orgName></affiliation></author><author><name sortKey="Wood, Bayden R" sort="Wood, Bayden R" uniqKey="Wood B" first="Bayden R" last="Wood">Bayden R. Wood</name><affiliation wicri:level="1"><nlm:aff id="A12">Centre for Biospectroscopy and School of Chemistry, Monash University, Clayton, Victoria, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Biospectroscopy and School of Chemistry, Monash University, Clayton, Victoria</wicri:regionArea><wicri:noRegion>Victoria</wicri:noRegion></affiliation></author><author><name sortKey="Gardner, Peter" sort="Gardner, Peter" uniqKey="Gardner P" first="Peter" last="Gardner">Peter Gardner</name><affiliation wicri:level="4"><nlm:aff id="A4">Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester</wicri:regionArea><placeName><settlement type="city">Manchester</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Manchester</region><settlement type="city">Manchester</settlement></placeName><orgName type="university">Université de Manchester</orgName></affiliation></author><author><name sortKey="Martin, Francis L" sort="Martin, Francis L" uniqKey="Martin F" first="Francis L" last="Martin">Francis L. Martin</name><affiliation wicri:level="1"><nlm:aff id="A2">Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24992094</idno><idno type="pmc">4480339</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4480339</idno><idno type="RBID">PMC:4480339</idno><idno type="doi">10.1038/nprot.2014.110</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">001E43</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001E43</idno><idno type="wicri:Area/Pmc/Curation">001C99</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001C99</idno><idno type="wicri:Area/Pmc/Checkpoint">001270</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001270</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">003536</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">003536</idno><idno type="wicri:Area/PubMed/Curation">003423</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">003423</idno><idno type="wicri:Area/PubMed/Checkpoint">003423</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">003423</idno><idno type="wicri:Area/Ncbi/Merge">001B94</idno><idno type="wicri:Area/Ncbi/Curation">001B94</idno><idno type="wicri:Area/Ncbi/Checkpoint">001B94</idno><idno type="wicri:doubleKey">1754-2189:2014:Baker M:using:fourier:transform</idno><idno type="wicri:Area/Main/Merge">003386</idno><idno type="wicri:Area/Main/Curation">003379</idno><idno type="wicri:Area/Main/Exploration">003379</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Using Fourier transform IR spectroscopy to analyze biological materials</title><author><name sortKey="Baker, Matthew J" sort="Baker, Matthew J" uniqKey="Baker M" first="Matthew J" last="Baker">Matthew J. Baker</name><affiliation wicri:level="1"><nlm:aff id="A1">Centre for Materials Science, Division of Chemistry, University of Central Lancashire, Preston, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Materials Science, Division of Chemistry, University of Central Lancashire, Preston</wicri:regionArea><wicri:noRegion>Preston</wicri:noRegion></affiliation></author><author><name sortKey="Trevisan, Julio" sort="Trevisan, Julio" uniqKey="Trevisan J" first="Júlio" last="Trevisan">Júlio Trevisan</name><affiliation wicri:level="1"><nlm:aff id="A2">Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A3">School of Computing and Communications, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>School of Computing and Communications, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation></author><author><name sortKey="Bassan, Paul" sort="Bassan, Paul" uniqKey="Bassan P" first="Paul" last="Bassan">Paul Bassan</name><affiliation wicri:level="4"><nlm:aff id="A4">Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester</wicri:regionArea><placeName><settlement type="city">Manchester</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Manchester</region><settlement type="city">Manchester</settlement></placeName><orgName type="university">Université de Manchester</orgName></affiliation></author><author><name sortKey="Bhargava, Rohit" sort="Bhargava, Rohit" uniqKey="Bhargava R" first="Rohit" last="Bhargava">Rohit Bhargava</name><affiliation wicri:level="2"><nlm:aff id="A5">Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Butler, Holly J" sort="Butler, Holly J" uniqKey="Butler H" first="Holly J" last="Butler">Holly J. Butler</name><affiliation wicri:level="1"><nlm:aff id="A2">Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation></author><author><name sortKey="Dorling, Konrad M" sort="Dorling, Konrad M" uniqKey="Dorling K" first="Konrad M" last="Dorling">Konrad M. Dorling</name><affiliation wicri:level="1"><nlm:aff id="A1">Centre for Materials Science, Division of Chemistry, University of Central Lancashire, Preston, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Materials Science, Division of Chemistry, University of Central Lancashire, Preston</wicri:regionArea><wicri:noRegion>Preston</wicri:noRegion></affiliation></author><author><name sortKey="Fielden, Peter R" sort="Fielden, Peter R" uniqKey="Fielden P" first="Peter R" last="Fielden">Peter R. Fielden</name><affiliation wicri:level="1"><nlm:aff id="A6">Department of Chemistry, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Chemistry, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation></author><author><name sortKey="Fogarty, Simon W" sort="Fogarty, Simon W" uniqKey="Fogarty S" first="Simon W" last="Fogarty">Simon W. Fogarty</name><affiliation wicri:level="1"><nlm:aff id="A2">Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A7">Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation></author><author><name sortKey="Fullwood, Nigel J" sort="Fullwood, Nigel J" uniqKey="Fullwood N" first="Nigel J" last="Fullwood">Nigel J. Fullwood</name><affiliation wicri:level="1"><nlm:aff id="A7">Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation></author><author><name sortKey="Heys, Kelly A" sort="Heys, Kelly A" uniqKey="Heys K" first="Kelly A" last="Heys">Kelly A. Heys</name><affiliation wicri:level="1"><nlm:aff id="A2">Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation></author><author><name sortKey="Hughes, Caryn" sort="Hughes, Caryn" uniqKey="Hughes C" first="Caryn" last="Hughes">Caryn Hughes</name><affiliation wicri:level="4"><nlm:aff id="A4">Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester</wicri:regionArea><placeName><settlement type="city">Manchester</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Manchester</region><settlement type="city">Manchester</settlement></placeName><orgName type="university">Université de Manchester</orgName></affiliation></author><author><name sortKey="Lasch, Peter" sort="Lasch, Peter" uniqKey="Lasch P" first="Peter" last="Lasch">Peter Lasch</name><affiliation wicri:level="3"><nlm:aff id="A8">Proteomics and Spectroscopy (ZBS 6), Robert-Koch-Institut, Berlin, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Proteomics and Spectroscopy (ZBS 6), Robert-Koch-Institut, Berlin</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Martin Hirsch, Pierre L" sort="Martin Hirsch, Pierre L" uniqKey="Martin Hirsch P" first="Pierre L" last="Martin-Hirsch">Pierre L. Martin-Hirsch</name><affiliation wicri:level="1"><nlm:aff id="A2">Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation></author><author><name sortKey="Obinaju, Blessing" sort="Obinaju, Blessing" uniqKey="Obinaju B" first="Blessing" last="Obinaju">Blessing Obinaju</name><affiliation wicri:level="1"><nlm:aff id="A2">Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation></author><author><name sortKey="Sockalingum, Ganesh D" sort="Sockalingum, Ganesh D" uniqKey="Sockalingum G" first="Ganesh D" last="Sockalingum">Ganesh D. Sockalingum</name><affiliation wicri:level="4"><nlm:aff id="A9">Equipe MéDIAN-Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, UnitéMEDyC, CNRS UMR7369, UFR Pharmacie, SFR CAP-Santé FED4231, Reims, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Equipe MéDIAN-Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, UnitéMEDyC, CNRS UMR7369, UFR Pharmacie, SFR CAP-Santé FED4231, Reims</wicri:regionArea><placeName><region type="region">Grand Est</region><region type="old region">Champagne-Ardenne</region><settlement type="city">Reims</settlement><settlement type="city">Reims</settlement></placeName><orgName type="university">Université de Reims Champagne-Ardenne</orgName></affiliation></author><author><name sortKey="Sule Suso, Josep" sort="Sule Suso, Josep" uniqKey="Sule Suso J" first="Josep" last="Sulé-Suso">Josep Sulé-Suso</name><affiliation wicri:level="1"><nlm:aff id="A10">Institute for Science and Technology in Medicine, School of Medicine, Keele University, Stoke-on-Trent, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Institute for Science and Technology in Medicine, School of Medicine, Keele University, Stoke-on-Trent</wicri:regionArea><wicri:noRegion>Stoke-on-Trent</wicri:noRegion></affiliation></author><author><name sortKey="Strong, Rebecca J" sort="Strong, Rebecca J" uniqKey="Strong R" first="Rebecca J" last="Strong">Rebecca J. Strong</name><affiliation wicri:level="1"><nlm:aff id="A2">Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation></author><author><name sortKey="Walsh, Michael J" sort="Walsh, Michael J" uniqKey="Walsh M" first="Michael J" last="Walsh">Michael J. Walsh</name><affiliation wicri:level="4"><nlm:aff id="A11">Department of Pathology, College of Medicine Research Building (COMRB), University of Illinois at Chicago, Chicago, Illinois, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, College of Medicine Research Building (COMRB), University of Illinois at Chicago, Chicago, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region><settlement type="city">Chicago</settlement></placeName><orgName type="university">Université de l'Illinois à Chicago</orgName></affiliation></author><author><name sortKey="Wood, Bayden R" sort="Wood, Bayden R" uniqKey="Wood B" first="Bayden R" last="Wood">Bayden R. Wood</name><affiliation wicri:level="1"><nlm:aff id="A12">Centre for Biospectroscopy and School of Chemistry, Monash University, Clayton, Victoria, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Biospectroscopy and School of Chemistry, Monash University, Clayton, Victoria</wicri:regionArea><wicri:noRegion>Victoria</wicri:noRegion></affiliation></author><author><name sortKey="Gardner, Peter" sort="Gardner, Peter" uniqKey="Gardner P" first="Peter" last="Gardner">Peter Gardner</name><affiliation wicri:level="4"><nlm:aff id="A4">Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester</wicri:regionArea><placeName><settlement type="city">Manchester</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Manchester</region><settlement type="city">Manchester</settlement></placeName><orgName type="university">Université de Manchester</orgName></affiliation></author><author><name sortKey="Martin, Francis L" sort="Martin, Francis L" uniqKey="Martin F" first="Francis L" last="Martin">Francis L. Martin</name><affiliation wicri:level="1"><nlm:aff id="A2">Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster</wicri:regionArea><wicri:noRegion>Lancaster</wicri:noRegion></affiliation></author></analytic><series><title level="j">Nature protocols</title><idno type="ISSN">1754-2189</idno><idno type="eISSN">1750-2799</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Colon (pathology)</term><term>Histocytological Preparation Techniques</term><term>Humans</term><term>Software</term><term>Spectroscopy, Fourier Transform Infrared (instrumentation)</term><term>Spectroscopy, Fourier Transform Infrared (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Côlon (anatomopathologie)</term><term>Humains</term><term>Logiciel</term><term>Spectroscopie infrarouge à transformée de Fourier ()</term><term>Spectroscopie infrarouge à transformée de Fourier (instrumentation)</term><term>Techniques de préparation histocytologique</term></keywords><keywords scheme="MESH" qualifier="anatomopathologie" xml:lang="fr"><term>Côlon</term></keywords><keywords scheme="MESH" qualifier="instrumentation" xml:lang="en"><term>Spectroscopy, Fourier Transform Infrared</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Spectroscopy, Fourier Transform Infrared</term></keywords><keywords scheme="MESH" qualifier="pathology" xml:lang="en"><term>Colon</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Histocytological Preparation Techniques</term><term>Humans</term><term>Software</term></keywords><keywords scheme="MESH" qualifier="instrumentation" xml:lang="fr"><term>Humains</term><term>Logiciel</term><term>Spectroscopie infrarouge à transformée de Fourier</term><term>Techniques de préparation histocytologique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P2">IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing.</p></div></front></TEI><affiliations><list><country><li>Allemagne</li><li>Australie</li><li>France</li><li>Royaume-Uni</li><li>États-Unis</li></country><region><li>Angleterre</li><li>Berlin</li><li>Champagne-Ardenne</li><li>Grand Est</li><li>Grand Manchester</li><li>Illinois</li></region><settlement><li>Berlin</li><li>Chicago</li><li>Manchester</li><li>Reims</li></settlement><orgName><li>Université de Manchester</li><li>Université de Reims Champagne-Ardenne</li><li>Université de l'Illinois à Chicago</li></orgName></list><tree><country name="Royaume-Uni"><noRegion><name sortKey="Baker, Matthew J" sort="Baker, Matthew J" uniqKey="Baker M" first="Matthew J" last="Baker">Matthew J. Baker</name></noRegion><name sortKey="Bassan, Paul" sort="Bassan, Paul" uniqKey="Bassan P" first="Paul" last="Bassan">Paul Bassan</name><name sortKey="Butler, Holly J" sort="Butler, Holly J" uniqKey="Butler H" first="Holly J" last="Butler">Holly J. Butler</name><name sortKey="Dorling, Konrad M" sort="Dorling, Konrad M" uniqKey="Dorling K" first="Konrad M" last="Dorling">Konrad M. Dorling</name><name sortKey="Fielden, Peter R" sort="Fielden, Peter R" uniqKey="Fielden P" first="Peter R" last="Fielden">Peter R. Fielden</name><name sortKey="Fogarty, Simon W" sort="Fogarty, Simon W" uniqKey="Fogarty S" first="Simon W" last="Fogarty">Simon W. Fogarty</name><name sortKey="Fogarty, Simon W" sort="Fogarty, Simon W" uniqKey="Fogarty S" first="Simon W" last="Fogarty">Simon W. Fogarty</name><name sortKey="Fullwood, Nigel J" sort="Fullwood, Nigel J" uniqKey="Fullwood N" first="Nigel J" last="Fullwood">Nigel J. Fullwood</name><name sortKey="Gardner, Peter" sort="Gardner, Peter" uniqKey="Gardner P" first="Peter" last="Gardner">Peter Gardner</name><name sortKey="Heys, Kelly A" sort="Heys, Kelly A" uniqKey="Heys K" first="Kelly A" last="Heys">Kelly A. Heys</name><name sortKey="Hughes, Caryn" sort="Hughes, Caryn" uniqKey="Hughes C" first="Caryn" last="Hughes">Caryn Hughes</name><name sortKey="Martin Hirsch, Pierre L" sort="Martin Hirsch, Pierre L" uniqKey="Martin Hirsch P" first="Pierre L" last="Martin-Hirsch">Pierre L. Martin-Hirsch</name><name sortKey="Martin, Francis L" sort="Martin, Francis L" uniqKey="Martin F" first="Francis L" last="Martin">Francis L. Martin</name><name sortKey="Obinaju, Blessing" sort="Obinaju, Blessing" uniqKey="Obinaju B" first="Blessing" last="Obinaju">Blessing Obinaju</name><name sortKey="Strong, Rebecca J" sort="Strong, Rebecca J" uniqKey="Strong R" first="Rebecca J" last="Strong">Rebecca J. Strong</name><name sortKey="Sule Suso, Josep" sort="Sule Suso, Josep" uniqKey="Sule Suso J" first="Josep" last="Sulé-Suso">Josep Sulé-Suso</name><name sortKey="Trevisan, Julio" sort="Trevisan, Julio" uniqKey="Trevisan J" first="Júlio" last="Trevisan">Júlio Trevisan</name><name sortKey="Trevisan, Julio" sort="Trevisan, Julio" uniqKey="Trevisan J" first="Júlio" last="Trevisan">Júlio Trevisan</name></country><country name="États-Unis"><region name="Illinois"><name sortKey="Bhargava, Rohit" sort="Bhargava, Rohit" uniqKey="Bhargava R" first="Rohit" last="Bhargava">Rohit Bhargava</name></region><name sortKey="Walsh, Michael J" sort="Walsh, Michael J" uniqKey="Walsh M" first="Michael J" last="Walsh">Michael J. Walsh</name></country><country name="Allemagne"><region name="Berlin"><name sortKey="Lasch, Peter" sort="Lasch, Peter" uniqKey="Lasch P" first="Peter" last="Lasch">Peter Lasch</name></region></country><country name="France"><region name="Grand Est"><name sortKey="Sockalingum, Ganesh D" sort="Sockalingum, Ganesh D" uniqKey="Sockalingum G" first="Ganesh D" last="Sockalingum">Ganesh D. Sockalingum</name></region></country><country name="Australie"><noRegion><name sortKey="Wood, Bayden R" sort="Wood, Bayden R" uniqKey="Wood B" first="Bayden R" last="Wood">Bayden R. Wood</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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