Biological Imaging Software Tools
Identifieur interne : 000328 ( Ncbi/Merge ); précédent : 000327; suivant : 000329Biological Imaging Software Tools
Auteurs : Kevin W. Eliceiri [États-Unis] ; Michael R. Berthold [Allemagne] ; Ilya G. Goldberg [États-Unis] ; Luis Ibá Ez [États-Unis] ; B. S. Manjunath [États-Unis] ; Maryann E. Martone [États-Unis] ; Robert F. Murphy [États-Unis] ; Hanchuan Peng ; Anne L. Plant [États-Unis] ; Badrinath Roysam ; Nico Stuurman [États-Unis] ; Jason R. Swedlow [Royaume-Uni] ; Pavel Tomancak [Allemagne] ; Anne E. Carpenter [États-Unis]Source :
- Nature methods [ 1548-7091 ] ; 2012.
Abstract
Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing hitherto unimagined capabilities. Almost all these advances have required the development of software to enable the acquisition, management, analysis, and visualization of the imaging data. We review each computational step that biologists encounter when dealing with digital images, the challenges in that domain, and the overall status of available software for bioimage informatics, focusing on open source options.
Url:
DOI: 10.1038/nmeth.2084
PubMed: 22743775
PubMed Central: 3659807
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000434
- to stream Pmc, to step Curation: 000434
- to stream Pmc, to step Checkpoint: 000437
Links to Exploration step
PMC:3659807Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Biological Imaging Software Tools</title><author><name sortKey="Eliceiri, Kevin W" sort="Eliceiri, Kevin W" uniqKey="Eliceiri K" first="Kevin W." last="Eliceiri">Kevin W. Eliceiri</name><affiliation wicri:level="2"><nlm:aff id="A1">LOCI, University of Wisconsin at Madison, Madison, Wisconsin, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>LOCI, University of Wisconsin at Madison, Madison, Wisconsin</wicri:regionArea><placeName><region type="state">Wisconsin</region></placeName></affiliation></author><author><name sortKey="Berthold, Michael R" sort="Berthold, Michael R" uniqKey="Berthold M" first="Michael R." last="Berthold">Michael R. Berthold</name><affiliation wicri:level="3"><nlm:aff id="A2">Department of Computer and Information Science, Universität Konstanz, Konstanz, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Computer and Information Science, Universität Konstanz, Konstanz</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Fribourg-en-Brisgau</region><settlement type="city">Constance (Allemagne)</settlement></placeName></affiliation></author><author><name sortKey="Goldberg, Ilya G" sort="Goldberg, Ilya G" uniqKey="Goldberg I" first="Ilya G." last="Goldberg">Ilya G. Goldberg</name><affiliation wicri:level="2"><nlm:aff id="A3">National Institute on Aging, NIH. Baltimore, Maryland, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Institute on Aging, NIH. Baltimore, Maryland</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Iba Ez, Luis" sort="Iba Ez, Luis" uniqKey="Iba Ez L" first="Luis" last="Ibá Ez">Luis Ibá Ez</name><affiliation wicri:level="2"><nlm:aff id="A4">Kitware Inc, New York, New York, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Kitware Inc, New York, New York</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Manjunath, B S" sort="Manjunath, B S" uniqKey="Manjunath B" first="B. S." last="Manjunath">B. S. Manjunath</name><affiliation wicri:level="2"><nlm:aff id="A5">Center for Bio-image Informatics, Department of Electrical and Computer Engineering, University of California, Santa Barbara, California, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Bio-image Informatics, Department of Electrical and Computer Engineering, University of California, Santa Barbara, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Martone, Maryann E" sort="Martone, Maryann E" uniqKey="Martone M" first="Maryann E." last="Martone">Maryann E. Martone</name><affiliation wicri:level="2"><nlm:aff id="A6">National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, California USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla</wicri:cityArea></affiliation></author><author><name sortKey="Murphy, Robert F" sort="Murphy, Robert F" uniqKey="Murphy R" first="Robert F." last="Murphy">Robert F. Murphy</name><affiliation wicri:level="4"><nlm:aff id="A7">Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation></author><author><name sortKey="Peng, Hanchuan" sort="Peng, Hanchuan" uniqKey="Peng H" first="Hanchuan" last="Peng">Hanchuan Peng</name><affiliation><nlm:aff id="A8">Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia USA</nlm:aff><wicri:noCountry code="subfield">Virginia USA</wicri:noCountry></affiliation></author><author><name sortKey="Plant, Anne L" sort="Plant, Anne L" uniqKey="Plant A" first="Anne L." last="Plant">Anne L. Plant</name><affiliation wicri:level="2"><nlm:aff id="A9">Biochemical Science Division, NIST, Gaithersburg, Maryland, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biochemical Science Division, NIST, Gaithersburg, Maryland</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Roysam, Badrinath" sort="Roysam, Badrinath" uniqKey="Roysam B" first="Badrinath" last="Roysam">Badrinath Roysam</name><affiliation><nlm:aff id="A10">Department of Electrical and Computer Engineering, University of Houston, Houston, Texas USA</nlm:aff><wicri:noCountry code="subfield">Texas USA</wicri:noCountry></affiliation></author><author><name sortKey="Stuurman, Nico" sort="Stuurman, Nico" uniqKey="Stuurman N" first="Nico" last="Stuurman">Nico Stuurman</name><affiliation wicri:level="2"><nlm:aff id="A11">Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Swedlow, Jason R" sort="Swedlow, Jason R" uniqKey="Swedlow J" first="Jason R." last="Swedlow">Jason R. Swedlow</name><affiliation wicri:level="1"><nlm:aff id="A12">Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee</wicri:regionArea><wicri:noRegion>Dundee</wicri:noRegion></affiliation></author><author><name sortKey="Tomancak, Pavel" sort="Tomancak, Pavel" uniqKey="Tomancak P" first="Pavel" last="Tomancak">Pavel Tomancak</name><affiliation wicri:level="3"><nlm:aff id="A13">Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute of Molecular Cell Biology and Genetics, Dresden</wicri:regionArea><placeName><region type="land" nuts="1">Saxe (Land)</region><region type="district" nuts="2">District de Dresde</region><settlement type="city">Dresde</settlement></placeName></affiliation></author><author><name sortKey="Carpenter, Anne E" sort="Carpenter, Anne E" uniqKey="Carpenter A" first="Anne E." last="Carpenter">Anne E. Carpenter</name><affiliation wicri:level="2"><nlm:aff id="A14">Imaging Platform, Broad Institute, Cambridge, Massachusetts, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Imaging Platform, Broad Institute, Cambridge, Massachusetts</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22743775</idno><idno type="pmc">3659807</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3659807</idno><idno type="RBID">PMC:3659807</idno><idno type="doi">10.1038/nmeth.2084</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000434</idno><idno type="wicri:Area/Pmc/Curation">000434</idno><idno type="wicri:Area/Pmc/Checkpoint">000437</idno><idno type="wicri:Area/Ncbi/Merge">000328</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Biological Imaging Software Tools</title><author><name sortKey="Eliceiri, Kevin W" sort="Eliceiri, Kevin W" uniqKey="Eliceiri K" first="Kevin W." last="Eliceiri">Kevin W. Eliceiri</name><affiliation wicri:level="2"><nlm:aff id="A1">LOCI, University of Wisconsin at Madison, Madison, Wisconsin, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>LOCI, University of Wisconsin at Madison, Madison, Wisconsin</wicri:regionArea><placeName><region type="state">Wisconsin</region></placeName></affiliation></author><author><name sortKey="Berthold, Michael R" sort="Berthold, Michael R" uniqKey="Berthold M" first="Michael R." last="Berthold">Michael R. Berthold</name><affiliation wicri:level="3"><nlm:aff id="A2">Department of Computer and Information Science, Universität Konstanz, Konstanz, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Computer and Information Science, Universität Konstanz, Konstanz</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Fribourg-en-Brisgau</region><settlement type="city">Constance (Allemagne)</settlement></placeName></affiliation></author><author><name sortKey="Goldberg, Ilya G" sort="Goldberg, Ilya G" uniqKey="Goldberg I" first="Ilya G." last="Goldberg">Ilya G. Goldberg</name><affiliation wicri:level="2"><nlm:aff id="A3">National Institute on Aging, NIH. Baltimore, Maryland, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Institute on Aging, NIH. Baltimore, Maryland</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Iba Ez, Luis" sort="Iba Ez, Luis" uniqKey="Iba Ez L" first="Luis" last="Ibá Ez">Luis Ibá Ez</name><affiliation wicri:level="2"><nlm:aff id="A4">Kitware Inc, New York, New York, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Kitware Inc, New York, New York</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Manjunath, B S" sort="Manjunath, B S" uniqKey="Manjunath B" first="B. S." last="Manjunath">B. S. Manjunath</name><affiliation wicri:level="2"><nlm:aff id="A5">Center for Bio-image Informatics, Department of Electrical and Computer Engineering, University of California, Santa Barbara, California, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Bio-image Informatics, Department of Electrical and Computer Engineering, University of California, Santa Barbara, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Martone, Maryann E" sort="Martone, Maryann E" uniqKey="Martone M" first="Maryann E." last="Martone">Maryann E. Martone</name><affiliation wicri:level="2"><nlm:aff id="A6">National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, California USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla</wicri:cityArea></affiliation></author><author><name sortKey="Murphy, Robert F" sort="Murphy, Robert F" uniqKey="Murphy R" first="Robert F." last="Murphy">Robert F. Murphy</name><affiliation wicri:level="4"><nlm:aff id="A7">Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation></author><author><name sortKey="Peng, Hanchuan" sort="Peng, Hanchuan" uniqKey="Peng H" first="Hanchuan" last="Peng">Hanchuan Peng</name><affiliation><nlm:aff id="A8">Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia USA</nlm:aff><wicri:noCountry code="subfield">Virginia USA</wicri:noCountry></affiliation></author><author><name sortKey="Plant, Anne L" sort="Plant, Anne L" uniqKey="Plant A" first="Anne L." last="Plant">Anne L. Plant</name><affiliation wicri:level="2"><nlm:aff id="A9">Biochemical Science Division, NIST, Gaithersburg, Maryland, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biochemical Science Division, NIST, Gaithersburg, Maryland</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Roysam, Badrinath" sort="Roysam, Badrinath" uniqKey="Roysam B" first="Badrinath" last="Roysam">Badrinath Roysam</name><affiliation><nlm:aff id="A10">Department of Electrical and Computer Engineering, University of Houston, Houston, Texas USA</nlm:aff><wicri:noCountry code="subfield">Texas USA</wicri:noCountry></affiliation></author><author><name sortKey="Stuurman, Nico" sort="Stuurman, Nico" uniqKey="Stuurman N" first="Nico" last="Stuurman">Nico Stuurman</name><affiliation wicri:level="2"><nlm:aff id="A11">Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Swedlow, Jason R" sort="Swedlow, Jason R" uniqKey="Swedlow J" first="Jason R." last="Swedlow">Jason R. Swedlow</name><affiliation wicri:level="1"><nlm:aff id="A12">Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee</wicri:regionArea><wicri:noRegion>Dundee</wicri:noRegion></affiliation></author><author><name sortKey="Tomancak, Pavel" sort="Tomancak, Pavel" uniqKey="Tomancak P" first="Pavel" last="Tomancak">Pavel Tomancak</name><affiliation wicri:level="3"><nlm:aff id="A13">Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute of Molecular Cell Biology and Genetics, Dresden</wicri:regionArea><placeName><region type="land" nuts="1">Saxe (Land)</region><region type="district" nuts="2">District de Dresde</region><settlement type="city">Dresde</settlement></placeName></affiliation></author><author><name sortKey="Carpenter, Anne E" sort="Carpenter, Anne E" uniqKey="Carpenter A" first="Anne E." last="Carpenter">Anne E. Carpenter</name><affiliation wicri:level="2"><nlm:aff id="A14">Imaging Platform, Broad Institute, Cambridge, Massachusetts, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Imaging Platform, Broad Institute, Cambridge, Massachusetts</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author></analytic><series><title level="j">Nature methods</title><idno type="ISSN">1548-7091</idno><idno type="eISSN">1548-7105</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing hitherto unimagined capabilities. Almost all these advances have required the development of software to enable the acquisition, management, analysis, and visualization of the imaging data. We review each computational step that biologists encounter when dealing with digital images, the challenges in that domain, and the overall status of available software for bioimage informatics, focusing on open source options.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">101215604</journal-id><journal-id journal-id-type="pubmed-jr-id">32338</journal-id><journal-id journal-id-type="nlm-ta">Nat Methods</journal-id><journal-id journal-id-type="iso-abbrev">Nat. Methods</journal-id><journal-title-group><journal-title>Nature methods</journal-title></journal-title-group><issn pub-type="ppub">1548-7091</issn><issn pub-type="epub">1548-7105</issn></journal-meta><article-meta><article-id pub-id-type="pmid">22743775</article-id><article-id pub-id-type="pmc">3659807</article-id><article-id pub-id-type="doi">10.1038/nmeth.2084</article-id><article-id pub-id-type="manuscript">NIHMS444059</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Biological Imaging Software Tools</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Eliceiri</surname><given-names>Kevin W.</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="corresp" rid="cor1">*</xref></contrib><contrib contrib-type="author"><name><surname>Berthold</surname><given-names>Michael R.</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Goldberg</surname><given-names>Ilya G.</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Ibáñez</surname><given-names>Luis</given-names></name><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Manjunath</surname><given-names>B.S.</given-names></name><xref ref-type="aff" rid="A5">5</xref></contrib><contrib contrib-type="author"><name><surname>Martone</surname><given-names>Maryann E.</given-names></name><xref ref-type="aff" rid="A6">6</xref></contrib><contrib contrib-type="author"><name><surname>Murphy</surname><given-names>Robert F.</given-names></name><xref ref-type="aff" rid="A7">7</xref></contrib><contrib contrib-type="author"><name><surname>Peng</surname><given-names>Hanchuan</given-names></name><xref ref-type="aff" rid="A8">8</xref></contrib><contrib contrib-type="author"><name><surname>Plant</surname><given-names>Anne L.</given-names></name><xref ref-type="aff" rid="A9">9</xref></contrib><contrib contrib-type="author"><name><surname>Roysam</surname><given-names>Badrinath</given-names></name><xref ref-type="aff" rid="A10">10</xref></contrib><contrib contrib-type="author"><name><surname>Stuurman</surname><given-names>Nico</given-names></name><xref ref-type="aff" rid="A11">11</xref></contrib><contrib contrib-type="author"><name><surname>Swedlow</surname><given-names>Jason R.</given-names></name><xref ref-type="aff" rid="A12">12</xref></contrib><contrib contrib-type="author"><name><surname>Tomancak</surname><given-names>Pavel</given-names></name><xref ref-type="aff" rid="A13">13</xref></contrib><contrib contrib-type="author"><name><surname>Carpenter</surname><given-names>Anne E.</given-names></name><xref ref-type="aff" rid="A14">14</xref><xref ref-type="corresp" rid="cor1">*</xref></contrib></contrib-group><aff id="A1"><label>1</label>LOCI, University of Wisconsin at Madison, Madison, Wisconsin, USA</aff><aff id="A2"><label>2</label>Department of Computer and Information Science, Universität Konstanz, Konstanz, Germany</aff><aff id="A3"><label>3</label>National Institute on Aging, NIH. Baltimore, Maryland, USA</aff><aff id="A4"><label>4</label>Kitware Inc, New York, New York, USA</aff><aff id="A5"><label>5</label>Center for Bio-image Informatics, Department of Electrical and Computer Engineering, University of California, Santa Barbara, California, USA</aff><aff id="A6"><label>6</label>National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, California USA</aff><aff id="A7"><label>7</label>Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA</aff><aff id="A8"><label>8</label>Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia USA</aff><aff id="A9"><label>9</label>Biochemical Science Division, NIST, Gaithersburg, Maryland, USA</aff><aff id="A10"><label>10</label>Department of Electrical and Computer Engineering, University of Houston, Houston, Texas USA</aff><aff id="A11"><label>11</label>Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA</aff><aff id="A12"><label>12</label>Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK</aff><aff id="A13"><label>13</label>Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany</aff><aff id="A14"><label>14</label>Imaging Platform, Broad Institute, Cambridge, Massachusetts, USA</aff><author-notes><corresp id="cor1"><label>*</label><bold>Corresponding authors</bold>: Kevin W. Eliceiri, Director, LOCI, University of Wisconsin at Madison, Madison, WI 53706, <email>eliceiri@wisc.edu</email>, Phone: 608-263-6288, Fax: 608-262-4570, Anne E. Carpenter, Director, Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, <email>anne@broadinstitute.org</email>, Phone: 617-714-7750, Fax: 617-714-8956</corresp></author-notes><pub-date pub-type="nihms-submitted"><day>2</day><month>5</month><year>2013</year></pub-date><pub-date pub-type="epub"><day>28</day><month>6</month><year>2012</year></pub-date><pub-date pub-type="pmc-release"><day>21</day><month>5</month><year>2013</year></pub-date><volume>9</volume><issue>7</issue><fpage>697</fpage><lpage>710</lpage><abstract><p id="P1">Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing hitherto unimagined capabilities. Almost all these advances have required the development of software to enable the acquisition, management, analysis, and visualization of the imaging data. We review each computational step that biologists encounter when dealing with digital images, the challenges in that domain, and the overall status of available software for bioimage informatics, focusing on open source options.</p></abstract><funding-group><award-group><funding-source country="United States">National Institute of General Medical Sciences : NIGMS</funding-source><award-id>RC2 GM092519 || GM</award-id></award-group><award-group><funding-source country="United States">National Institute of General Medical Sciences : NIGMS</funding-source><award-id>R01 GM089652 || GM</award-id></award-group></funding-group></article-meta></front></pmc><affiliations><list><country><li>Allemagne</li><li>Royaume-Uni</li><li>États-Unis</li></country><region><li>Bade-Wurtemberg</li><li>Californie</li><li>District de Dresde</li><li>District de Fribourg-en-Brisgau</li><li>Maryland</li><li>Massachusetts</li><li>Pennsylvanie</li><li>Saxe (Land)</li><li>Wisconsin</li><li>État de New York</li></region><settlement><li>Constance (Allemagne)</li><li>Dresde</li><li>Pittsburgh</li></settlement><orgName><li>Université Carnegie-Mellon</li></orgName></list><tree><noCountry><name sortKey="Peng, Hanchuan" sort="Peng, Hanchuan" uniqKey="Peng H" first="Hanchuan" last="Peng">Hanchuan Peng</name><name sortKey="Roysam, Badrinath" sort="Roysam, Badrinath" uniqKey="Roysam B" first="Badrinath" last="Roysam">Badrinath Roysam</name></noCountry><country name="États-Unis"><region name="Wisconsin"><name sortKey="Eliceiri, Kevin W" sort="Eliceiri, Kevin W" uniqKey="Eliceiri K" first="Kevin W." last="Eliceiri">Kevin W. Eliceiri</name></region><name sortKey="Carpenter, Anne E" sort="Carpenter, Anne E" uniqKey="Carpenter A" first="Anne E." last="Carpenter">Anne E. Carpenter</name><name sortKey="Goldberg, Ilya G" sort="Goldberg, Ilya G" uniqKey="Goldberg I" first="Ilya G." last="Goldberg">Ilya G. Goldberg</name><name sortKey="Iba Ez, Luis" sort="Iba Ez, Luis" uniqKey="Iba Ez L" first="Luis" last="Ibá Ez">Luis Ibá Ez</name><name sortKey="Manjunath, B S" sort="Manjunath, B S" uniqKey="Manjunath B" first="B. S." last="Manjunath">B. S. Manjunath</name><name sortKey="Martone, Maryann E" sort="Martone, Maryann E" uniqKey="Martone M" first="Maryann E." last="Martone">Maryann E. Martone</name><name sortKey="Murphy, Robert F" sort="Murphy, Robert F" uniqKey="Murphy R" first="Robert F." last="Murphy">Robert F. Murphy</name><name sortKey="Plant, Anne L" sort="Plant, Anne L" uniqKey="Plant A" first="Anne L." last="Plant">Anne L. Plant</name><name sortKey="Stuurman, Nico" sort="Stuurman, Nico" uniqKey="Stuurman N" first="Nico" last="Stuurman">Nico Stuurman</name></country><country name="Allemagne"><region name="Bade-Wurtemberg"><name sortKey="Berthold, Michael R" sort="Berthold, Michael R" uniqKey="Berthold M" first="Michael R." last="Berthold">Michael R. Berthold</name></region><name sortKey="Tomancak, Pavel" sort="Tomancak, Pavel" uniqKey="Tomancak P" first="Pavel" last="Tomancak">Pavel Tomancak</name></country><country name="Royaume-Uni"><noRegion><name sortKey="Swedlow, Jason R" sort="Swedlow, Jason R" uniqKey="Swedlow J" first="Jason R." last="Swedlow">Jason R. Swedlow</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Ncbi/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000328 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd -nk 000328 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Ticri/CIDE
|area= CyberinfraV1
|flux= Ncbi
|étape= Merge
|type= RBID
|clé= PMC:3659807
|texte= Biological Imaging Software Tools
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/RBID.i -Sk "pubmed:22743775" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd \
| NlmPubMed2Wicri -a CyberinfraV1
| This area was generated with Dilib version V0.6.25. |  |