CyberinfraV1, Pmc, Corpus, bibRecord, 000434

Biological Imaging Software Tools

Identifieur interne : 000434 ( Pmc/Corpus ); précédent : 000433; suivant : 000435

Biological Imaging Software Tools

Auteurs : Kevin W. Eliceiri ; Michael R. Berthold ; Ilya G. Goldberg ; Luis Ibá Ez ; B. S. Manjunath ; Maryann E. Martone ; Robert F. Murphy ; Hanchuan Peng ; Anne L. Plant ; Badrinath Roysam ; Nico Stuurman ; Jason R. Swedlow ; Pavel Tomancak ; Anne E. Carpenter

Source :

Nature methods [ 1548-7091 ] ; 2012.

RBID : PMC:3659807

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:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3659807

DOI: 10.1038/nmeth.2084
PubMed: 22743775
PubMed Central: 3659807

Links to Exploration step

PMC:3659807

Le 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><nlm:aff id="A1">LOCI, University of Wisconsin at Madison, Madison, Wisconsin, USA</nlm:aff>
</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><nlm:aff id="A2">Department of Computer and Information Science, Universität Konstanz, Konstanz, Germany</nlm:aff>
</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><nlm:aff id="A3">National Institute on Aging, NIH. Baltimore, Maryland, USA</nlm:aff>
</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><nlm:aff id="A4">Kitware Inc, New York, New York, USA</nlm:aff>
</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><nlm:aff id="A5">Center for Bio-image Informatics, Department of Electrical and Computer Engineering, University of California, Santa Barbara, California, USA</nlm:aff>
</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><nlm:aff id="A6">National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, California USA</nlm:aff>
</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><nlm:aff id="A7">Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA</nlm:aff>
</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>
</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><nlm:aff id="A9">Biochemical Science Division, NIST, Gaithersburg, Maryland, USA</nlm:aff>
</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>
</affiliation>
</author>
<author><name sortKey="Stuurman, Nico" sort="Stuurman, Nico" uniqKey="Stuurman N" first="Nico" last="Stuurman">Nico Stuurman</name>
<affiliation><nlm:aff id="A11">Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA</nlm:aff>
</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><nlm:aff id="A12">Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Tomancak, Pavel" sort="Tomancak, Pavel" uniqKey="Tomancak P" first="Pavel" last="Tomancak">Pavel Tomancak</name>
<affiliation><nlm:aff id="A13">Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany</nlm:aff>
</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><nlm:aff id="A14">Imaging Platform, Broad Institute, Cambridge, Massachusetts, USA</nlm:aff>
</affiliation>
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<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>
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<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><nlm:aff id="A1">LOCI, University of Wisconsin at Madison, Madison, Wisconsin, USA</nlm:aff>
</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><nlm:aff id="A2">Department of Computer and Information Science, Universität Konstanz, Konstanz, Germany</nlm:aff>
</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><nlm:aff id="A3">National Institute on Aging, NIH. Baltimore, Maryland, USA</nlm:aff>
</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><nlm:aff id="A4">Kitware Inc, New York, New York, USA</nlm:aff>
</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><nlm:aff id="A5">Center for Bio-image Informatics, Department of Electrical and Computer Engineering, University of California, Santa Barbara, California, USA</nlm:aff>
</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><nlm:aff id="A6">National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, California USA</nlm:aff>
</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><nlm:aff id="A7">Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA</nlm:aff>
</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>
</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><nlm:aff id="A9">Biochemical Science Division, NIST, Gaithersburg, Maryland, USA</nlm:aff>
</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>
</affiliation>
</author>
<author><name sortKey="Stuurman, Nico" sort="Stuurman, Nico" uniqKey="Stuurman N" first="Nico" last="Stuurman">Nico Stuurman</name>
<affiliation><nlm:aff id="A11">Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA</nlm:aff>
</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><nlm:aff id="A12">Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Tomancak, Pavel" sort="Tomancak, Pavel" uniqKey="Tomancak P" first="Pavel" last="Tomancak">Pavel Tomancak</name>
<affiliation><nlm:aff id="A13">Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany</nlm:aff>
</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><nlm:aff id="A14">Imaging Platform, Broad Institute, Cambridge, Massachusetts, USA</nlm:aff>
</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>
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<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>
</record>

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Biological Imaging Software Tools

Biological Imaging Software Tools

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Abstract

Links to Exploration step

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