Journal article Open Access

ChipSeg: An Automatic Tool to Segment Bacterial and Mammalian Cells Cultured in Microfluidic Devices

de Cesare, Irene; Zamora-Chimal, Criseida G.; Postiglione, Lorena; Khazim, Mahmoud; Pedone, Elisa; Shannon, Barbara; Fiore, Gianfranco; Perrino, Giansimone; Napolitano, Sara; di Bernardo, Diego; Savery, Nigel J.; Grierson, Claire; di Bernardo, Mario; Marucci, Lucia


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  <identifier identifierType="URL">https://zenodo.org/record/4822255</identifier>
  <creators>
    <creator>
      <creatorName>de Cesare, Irene</creatorName>
      <givenName>Irene</givenName>
      <familyName>de Cesare</familyName>
      <affiliation>Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K.</affiliation>
    </creator>
    <creator>
      <creatorName>Zamora-Chimal, Criseida G.</creatorName>
      <givenName>Criseida G.</givenName>
      <familyName>Zamora-Chimal</familyName>
      <affiliation>Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K.  - BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.</affiliation>
    </creator>
    <creator>
      <creatorName>Postiglione, Lorena</creatorName>
      <givenName>Lorena</givenName>
      <familyName>Postiglione</familyName>
      <affiliation>Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K.</affiliation>
    </creator>
    <creator>
      <creatorName>Khazim, Mahmoud</creatorName>
      <givenName>Mahmoud</givenName>
      <familyName>Khazim</familyName>
      <affiliation>Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K. - School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, U.K.</affiliation>
    </creator>
    <creator>
      <creatorName>Pedone, Elisa</creatorName>
      <givenName>Elisa</givenName>
      <familyName>Pedone</familyName>
      <affiliation>Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K. - School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, U.K.</affiliation>
    </creator>
    <creator>
      <creatorName>Shannon, Barbara</creatorName>
      <givenName>Barbara</givenName>
      <familyName>Shannon</familyName>
      <affiliation>BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K. - School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.</affiliation>
    </creator>
    <creator>
      <creatorName>Fiore, Gianfranco</creatorName>
      <givenName>Gianfranco</givenName>
      <familyName>Fiore</familyName>
      <affiliation>Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K. - BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.</affiliation>
    </creator>
    <creator>
      <creatorName>Perrino, Giansimone</creatorName>
      <givenName>Giansimone</givenName>
      <familyName>Perrino</familyName>
      <affiliation>Telethon Institute of Genetic and Medicine Via Campi Flegrei 34, 80078 Pozzuoli, Italy</affiliation>
    </creator>
    <creator>
      <creatorName>Napolitano, Sara</creatorName>
      <givenName>Sara</givenName>
      <familyName>Napolitano</familyName>
      <affiliation>Telethon Institute of Genetic and Medicine Via Campi Flegrei 34, 80078 Pozzuoli, Italy</affiliation>
    </creator>
    <creator>
      <creatorName>di Bernardo, Diego</creatorName>
      <givenName>Diego</givenName>
      <familyName>di Bernardo</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-1911-7407</nameIdentifier>
      <affiliation>Telethon Institute of Genetic and Medicine Via Campi Flegrei 34, 80078 Pozzuoli, Italy - Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, 80125 Naples, Italy</affiliation>
    </creator>
    <creator>
      <creatorName>Savery, Nigel J.</creatorName>
      <givenName>Nigel J.</givenName>
      <familyName>Savery</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-0803-4075</nameIdentifier>
      <affiliation>BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K. -  School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.</affiliation>
    </creator>
    <creator>
      <creatorName>Grierson, Claire</creatorName>
      <givenName>Claire</givenName>
      <familyName>Grierson</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-4000-0975</nameIdentifier>
      <affiliation>BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K. - School of Biological Sciences, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.</affiliation>
    </creator>
    <creator>
      <creatorName>di Bernardo, Mario</creatorName>
      <givenName>Mario</givenName>
      <familyName>di Bernardo</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-2171-4745</nameIdentifier>
      <affiliation>Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K. - BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K. - Department of EE and ICT, University of Naples Federico II, Via Claudio 21, 80125 Naples, Italy</affiliation>
    </creator>
    <creator>
      <creatorName>Marucci, Lucia</creatorName>
      <givenName>Lucia</givenName>
      <familyName>Marucci</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-7553-6358</nameIdentifier>
      <affiliation>Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K. - BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K. - School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, U.K.</affiliation>
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  <titles>
    <title>ChipSeg: An Automatic Tool to Segment Bacterial and Mammalian Cells Cultured in Microfluidic Devices</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <dates>
    <date dateType="Issued">2021-01-18</date>
  </dates>
  <resourceType resourceTypeGeneral="Text">Journal article</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4822255</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsIdenticalTo">10.1021/acsomega.0c03906</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/cosy-bio</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;strong&gt;Abstract&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;Extracting quantitative measurements from time-lapse images is necessary in external feedback control applications, where segmentation results are used to inform control algorithms. We describe ChipSeg, a computational tool that segments bacterial and mammalian cells cultured in microfluidic devices and imaged by time-lapse microscopy, which can be used also in the context of external feedback control. The method is based on thresholding and uses the same core functions for both cell types. It allows us to segment individual cells in high cell density microfluidic devices, to quantify fluorescent protein expression over a time-lapse experiment, and to track individual mammalian cells. ChipSeg enables robust segmentation in external feedback control experiments and can be easily customized for other experimental settings and research aims.&lt;/p&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/H2020/766840/">766840</awardNumber>
      <awardTitle>Control Engineering of Biological Systems for Reliable Synthetic Biology Applications</awardTitle>
    </fundingReference>
  </fundingReferences>
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