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


DCAT Export

<?xml version='1.0' encoding='utf-8'?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:adms="http://www.w3.org/ns/adms#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dct="http://purl.org/dc/terms/" xmlns:dctype="http://purl.org/dc/dcmitype/" xmlns:dcat="http://www.w3.org/ns/dcat#" xmlns:duv="http://www.w3.org/ns/duv#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:frapo="http://purl.org/cerif/frapo/" xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:gsp="http://www.opengis.net/ont/geosparql#" xmlns:locn="http://www.w3.org/ns/locn#" xmlns:org="http://www.w3.org/ns/org#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:schema="http://schema.org/" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:vcard="http://www.w3.org/2006/vcard/ns#" xmlns:wdrs="http://www.w3.org/2007/05/powder-s#">
  <rdf:Description rdf:about="https://zenodo.org/record/4822255">
    <rdf:type rdf:resource="http://www.w3.org/ns/dcat#Dataset"/>
    <dct:type rdf:resource="http://purl.org/dc/dcmitype/Text"/>
    <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/record/4822255</dct:identifier>
    <foaf:page rdf:resource="https://zenodo.org/record/4822255"/>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>de Cesare, Irene</foaf:name>
        <foaf:givenName>Irene</foaf:givenName>
        <foaf:familyName>de Cesare</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K.</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Zamora-Chimal, Criseida G.</foaf:name>
        <foaf:givenName>Criseida G.</foaf:givenName>
        <foaf:familyName>Zamora-Chimal</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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.</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Postiglione, Lorena</foaf:name>
        <foaf:givenName>Lorena</foaf:givenName>
        <foaf:familyName>Postiglione</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol BS8 1UB, U.K.</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Khazim, Mahmoud</foaf:name>
        <foaf:givenName>Mahmoud</foaf:givenName>
        <foaf:familyName>Khazim</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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.</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Pedone, Elisa</foaf:name>
        <foaf:givenName>Elisa</foaf:givenName>
        <foaf:familyName>Pedone</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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.</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Shannon, Barbara</foaf:name>
        <foaf:givenName>Barbara</foaf:givenName>
        <foaf:familyName>Shannon</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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.</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Fiore, Gianfranco</foaf:name>
        <foaf:givenName>Gianfranco</foaf:givenName>
        <foaf:familyName>Fiore</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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.</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Perrino, Giansimone</foaf:name>
        <foaf:givenName>Giansimone</foaf:givenName>
        <foaf:familyName>Perrino</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Telethon Institute of Genetic and Medicine Via Campi Flegrei 34, 80078 Pozzuoli, Italy</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Napolitano, Sara</foaf:name>
        <foaf:givenName>Sara</foaf:givenName>
        <foaf:familyName>Napolitano</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Telethon Institute of Genetic and Medicine Via Campi Flegrei 34, 80078 Pozzuoli, Italy</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-1911-7407">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0002-1911-7407</dct:identifier>
        <foaf:name>di Bernardo, Diego</foaf:name>
        <foaf:givenName>Diego</foaf:givenName>
        <foaf:familyName>di Bernardo</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-0803-4075">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0002-0803-4075</dct:identifier>
        <foaf:name>Savery, Nigel J.</foaf:name>
        <foaf:givenName>Nigel J.</foaf:givenName>
        <foaf:familyName>Savery</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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.</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-4000-0975">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0002-4000-0975</dct:identifier>
        <foaf:name>Grierson, Claire</foaf:name>
        <foaf:givenName>Claire</foaf:givenName>
        <foaf:familyName>Grierson</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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.</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-2171-4745">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0002-2171-4745</dct:identifier>
        <foaf:name>di Bernardo, Mario</foaf:name>
        <foaf:givenName>Mario</foaf:givenName>
        <foaf:familyName>di Bernardo</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-7553-6358">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0002-7553-6358</dct:identifier>
        <foaf:name>Marucci, Lucia</foaf:name>
        <foaf:givenName>Lucia</foaf:givenName>
        <foaf:familyName>Marucci</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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.</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:title>ChipSeg: An Automatic Tool to Segment Bacterial and Mammalian Cells Cultured in Microfluidic Devices</dct:title>
    <dct:publisher>
      <foaf:Agent>
        <foaf:name>Zenodo</foaf:name>
      </foaf:Agent>
    </dct:publisher>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2021</dct:issued>
    <frapo:isFundedBy rdf:resource="info:eu-repo/grantAgreement/EC/H2020/766840/"/>
    <schema:funder>
      <foaf:Organization>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10.13039/501100000780</dct:identifier>
        <foaf:name>European Commission</foaf:name>
      </foaf:Organization>
    </schema:funder>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-01-18</dct:issued>
    <owl:sameAs rdf:resource="https://zenodo.org/record/4822255"/>
    <adms:identifier>
      <adms:Identifier>
        <skos:notation rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/record/4822255</skos:notation>
        <adms:schemeAgency>url</adms:schemeAgency>
      </adms:Identifier>
    </adms:identifier>
    <owl:sameAs rdf:resource="https://doi.org/10.1021/acsomega.0c03906"/>
    <dct:isPartOf rdf:resource="https://zenodo.org/communities/cosy-bio"/>
    <dct:description>&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;</dct:description>
    <dct:accessRights rdf:resource="http://publications.europa.eu/resource/authority/access-right/PUBLIC"/>
    <dct:accessRights>
      <dct:RightsStatement rdf:about="info:eu-repo/semantics/openAccess">
        <rdfs:label>Open Access</rdfs:label>
      </dct:RightsStatement>
    </dct:accessRights>
    <dcat:distribution>
      <dcat:Distribution>
        <dct:license rdf:resource="https://creativecommons.org/licenses/by/4.0/legalcode"/>
        <dcat:accessURL rdf:resource="https://zenodo.org/record/4822255"/>
      </dcat:Distribution>
    </dcat:distribution>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL>https://doi.org/10.1021/acsomega.0c03906</dcat:accessURL>
        <dcat:byteSize>1419341</dcat:byteSize>
        <dcat:downloadURL rdf:resource="https://zenodo.org/record/4822255/files/De Cesare et al 2021 acsomega.pdf">https://zenodo.org/record/4822255/files/De Cesare et al 2021 acsomega.pdf</dcat:downloadURL>
        <dcat:mediaType>application/pdf</dcat:mediaType>
      </dcat:Distribution>
    </dcat:distribution>
  </rdf:Description>
  <foaf:Project rdf:about="info:eu-repo/grantAgreement/EC/H2020/766840/">
    <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">766840</dct:identifier>
    <dct:title>Control Engineering of Biological Systems for Reliable Synthetic Biology Applications</dct:title>
    <frapo:isAwardedBy>
      <foaf:Organization>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10.13039/501100000780</dct:identifier>
        <foaf:name>European Commission</foaf:name>
      </foaf:Organization>
    </frapo:isAwardedBy>
  </foaf:Project>
</rdf:RDF>
10
8
views
downloads
Views 10
Downloads 8
Data volume 11.4 MB
Unique views 8
Unique downloads 7

Share

Cite as