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ZFBONE: an ImageJ toolset for semi-automatic analysis of zebrafish bone structures

2020-09Journal article Restricted
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dc.contributor.authorTarasco, Marco
dc.contributor.authorCordelieres, Fabrice P.
dc.contributor.authorCancela, M. Leonor
dc.contributor.authorLaizé, Vincent
dc.date.accessioned2021-06-24T11:35:20Z
dc.date.available2021-06-24T11:35:20Z
dc.date.issued2020-09
dc.description.abstractThe last decade has seen an increased interest in the discovery of compounds with bone anabolic activity to treat skeletal disorders such as osteoporosis and increase the well-being of patients. Due to the many technical advantages over classical rodent systems, zebrafish (Danio rerio) has been increasingly used in screening pipelines, in particular those aiming at identifying osteoactive compounds with pharmacological potential. Because compound osteoactivity is mostly determined in zebrafish through the morphometric analysis of bone structures, image analysis, rather than screening assay implementation, molecule availability and image acquisition, represents a bottleneck to the screening throughput. The absence of auto/semi-automatic tools for image analysis of fish bone structures is also a limitation to a broader usage of zebrafish screening pipelines. We present here ZFBONE (for ZebraFish BONE), an open-source, freely available, user-friendly, rapid and reliable toolset, aiming at accelerating image analysis by automating the morphometric assessment of zebrafish bone structures, but also at increasing data accuracy by reducing operator bias. Tools included in ZFBONE allow users to assess, from 2D images, morphometric parameters of several bone structures (e.g. operculum, caudal fin rays and scales) but also the extent and the intensity of bone-specific colorations. ZFBONE has been developed using the open-source ImageJ software, to make it available to the whole zebrafish research community, but also to have it easily modifiable according to user demands. ZFBONE can also be used toward the standardization of zebrafish screening protocols in academia and industry.
dc.description.sponsorshipPortuguese Foundation for Science and Technology (FCT)Portuguese Foundation for Science and Technology [UIDB/04326/2020]
dc.description.sponsorshipEuropean Maritime and Fisheries Fund (EMFF/FEAMP) through the National Operational Programme MAR2020
dc.description.sponsorshipFCTPortuguese Foundation for Science and TechnologyEuropean Commission [SFRH/BD/128634/2017]
dc.description.sponsorshipNEUBIAS-COST STSM program [CA15124]
dc.description.sponsorshipFrench National Research AgencyFrench National Research Agency (ANR) [ANR-10-INBS-04]
dc.description.sponsorshipproject OSTEOMAR [16-02-01-FMP-0057]
dc.description.versioninfo:eu-repo/semantics/publishedVersion
dc.identifier.doi10.1016/j.bone.2020.115480
dc.identifier.issn8756-3282
dc.identifier.urihttp://hdl.handle.net/10400.1/16409
dc.language.isoeng
dc.peerreviewedyes
dc.publisherElsevier
dc.relationAlgarve Centre for Marine Sciences
dc.relationHow microplastics and adsorbed pollutants affect zebrafish development
dc.subjectImageJ
dc.subjectZebrafish
dc.subjectBone
dc.subjectOsteoactive compounds screening
dc.subjectMorphometric analysis
dc.subject.otherEndocrinology & Metabolism
dc.titleZFBONE: an ImageJ toolset for semi-automatic analysis of zebrafish bone structures
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleAlgarve Centre for Marine Sciences
oaire.awardTitleHow microplastics and adsorbed pollutants affect zebrafish development
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F04326%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/OE/SFRH%2FBD%2F128634%2F2017/PT
oaire.citation.startPage115480
oaire.citation.titleBone
oaire.citation.volume138
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStreamOE
person.familyNameTarasco
person.familyNameCancela
person.familyNameLaizé
person.givenNameMarco
person.givenNameM. Leonor
person.givenNameVincent
person.identifier.ciencia-id2B1F-0392-9ABE
person.identifier.orcid0000-0001-5894-6526
person.identifier.orcid0000-0003-3114-6662
person.identifier.orcid0000-0001-9565-9198
person.identifier.ridG-9575-2017
person.identifier.ridB-4463-2008
person.identifier.scopus-author-id57194105105
person.identifier.scopus-author-id6602982778
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsrestrictedAccess
rcaap.typearticle
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