HyLength: a semi-automated digital image analysis tool for measuring the length of roots and fungal hyphae of dense mycelia.
Identifieur interne : 000116 ( Main/Corpus ); précédent : 000115; suivant : 000117HyLength: a semi-automated digital image analysis tool for measuring the length of roots and fungal hyphae of dense mycelia.
Auteurs : Alessio Cardini ; Elisa Pellegrino ; Emanuela Del Dottore ; Hannes A. Gamper ; Barbara Mazzolai ; Laura ErcoliSource :
- Mycorrhiza [ 1432-1890 ] ; 2020.
English descriptors
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- MESH :
Abstract
In plant-fungus phenotyping, determining fungal hyphal and plant root lengths by digital image analysis can reduce labour and increase data reproducibility. However, the degree of software sophistication is often prohibitive and manual measuring is still used, despite being very time-consuming. We developed the HyLength tool for measuring the lengths of hyphae and roots in in vivo and in vitro systems. The HyLength was successfully validated against manual measures of roots and fungal hyphae obtained from all systems. Compared with manual methods, the HyLength underestimated Medicago sativa roots in the in vivo system and Rhizophagus irregularis hyphae in the in vitro system by about 12 cm per m and allowed to save about 1 h for a single experimental unit. As regards hyphae of R. irregularis in the in vivo system, the HyLength overestimated the length by about 21 cm per m compared with manual measures, but time saving was up to 20.5 h per single experimental unit. Finally, with hyphae of Aspergillus oryzae, the underestimation was about 8 cm per m with a time saving of about 10 min for a single germinating spore. By benchmarking the HyLength against the AnaMorf plugin of the ImageJ/Fiji, we found that the HyLength performed better for dense fungal hyphae, also strongly reducing the measuring time. The HyLength can allow measuring the length over a whole experimental unit, eliminating the error due to sub-area selection by the user and allowing processing a high number of samples. Therefore, we propose the HyLength as a useful freeware tool for measuring fungal hyphae of dense mycelia.
DOI: 10.1007/s00572-020-00956-w
PubMed: 32300867
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Gamper</name><affiliation><nlm:affiliation>Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Free University of Bozen-Bolzano, Faculty of Science and Technology, Universitätsplatz 5 - piazza Università 5, 39100, Bozen-Bolzano, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Mazzolai, Barbara" sort="Mazzolai, Barbara" uniqKey="Mazzolai B" first="Barbara" last="Mazzolai">Barbara Mazzolai</name><affiliation><nlm:affiliation>Center for Micro-BioRobotics, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025, Pontedera, Pisa, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Ercoli, Laura" sort="Ercoli, Laura" uniqKey="Ercoli L" first="Laura" last="Ercoli">Laura Ercoli</name><affiliation><nlm:affiliation>Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32300867</idno><idno type="pmid">32300867</idno><idno type="doi">10.1007/s00572-020-00956-w</idno><idno type="wicri:Area/Main/Corpus">000116</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000116</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">HyLength: a semi-automated digital image analysis tool for measuring the length of roots and fungal hyphae of dense mycelia.</title><author><name sortKey="Cardini, Alessio" sort="Cardini, Alessio" uniqKey="Cardini A" first="Alessio" last="Cardini">Alessio Cardini</name><affiliation><nlm:affiliation>Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Pellegrino, Elisa" sort="Pellegrino, Elisa" uniqKey="Pellegrino E" first="Elisa" last="Pellegrino">Elisa Pellegrino</name><affiliation><nlm:affiliation>Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. elisa.pellegrino@santannapisa.it.</nlm:affiliation></affiliation></author><author><name sortKey="Del Dottore, Emanuela" sort="Del Dottore, Emanuela" uniqKey="Del Dottore E" first="Emanuela" last="Del Dottore">Emanuela Del Dottore</name><affiliation><nlm:affiliation>Center for Micro-BioRobotics, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025, Pontedera, Pisa, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Gamper, Hannes A" sort="Gamper, Hannes A" uniqKey="Gamper H" first="Hannes A" last="Gamper">Hannes A. Gamper</name><affiliation><nlm:affiliation>Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Free University of Bozen-Bolzano, Faculty of Science and Technology, Universitätsplatz 5 - piazza Università 5, 39100, Bozen-Bolzano, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Mazzolai, Barbara" sort="Mazzolai, Barbara" uniqKey="Mazzolai B" first="Barbara" last="Mazzolai">Barbara Mazzolai</name><affiliation><nlm:affiliation>Center for Micro-BioRobotics, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025, Pontedera, Pisa, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Ercoli, Laura" sort="Ercoli, Laura" uniqKey="Ercoli L" first="Laura" last="Ercoli">Laura Ercoli</name><affiliation><nlm:affiliation>Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Mycorrhiza</title><idno type="eISSN">1432-1890</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Hyphae (MeSH)</term><term>Mycorrhizae (MeSH)</term><term>Plant Roots (MeSH)</term><term>Reproducibility of Results (MeSH)</term><term>Spores, Fungal (MeSH)</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Hyphae</term><term>Mycorrhizae</term><term>Plant Roots</term><term>Reproducibility of Results</term><term>Spores, Fungal</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In plant-fungus phenotyping, determining fungal hyphal and plant root lengths by digital image analysis can reduce labour and increase data reproducibility. However, the degree of software sophistication is often prohibitive and manual measuring is still used, despite being very time-consuming. We developed the HyLength tool for measuring the lengths of hyphae and roots in in vivo and in vitro systems. The HyLength was successfully validated against manual measures of roots and fungal hyphae obtained from all systems. Compared with manual methods, the HyLength underestimated Medicago sativa roots in the in vivo system and Rhizophagus irregularis hyphae in the in vitro system by about 12 cm per m and allowed to save about 1 h for a single experimental unit. As regards hyphae of R. irregularis in the in vivo system, the HyLength overestimated the length by about 21 cm per m compared with manual measures, but time saving was up to 20.5 h per single experimental unit. Finally, with hyphae of Aspergillus oryzae, the underestimation was about 8 cm per m with a time saving of about 10 min for a single germinating spore. By benchmarking the HyLength against the AnaMorf plugin of the ImageJ/Fiji, we found that the HyLength performed better for dense fungal hyphae, also strongly reducing the measuring time. The HyLength can allow measuring the length over a whole experimental unit, eliminating the error due to sub-area selection by the user and allowing processing a high number of samples. Therefore, we propose the HyLength as a useful freeware tool for measuring fungal hyphae of dense mycelia.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Automated" Owner="NLM"><PMID Version="1">32300867</PMID><DateCompleted><Year>2020</Year><Month>05</Month><Day>19</Day></DateCompleted><DateRevised><Year>2020</Year><Month>05</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1432-1890</ISSN><JournalIssue CitedMedium="Internet"><Volume>30</Volume><Issue>2-3</Issue><PubDate><Year>2020</Year><Month>May</Month></PubDate></JournalIssue><Title>Mycorrhiza</Title><ISOAbbreviation>Mycorrhiza</ISOAbbreviation></Journal><ArticleTitle>HyLength: a semi-automated digital image analysis tool for measuring the length of roots and fungal hyphae of dense mycelia.</ArticleTitle><Pagination><MedlinePgn>229-242</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00572-020-00956-w</ELocationID><Abstract><AbstractText>In plant-fungus phenotyping, determining fungal hyphal and plant root lengths by digital image analysis can reduce labour and increase data reproducibility. However, the degree of software sophistication is often prohibitive and manual measuring is still used, despite being very time-consuming. We developed the HyLength tool for measuring the lengths of hyphae and roots in in vivo and in vitro systems. The HyLength was successfully validated against manual measures of roots and fungal hyphae obtained from all systems. Compared with manual methods, the HyLength underestimated Medicago sativa roots in the in vivo system and Rhizophagus irregularis hyphae in the in vitro system by about 12 cm per m and allowed to save about 1 h for a single experimental unit. As regards hyphae of R. irregularis in the in vivo system, the HyLength overestimated the length by about 21 cm per m compared with manual measures, but time saving was up to 20.5 h per single experimental unit. Finally, with hyphae of Aspergillus oryzae, the underestimation was about 8 cm per m with a time saving of about 10 min for a single germinating spore. By benchmarking the HyLength against the AnaMorf plugin of the ImageJ/Fiji, we found that the HyLength performed better for dense fungal hyphae, also strongly reducing the measuring time. The HyLength can allow measuring the length over a whole experimental unit, eliminating the error due to sub-area selection by the user and allowing processing a high number of samples. Therefore, we propose the HyLength as a useful freeware tool for measuring fungal hyphae of dense mycelia.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cardini</LastName><ForeName>Alessio</ForeName><Initials>A</Initials><Identifier Source="ORCID">https://orcid.org/0000-0001-9687-6047</Identifier><AffiliationInfo><Affiliation>Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pellegrino</LastName><ForeName>Elisa</ForeName><Initials>E</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-2482-1327</Identifier><AffiliationInfo><Affiliation>Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. elisa.pellegrino@santannapisa.it.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Del Dottore</LastName><ForeName>Emanuela</ForeName><Initials>E</Initials><Identifier Source="ORCID">https://orcid.org/0000-0001-6874-1970</Identifier><AffiliationInfo><Affiliation>Center for Micro-BioRobotics, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025, Pontedera, Pisa, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gamper</LastName><ForeName>Hannes A</ForeName><Initials>HA</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-8185-3472</Identifier><AffiliationInfo><Affiliation>Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Free University of Bozen-Bolzano, Faculty of Science and Technology, Universitätsplatz 5 - piazza Università 5, 39100, Bozen-Bolzano, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mazzolai</LastName><ForeName>Barbara</ForeName><Initials>B</Initials><Identifier Source="ORCID">https://orcid.org/0000-0003-0722-8350</Identifier><AffiliationInfo><Affiliation>Center for Micro-BioRobotics, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025, Pontedera, Pisa, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ercoli</LastName><ForeName>Laura</ForeName><Initials>L</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-7942-2120</Identifier><AffiliationInfo><Affiliation>Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>04</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Mycorrhiza</MedlineTA><NlmUniqueID>100955036</NlmUniqueID><ISSNLinking>0940-6360</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D025301" MajorTopicYN="Y">Hyphae</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="Y">Mycorrhizae</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013172" MajorTopicYN="N">Spores, Fungal</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Arbuscular mycorrhizal fungi</Keyword><Keyword MajorTopicYN="N">Digital image analysis</Keyword><Keyword MajorTopicYN="N">Extraradical mycelium</Keyword><Keyword MajorTopicYN="N">Hyphal length</Keyword><Keyword MajorTopicYN="N">Plant-fungus phenotyping</Keyword><Keyword MajorTopicYN="N">Root length</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>01</Month><Day>10</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>03</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>4</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>5</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>4</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32300867</ArticleId><ArticleId IdType="doi">10.1007/s00572-020-00956-w</ArticleId><ArticleId IdType="pii">10.1007/s00572-020-00956-w</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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