Ensemble Neuron Tracer for 3D Neuron Reconstruction
Tracing of neuron paths is important in neuroscience. Recent studies have shown that it is possible to segment and reconstruct three-dimensional morphology of axons and dendrites using fully automatic neuron tracing methods. A specific tracer may be better than others for a specific dataset, but ano...
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| Veröffentlicht in: | Neuroinformatics (Totowa, N.J.) N.J.), 2017-04, Vol.15 (2), p.185-198 |
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| container_title | Neuroinformatics (Totowa, N.J.) |
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| creator | Wang, Ching-Wei Lee, Yu-Ching Pradana, Hilmil Zhou, Zhi Peng, Hanchuan |
| description | Tracing of neuron paths is important in neuroscience. Recent studies have shown that it is possible to segment and reconstruct three-dimensional morphology of axons and dendrites using fully automatic neuron tracing methods. A specific tracer may be better than others for a specific dataset, but another tracer could perform better for some other datasets. Ensemble of learners is an effective way to improve learning accuracy in machine learning. We developed automatic ensemble neuron tracers, which consistently perform well on 57 datasets of 5 species collected from 7 laboratories worldwide. Quantitative evaluation based on the data generated by human annotators shows that the proposed ensemble tracers are valuable for 3D neuron tracing and can be widely applied to different datasets. |
| doi_str_mv | 10.1007/s12021-017-9325-1 |
| format | Article |
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Recent studies have shown that it is possible to segment and reconstruct three-dimensional morphology of axons and dendrites using fully automatic neuron tracing methods. A specific tracer may be better than others for a specific dataset, but another tracer could perform better for some other datasets. Ensemble of learners is an effective way to improve learning accuracy in machine learning. We developed automatic ensemble neuron tracers, which consistently perform well on 57 datasets of 5 species collected from 7 laboratories worldwide. Quantitative evaluation based on the data generated by human annotators shows that the proposed ensemble tracers are valuable for 3D neuron tracing and can be widely applied to different datasets.</description><identifier>ISSN: 1539-2791</identifier><identifier>EISSN: 1559-0089</identifier><identifier>DOI: 10.1007/s12021-017-9325-1</identifier><identifier>PMID: 28185058</identifier><language>eng</language><publisher>New York: Springer US</publisher><subject>Algorithms ; Animals ; Automatic Data Processing ; Axons ; Bioinformatics ; Biomedical and Life Sciences ; Biomedicine ; Brain - cytology ; Brain - diagnostic imaging ; Computational Biology/Bioinformatics ; Computer Appl. in Life Sciences ; Databases, Factual ; Datasets ; Dendrites ; Dendrites - ultrastructure ; Humans ; Imaging, Three-Dimensional - methods ; Learning algorithms ; Magnetic Resonance Imaging ; Nervous system ; Neurology ; Neurons - physiology ; Neurons - ultrastructure ; Neurosciences ; Original Article ; Quantitative analysis ; Tracers</subject><ispartof>Neuroinformatics (Totowa, N.J.), 2017-04, Vol.15 (2), p.185-198</ispartof><rights>Springer Science+Business Media New York 2017</rights><rights>Neuroinformatics is a copyright of Springer, 2017.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-p212t-d4fdfd1212b2838fc9793fbf498bb101e3f3e49c9995c94f915b02f9084ed5543</cites><orcidid>0000-0001-9992-6863</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s12021-017-9325-1$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s12021-017-9325-1$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28185058$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, Ching-Wei</creatorcontrib><creatorcontrib>Lee, Yu-Ching</creatorcontrib><creatorcontrib>Pradana, Hilmil</creatorcontrib><creatorcontrib>Zhou, Zhi</creatorcontrib><creatorcontrib>Peng, Hanchuan</creatorcontrib><title>Ensemble Neuron Tracer for 3D Neuron Reconstruction</title><title>Neuroinformatics (Totowa, N.J.)</title><addtitle>Neuroinform</addtitle><addtitle>Neuroinformatics</addtitle><description>Tracing of neuron paths is important in neuroscience. 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Quantitative evaluation based on the data generated by human annotators shows that the proposed ensemble tracers are valuable for 3D neuron tracing and can be widely applied to different datasets.</description><subject>Algorithms</subject><subject>Animals</subject><subject>Automatic Data Processing</subject><subject>Axons</subject><subject>Bioinformatics</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>Brain - cytology</subject><subject>Brain - diagnostic imaging</subject><subject>Computational Biology/Bioinformatics</subject><subject>Computer Appl. in Life Sciences</subject><subject>Databases, Factual</subject><subject>Datasets</subject><subject>Dendrites</subject><subject>Dendrites - ultrastructure</subject><subject>Humans</subject><subject>Imaging, Three-Dimensional - methods</subject><subject>Learning algorithms</subject><subject>Magnetic Resonance Imaging</subject><subject>Nervous system</subject><subject>Neurology</subject><subject>Neurons - physiology</subject><subject>Neurons - ultrastructure</subject><subject>Neurosciences</subject><subject>Original Article</subject><subject>Quantitative analysis</subject><subject>Tracers</subject><issn>1539-2791</issn><issn>1559-0089</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNpdkMtKA0EQRRtRTIx-gBsZcOOmtaofma6lJPEBQUHiuplHtyTMI3bPLPx7JyQBcVWXqsOlOIxdI9wjQPoQUYBADphykkJzPGFj1Jo4gKHTXZbERUo4YhcxbgDENAU4ZyNh0GjQZszkoomuziuXvLk-tE2yClnhQuLbkMj5cfnhiraJXeiLbt02l-zMZ1V0V4c5YZ9Pi9XshS_fn19nj0u-FSg6Xipf-hKHnAsjjS8oJelzr8jkOQI66aVTVBCRLkh5Qp2D8ARGuVJrJSfsbt-7De1372Jn63UsXFVljWv7aNFMU61Qq3RAb_-hm7YPzfCdRQIBeqoMDNTNgerz2pV2G9Z1Fn7sUccAiD0Qh1Pz5cKfGrA753bv3A7O7c65RfkL2O1vBQ</recordid><startdate>20170401</startdate><enddate>20170401</enddate><creator>Wang, Ching-Wei</creator><creator>Lee, Yu-Ching</creator><creator>Pradana, Hilmil</creator><creator>Zhou, Zhi</creator><creator>Peng, Hanchuan</creator><general>Springer US</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>3V.</scope><scope>7TK</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88G</scope><scope>8AO</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2M</scope><scope>M7P</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PSYQQ</scope><scope>Q9U</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-9992-6863</orcidid></search><sort><creationdate>20170401</creationdate><title>Ensemble Neuron Tracer for 3D Neuron Reconstruction</title><author>Wang, Ching-Wei ; Lee, Yu-Ching ; Pradana, Hilmil ; Zhou, Zhi ; Peng, Hanchuan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-p212t-d4fdfd1212b2838fc9793fbf498bb101e3f3e49c9995c94f915b02f9084ed5543</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Algorithms</topic><topic>Animals</topic><topic>Automatic Data Processing</topic><topic>Axons</topic><topic>Bioinformatics</topic><topic>Biomedical and Life Sciences</topic><topic>Biomedicine</topic><topic>Brain - cytology</topic><topic>Brain - diagnostic imaging</topic><topic>Computational Biology/Bioinformatics</topic><topic>Computer Appl. in Life Sciences</topic><topic>Databases, Factual</topic><topic>Datasets</topic><topic>Dendrites</topic><topic>Dendrites - ultrastructure</topic><topic>Humans</topic><topic>Imaging, Three-Dimensional - methods</topic><topic>Learning algorithms</topic><topic>Magnetic Resonance Imaging</topic><topic>Nervous system</topic><topic>Neurology</topic><topic>Neurons - physiology</topic><topic>Neurons - ultrastructure</topic><topic>Neurosciences</topic><topic>Original Article</topic><topic>Quantitative analysis</topic><topic>Tracers</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, Ching-Wei</creatorcontrib><creatorcontrib>Lee, Yu-Ching</creatorcontrib><creatorcontrib>Pradana, Hilmil</creatorcontrib><creatorcontrib>Zhou, Zhi</creatorcontrib><creatorcontrib>Peng, Hanchuan</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>ProQuest Central (Corporate)</collection><collection>Neurosciences Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Psychology Database (Alumni)</collection><collection>ProQuest Pharma Collection</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>ProQuest Psychology</collection><collection>Biological Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest One Psychology</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><jtitle>Neuroinformatics (Totowa, N.J.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Ching-Wei</au><au>Lee, Yu-Ching</au><au>Pradana, Hilmil</au><au>Zhou, Zhi</au><au>Peng, Hanchuan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Ensemble Neuron Tracer for 3D Neuron Reconstruction</atitle><jtitle>Neuroinformatics (Totowa, N.J.)</jtitle><stitle>Neuroinform</stitle><addtitle>Neuroinformatics</addtitle><date>2017-04-01</date><risdate>2017</risdate><volume>15</volume><issue>2</issue><spage>185</spage><epage>198</epage><pages>185-198</pages><issn>1539-2791</issn><eissn>1559-0089</eissn><abstract>Tracing of neuron paths is important in neuroscience. 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| subjects | Algorithms Animals Automatic Data Processing Axons Bioinformatics Biomedical and Life Sciences Biomedicine Brain - cytology Brain - diagnostic imaging Computational Biology/Bioinformatics Computer Appl. in Life Sciences Databases, Factual Datasets Dendrites Dendrites - ultrastructure Humans Imaging, Three-Dimensional - methods Learning algorithms Magnetic Resonance Imaging Nervous system Neurology Neurons - physiology Neurons - ultrastructure Neurosciences Original Article Quantitative analysis Tracers |
| title | Ensemble Neuron Tracer for 3D Neuron Reconstruction |
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