{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T17:18:42Z","timestamp":1785345522349,"version":"3.55.0"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2017,3,30]],"date-time":"2017-03-30T00:00:00Z","timestamp":1490832000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>State-of-the-art light and electron microscopes are capable of acquiring large image datasets, but quantitatively evaluating the data often involves manually annotating structures of interest. This process is time-consuming and often a major bottleneck in the evaluation pipeline. To overcome this problem, we have introduced the Trainable Weka Segmentation (TWS), a machine learning tool that leverages a limited number of manual annotations in order to train a classifier and segment the remaining data automatically. In addition, TWS can provide unsupervised segmentation learning schemes (clustering) and can be customized to employ user-designed image features or classifiers.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>TWS is distributed as open-source software as part of the Fiji image processing distribution of ImageJ at http:\/\/imagej.net\/Trainable_Weka_Segmentation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx180","type":"journal-article","created":{"date-parts":[[2017,3,28]],"date-time":"2017-03-28T14:04:40Z","timestamp":1490709880000},"page":"2424-2426","source":"Crossref","is-referenced-by-count":2261,"title":["Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification"],"prefix":"10.1093","volume":"33","author":[{"given":"Ignacio","family":"Arganda-Carreras","sequence":"first","affiliation":[{"name":"Ikerbasque, Basque Foundation for Science, Bilbao, Spain"},{"name":"Computer Science and Artificial Intelligence Department, Basque Country University, San Sebastian, Spain"},{"name":"Donostia International Physics Center, San Sebastian, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Verena","family":"Kaynig","sequence":"additional","affiliation":[{"name":"Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Curtis","family":"Rueden","sequence":"additional","affiliation":[{"name":"Laboratory for Optical and Computational Instrumentation, University of Wisconsin, Madison, WI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin W","family":"Eliceiri","sequence":"additional","affiliation":[{"name":"Laboratory for Optical and Computational Instrumentation, University of Wisconsin, Madison, WI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johannes","family":"Schindelin","sequence":"additional","affiliation":[{"name":"Laboratory for Optical and Computational Instrumentation, University of Wisconsin, Madison, WI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Albert","family":"Cardona","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H","family":"Sebastian Seung","sequence":"additional","affiliation":[{"name":"Neuroscience Institute and Computer Science Department, Princeton University, NJ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,3,30]]},"reference":[{"key":"2023063012504785400_btx180-B1","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1007\/978-3-319-28549-8_7","volume-title":"Focus on Bio-Image Informatics","author":"Dietz","year":"2016"},{"key":"2023063012504785400_btx180-B2","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1145\/1656274.1656278","article-title":"The weka data mining software: an update","volume":"11","author":"Hall","year":"2009","journal-title":"ACM SIGKDD Explor. 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Methods"},{"key":"2023063012504785400_btx180-B7","author":"Sommer","year":"2011"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/15\/2424\/50756582\/bioinformatics_33_15_2424.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/15\/2424\/50756582\/bioinformatics_33_15_2424.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,30]],"date-time":"2023-06-30T12:50:59Z","timestamp":1688129459000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/15\/2424\/3092362"}},"subtitle":[],"editor":[{"given":"Robert","family":"Murphy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,3,30]]},"references-count":7,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2017,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx180","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,8,1]]},"published":{"date-parts":[[2017,3,30]]}}}