{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T05:59:57Z","timestamp":1775887197745,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,1,17]],"date-time":"2020-01-17T00:00:00Z","timestamp":1579219200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"LENDULET-BIOMAG","award":["2018-342"],"award-info":[{"award-number":["2018-342"]}]},{"name":"European Regional Development Funds","award":["GINOP-2.3.2-15-2016-00026"],"award-info":[{"award-number":["GINOP-2.3.2-15-2016-00026"]}]},{"name":"European Regional Development Funds","award":["GINOP-2.3.2-15-2016-00037"],"award-info":[{"award-number":["GINOP-2.3.2-15-2016-00037"]}]},{"DOI":"10.13039\/100010260","name":"Union for International Cancer Control","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010260","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004432","name":"UICC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004432","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UICC Technical Fellowship","award":["UICC-TF\/19\/640197"],"award-info":[{"award-number":["UICC-TF\/19\/640197"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Segmentation of single cells in microscopy images is one of the major challenges in computational biology. It is the first step of most bioimage analysis tasks, and essential to create training sets for more advanced deep learning approaches. Here, we propose 3D-Cell-Annotator to solve this task using 3D active surfaces together with shape descriptors as prior information in a semi-automated fashion. The software uses the convenient 3D interface of the widely used Medical Imaging Interaction Toolkit (MITK). Results on 3D biological structures (e.g. spheroids, organoids and embryos) show that the precision of the segmentation reaches the level of a human expert.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>3D-Cell-Annotator is implemented in CUDA\/C++ as a patch for the segmentation module of MITK. The 3D-Cell-Annotator enabled MITK distribution can be downloaded at: www.3D-cell-annotator.org. It works under Windows 64-bit systems and recent Linux distributions even on a consumer level laptop with a CUDA-enabled video card using recent NVIDIA drivers.<\/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\/btaa029","type":"journal-article","created":{"date-parts":[[2020,1,15]],"date-time":"2020-01-15T07:10:58Z","timestamp":1579072258000},"page":"2948-2949","source":"Crossref","is-referenced-by-count":25,"title":["3D-Cell-Annotator: an open-source active surface tool for single-cell segmentation in 3D microscopy images"],"prefix":"10.1093","volume":"36","author":[{"given":"Ervin A","family":"Tasnadi","sequence":"first","affiliation":[{"name":"Synthetic and System Biology Unit , Biological Research Centre (BRC), Szeged H-6726, Hungary"}]},{"given":"Timea","family":"Toth","sequence":"additional","affiliation":[{"name":"Synthetic and System Biology Unit , Biological Research Centre (BRC), Szeged H-6726, Hungary"}]},{"given":"Maria","family":"Kovacs","sequence":"additional","affiliation":[{"name":"Synthetic and System Biology Unit , Biological Research Centre (BRC), Szeged H-6726, Hungary"}]},{"given":"Akos","family":"Diosdi","sequence":"additional","affiliation":[{"name":"Synthetic and System Biology Unit , Biological Research Centre (BRC), Szeged H-6726, Hungary"}]},{"given":"Francesco","family":"Pampaloni","sequence":"additional","affiliation":[{"name":"Buchmann Institute for Molecular Life Sciences (BMLS) , Goethe University of Frankfurt, DE-60438 Frankfurt, Germany"}]},{"given":"Jozsef","family":"Molnar","sequence":"additional","affiliation":[{"name":"Synthetic and System Biology Unit , Biological Research Centre (BRC), Szeged H-6726, Hungary"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0371-7782","authenticated-orcid":false,"given":"Filippo","family":"Piccinini","sequence":"additional","affiliation":[{"name":"Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS , I-47014 Meldola (FC), Italy"}]},{"given":"Peter","family":"Horvath","sequence":"additional","affiliation":[{"name":"Synthetic and System Biology Unit , Biological Research Centre (BRC), Szeged H-6726, Hungary"},{"name":"Institute for Molecular Medicine Finland University of Helsinki , FI-00014 Helsinki, Finland"},{"name":"Single-Cell Technologies Ltd , H-6726 Szeged, Hungary"}]}],"member":"286","published-online":{"date-parts":[[2020,1,17]]},"reference":[{"key":"2023013111480498500_btaa029-B1","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1038\/nrd.2018.99","article-title":"Concerns, challenges and promises of high-content analysis of 3D cellular models","volume":"17","author":"Carragher","year":"2018","journal-title":"Nat. Rev. Drug Discov"},{"key":"2023013111480498500_btaa029-B2","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.1093\/bioinformatics\/btw093","article-title":"OpenSegSPIM: a user-friendly segmentation tool for SPIM data","volume":"32","author":"Gole","year":"2016","journal-title":"Bioinformatics"},{"key":"2023013111480498500_btaa029-B3","doi-asserted-by":"crossref","DOI":"10.1101\/580605","article-title":"A deep learning framework for nucleus segmentation using image style transfer","author":"Hollandi","year":"2019"},{"key":"2023013111480498500_btaa029-B4","author":"Molnar","year":"2017"},{"key":"2023013111480498500_btaa029-B5","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1007\/s11548-013-0840-8","article-title":"The Medical Imaging Interaction Toolkit: challenges and advances","volume":"8","author":"Nolden","year":"2013","journal-title":"Int. J. Comput. Assist. Radiol. Surg"},{"key":"2023013111480498500_btaa029-B6","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1093\/bioinformatics\/btu774","article-title":"NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei","volume":"31","author":"Poulet","year":"2015","journal-title":"Bioinformatics"},{"key":"2023013111480498500_btaa029-B7","first-page":"e53654","article-title":"Quantitative analysis of protein expression to study lineage specification in mouse preimplantation embryos","volume":"108","author":"Saiz","year":"2016","journal-title":"J. Vis. Exp"},{"key":"2023013111480498500_btaa029-B8","doi-asserted-by":"crossref","first-page":"19103","DOI":"10.1038\/srep19103","article-title":"3D tumor spheroid models for in vitro therapeutic screening: a systematic approach to enhance the biological relevance of data obtained","volume":"6","author":"Zanoni","year":"2016","journal-title":"Sci. Rep"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa029\/32318930\/btaa029.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/9\/2948\/48983963\/bioinformatics_36_9_2948.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/9\/2948\/48983963\/bioinformatics_36_9_2948.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T15:50:46Z","timestamp":1675180246000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/9\/2948\/5709038"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,1,17]]},"references-count":8,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2020,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa029","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/677294","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,5,1]]},"published":{"date-parts":[[2020,1,17]]}}}