{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T20:03:44Z","timestamp":1760731424441,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2021,3,2]],"date-time":"2021-03-02T00:00:00Z","timestamp":1614643200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2017YFC1201200","2016YFB0201700","2017YFC0908400"],"award-info":[{"award-number":["2017YFC1201200","2016YFB0201700","2017YFC0908400"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Microscopy technology plays important roles in many biological research fields. Solvent-cleared brain high-resolution (HR) 3D image reconstruction is an important microscopy application. However, 3D microscopy image generation is time-consuming and expensive. Therefore, we have developed a deep learning framework (DeepS) for both image optical sectioning and super resolution microscopy.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Using DeepS to perform super resolution solvent-cleared mouse brain microscopy 3D image yields improved performance in comparison with the standard image processing workflow. We have also developed a web server to allow online usage of DeepS. Users can train their own models with only one pair of training images using the transfer learning function of the web server.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availabilityand implementation<\/jats:title>\n                  <jats:p>http:\/\/deeps.cibr.ac.cn.<\/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\/btab144","type":"journal-article","created":{"date-parts":[[2021,2,26]],"date-time":"2021-02-26T12:24:23Z","timestamp":1614342263000},"page":"3086-3087","source":"Crossref","is-referenced-by-count":3,"title":["DeepS: a web server for image optical sectioning and super resolution microscopy based on a deep learning framework"],"prefix":"10.1093","volume":"37","author":[{"given":"Qingjie","family":"Zhu","sequence":"first","affiliation":[{"name":"Chinese Institute for Brain Research (CIBR) , Beijing 102206, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Shao","sequence":"additional","affiliation":[{"name":"Chinese Institute for Brain Research (CIBR) , Beijing 102206, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhicheng","family":"Wang","sequence":"additional","affiliation":[{"name":"Chinese Institute for Brain Research (CIBR) , Beijing 102206, China"},{"name":"Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xingjun","family":"Chen","sequence":"additional","affiliation":[{"name":"Chinese Institute for Brain Research (CIBR) , Beijing 102206, China"},{"name":"Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chunqiong","family":"Li","sequence":"additional","affiliation":[{"name":"Chinese Institute for Brain Research (CIBR) , Beijing 102206, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zihan","family":"Liang","sequence":"additional","affiliation":[{"name":"Department of Bio-engineering, Southwest Jiaotong University , Chengdu, Sichuan 611756, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mingyue","family":"Jia","sequence":"additional","affiliation":[{"name":"Chinese Institute for Brain Research (CIBR) , Beijing 102206, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qingchun","family":"Guo","sequence":"additional","affiliation":[{"name":"Chinese Institute for Brain Research (CIBR) , Beijing 102206, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hu","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Comprehensive Dentistry, Texas A&M University , Dallas, TX 75246, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lei","family":"Kong","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University , Beijing 100871, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0698-0754","authenticated-orcid":false,"given":"Li","family":"Zhang","sequence":"additional","affiliation":[{"name":"Chinese Institute for Brain Research (CIBR) , Beijing 102206, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,3,2]]},"reference":[{"key":"2023061310542054300_btab144-B1","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1109\/TPAMI.2015.2439281","article-title":"Image super-resolution using deep convolutional networks","volume":"38","author":"Dong","year":"2016","journal-title":"IEEE Trans. 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