{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T13:49:04Z","timestamp":1782308944359,"version":"3.54.5"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T00:00:00Z","timestamp":1779408000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFF0704300"],"award-info":[{"award-number":["2021YFF0704300"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003453","name":"Natural Science Foundation of Guangdong Province","doi-asserted-by":"publisher","award":["2025A1515010342"],"award-info":[{"award-number":["2025A1515010342"]}],"id":[{"id":"10.13039\/501100003453","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Dubai Future Foundation","award":["2024CANAD-MES-061"],"award-info":[{"award-number":["2024CANAD-MES-061"]}]},{"name":"Fundamental Research Funds for the Central Universities, and the Natural Science Foundation of Ningxia Province","award":["2026AAC040016"],"award-info":[{"award-number":["2026AAC040016"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Serial section electron microscopy (ssEM) is essential for studying biological cell structures at nanometer resolution. However, supporting film folding (SFF) degradation frequently occurs during sample preparation, causing structural distortions and information loss that severely impair downstream analyses such as 3D reconstruction and neuron segmentation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose RegInpaint, a novel recovery framework that jointly addresses deformation correction and missing-information restoration caused by SFF degradation. RegInpaint formulates SFF recovery as a joint problem of 3D elastic registration and image inpainting, providing a generalizable solution for ssEM restoration. Experiments on four EM datasets show that RegInpaint consistently outperforms existing methods in image restoration quality and significantly improves neuron segmentation accuracy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Source code is freely available at https:\/\/github.com\/zhangzhenbang2021\/RegInpaint.git.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag329","type":"journal-article","created":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T11:43:17Z","timestamp":1779277397000},"source":"Crossref","is-referenced-by-count":0,"title":["3D registration-guided deformable residual inpainting for ssEM restoration"],"prefix":"10.1093","volume":"42","author":[{"given":"Zhenbang","family":"Zhang","sequence":"first","affiliation":[{"name":"Shenzhen Research Institute of Shandong University , Shenzhen, 518000,","place":["China"]},{"name":"Research Center for Mathematics and Interdisciplinary Sciences, Frontiers Science Center for Nonlinear Expectations (Ministry of Education), Shandong University , Qingdao, 266237,","place":["China"]},{"name":"Department of Machine Learning, Mohamed bin Zayed University of Artificial Intelligence , Abu Dhabi, 7909,","place":["United Arab Emirates"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingtong","family":"Feng","sequence":"additional","affiliation":[{"name":"Research Center for Mathematics and Interdisciplinary Sciences, Frontiers Science Center for Nonlinear Expectations (Ministry of Education), Shandong University , Qingdao, 266237,","place":["China"]},{"name":"College of Medical Information and Engineering, Ningxia Medical University , Ningxia, 750004,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7016-421X","authenticated-orcid":false,"given":"Hongjia","family":"Li","sequence":"additional","affiliation":[{"name":"School of Medical Technology, Beijing Institute of Technology , Beijing, 100081,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haythem","family":"El-Messiry","sequence":"additional","affiliation":[{"name":"Canadian University Dubai , Dubai, 117781,","place":["United Arab Emirates"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiqiang","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Machine Learning, Mohamed bin Zayed University of Artificial Intelligence , Abu Dhabi, 7909,","place":["United Arab 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