{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T03:58:05Z","timestamp":1778903885079,"version":"3.51.4"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2019,7,8]],"date-time":"2019-07-08T00:00:00Z","timestamp":1562544000000},"content-version":"vor","delay-in-days":7,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004052","name":"King Abdullah University of Science and Technology","doi-asserted-by":"publisher","award":["FCC\/1\/1976-04"],"award-info":[{"award-number":["FCC\/1\/1976-04"]}],"id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004052","name":"King Abdullah University of Science and Technology","doi-asserted-by":"publisher","award":["URF\/1\/2601-01"],"award-info":[{"award-number":["URF\/1\/2601-01"]}],"id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004052","name":"King Abdullah University of Science and Technology","doi-asserted-by":"publisher","award":["URF\/1\/3007-01"],"award-info":[{"award-number":["URF\/1\/3007-01"]}],"id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"U.S. National Institutes of Health","doi-asserted-by":"crossref","award":["P41 GM103712"],"award-info":[{"award-number":["P41 GM103712"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Carnegie Mellon University's Center for Machine Learning and Health"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Electron tomography (ET) is a widely used technology for 3D macro-molecular structure reconstruction. To obtain a satisfiable tomogram reconstruction, several key processes are involved, one of which is the calibration of projection parameters of the tilt series. Although fiducial marker-based alignment for tilt series has been well studied, marker-free alignment remains a challenge, which requires identifying and tracking the identical objects (landmarks) through different projections. However, the tracking of these landmarks is usually affected by the pixel density (intensity) change caused by the geometry difference in different views. The tracked landmarks will be used to determine the projection parameters. Meanwhile, different projection parameters will also affect the localization of landmarks. Currently, there is no alignment method that takes interrelationship between the projection parameters and the landmarks.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we propose a novel, joint method for marker-free alignment of tilt series in ET, by utilizing the information underlying the interrelationship between the projection model and the landmarks. The proposed method is the first joint solution that combines the extrinsic (track-based) alignment and the intrinsic (intensity-based) alignment, in which the localization of landmarks and projection parameters keep refining each other until convergence. This iterative approach makes our solution robust to different initial parameters and extreme geometric changes, which ensures a better reconstruction for marker-free ET. Comprehensive experimental results on three real datasets show that our new method achieved a significant improvement in alignment accuracy and reconstruction quality, compared to the state-of-the-art methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The main program is available at https:\/\/github.com\/icthrm\/joint-marker-free-alignment.<\/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\/btz323","type":"journal-article","created":{"date-parts":[[2019,5,9]],"date-time":"2019-05-09T19:21:53Z","timestamp":1557429713000},"page":"i249-i259","source":"Crossref","is-referenced-by-count":10,"title":["A joint method for marker-free alignment of tilt series in electron tomography"],"prefix":"10.1093","volume":"35","author":[{"given":"Renmin","family":"Han","sequence":"first","affiliation":[{"name":"Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhipeng","family":"Bao","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering, Tsinghua University, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiangrui","family":"Zeng","sequence":"additional","affiliation":[{"name":"Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tongxin","family":"Niu","sequence":"additional","affiliation":[{"name":"National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fa","family":"Zhang","sequence":"additional","affiliation":[{"name":"High Performance Computer Research Center, Chinese Academy of Sciences, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Min","family":"Xu","sequence":"additional","affiliation":[{"name":"Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin","family":"Gao","sequence":"additional","affiliation":[{"name":"Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,7,5]]},"reference":[{"key":"2023062712350592900_btz323-B1","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1177\/016173468400600107","article-title":"Simultaneous algebraic reconstruction technique (SART): a superior implementation of the art algorithm","volume":"6","author":"Andersen","year":"1984","journal-title":"Ultrasonic Imaging"},{"key":"2023062712350592900_btz323-B2","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1145\/361002.361007","article-title":"Multidimensional binary search trees used for associative searching","volume":"18","author":"Bentley","year":"1975","journal-title":"Commun. 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