{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T09:42:36Z","timestamp":1792489356859,"version":"4.5.0"},"reference-count":21,"publisher":"International Union of Crystallography (IUCr)","issue":"10","license":[{"start":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:00:00Z","timestamp":1790121600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/legalcode"},{"start":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:00:00Z","timestamp":1790121600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/legalcode"}],"funder":[{"DOI":"10.13039\/100019180","name":"European Research Council, HORIZON EUROPE European Research Council","doi-asserted-by":"publisher","award":["101055413"],"award-info":[{"award-number":["101055413"]}],"id":[{"id":"10.13039\/100019180","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["iucr.org","wiley.com","iucrj.org"],"crossmark-restriction":true},"short-container-title":["Acta Crystallogr D Struct Biol","Acta Crystallogr D","Acta Cryst D","Acta Cryst D Struct Biol","Acta Cryst Sect D","Acta Cryst Sect D Struct Biol","Acta Crystallogr Sect D","Acta Crystallogr Sect D Struct Biol","Acta Crystallogr D Biol Crystallogr","Acta Cryst D Biol Cryst"],"accepted":{"date-parts":[[2026,9,15]]},"published-print":{"date-parts":[[2026,10,1]]},"abstract":"<jats:p>\n                    Four-dimensional scanning transmission electron microscopy (4D-STEM) enables the acquisition of diffraction patterns at every probe position in a dense array. For imaging applications this approach offers significant benefits in terms of spatial resolution and contrast enhancement. In this work, we present an update on our open\n                    <jats:italic>SavvyScan<\/jats:italic>\n                    platform, consisting of a synchronous scan generator integrated by software with\n                    <jats:italic>SerialEM<\/jats:italic>\n                    to enable the automation of complex experimental protocols such as tomography. The proposed hardware functions as an interface between\n                    <jats:italic>SerialEM<\/jats:italic>\n                    , the scan controls of the microscope, a fast annular dark-field detector and a synchronized trigger for a pixelated detector. Our previous implementation relied on a dedicated computer equipped with a multichannel acquisition and signal-generation cards, as well as a separate microcontroller for synchronization. Here, we report a low-cost implementation based on a Red Pitaya board, utilizing direct programming of its embedded FPGA and Linux server components. We provide detailed instructions for system installation and operation, along with practical guidance for modifying the source code. System performance is validated through oscilloscope measurements and imaging of a replica grating sample. The utility of the approach is further demonstrated by generating a 3D electron tomogram of a cryogenic sample of mitochondria from a tilt series of shadow montage projections.\n                  <\/jats:p>","DOI":"10.1107\/s2059798326009630","type":"journal-article","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T10:54:10Z","timestamp":1789988050000},"page":"1203-1211","update-policy":"https:\/\/doi.org\/10.1107\/cm_01","source":"Crossref","is-referenced-by-count":0,"title":["FPGA-based scanner and\n                    <i>SerialEM<\/i>\n                    server for 4D-STEM electron tomography"],"prefix":"10.1107","volume":"82","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3168-0577","authenticated-orcid":true,"given":"Shahar","family":"Seifer","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0316ej306","id-type":"ROR","asserted-by":"publisher"}],"department":["Chemical and Biological Physics"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7915-5512","authenticated-orcid":true,"given":"Michael","family":"Elbaum","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0316ej306","id-type":"ROR","asserted-by":"publisher"}],"department":["Chemical and Biological Physics"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"329","published-online":{"date-parts":[[2026,9,23]]},"reference":[{"key":"sor5007_bb1","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.jsb.2014.11.009","volume":"189","author":"Agulleiro","year":"2015","journal-title":"J. Struct. Biol."},{"key":"sor5007_bb2","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s42649-026-00137-7","volume":"56","author":"Gong","year":"2026","journal-title":"Appl. Microsc."},{"key":"sor5007_bb3","doi-asserted-by":"crossref","first-page":"1587","DOI":"10.1021\/acscentsci.8b00760","volume":"4","author":"Jones","year":"2018","journal-title":"ACS Cent. Sci."},{"key":"sor5007_bb4","unstructured":"Kirchweger, P., Mullick, D., Wolf, S. G. & Elbaum, M. (2023). J. Vis. Exp., e65052."},{"key":"sor5007_bb5","first-page":"20251126690630","author":"Kirchweger","year":"2025","journal-title":"bioRxiv"},{"key":"sor5007_bb6","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1006\/jsbi.1996.0013","volume":"116","author":"Kremer","year":"1996","journal-title":"J. Struct. Biol."},{"key":"sor5007_bb7","doi-asserted-by":"crossref","first-page":"8062","DOI":"10.1038\/s41467-024-52403-5","volume":"15","author":"K\u00fc\u00e7\u00fcko\u011flu","year":"2024","journal-title":"Nat. Commun."},{"key":"sor5007_bb8","doi-asserted-by":"crossref","first-page":"1182","DOI":"10.1017\/S1431927603445911","volume":"9","author":"Mastronarde","year":"2003","journal-title":"Microsc. Microanal."},{"key":"sor5007_bb9","unstructured":"Nexperion. (2026). The SerialEM Script Repository. https:\/\/serialemscripts.nexperion.net\/category."},{"key":"sor5007_bb10","unstructured":"Seifer, S. (2026). Shadow Montage Scripts. https:\/\/github.com\/Pr4Et\/Supplementaries\/tree\/main\/Shadow_Montage."},{"key":"sor5007_bb11","unstructured":"Seifer, S., Dalaloyan, A., Kirchweger, P. & Elbaum, M. (2026). 4D-STEM Tilt-series of Mitochondria in U2OS Cell. https:\/\/zenodo.org\/doi\/10.5281\/zenodo.20544863."},{"key":"sor5007_bb12","doi-asserted-by":"crossref","first-page":"e00431","DOI":"10.1016\/j.ohx.2023.e00431","volume":"14","author":"Seifer","year":"2023","journal-title":"HardwareX"},{"key":"sor5007_bb13","doi-asserted-by":"crossref","first-page":"1476","DOI":"10.1017\/S1431927621012861","volume":"27","author":"Seifer","year":"2021","journal-title":"Microsc. Microanal."},{"key":"sor5007_bb14","doi-asserted-by":"crossref","first-page":"113936","DOI":"10.1016\/j.ultramic.2024.113936","volume":"259","author":"Seifer","year":"2024","journal-title":"Ultramicroscopy"},{"key":"sor5007_bb15","doi-asserted-by":"crossref","first-page":"ozaf126","DOI":"10.1093\/mam\/ozaf126","volume":"32","author":"Seifer","year":"2026","journal-title":"Microsc. Microanal."},{"key":"sor5007_bb16","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1093\/mam\/ozae050","volume":"30","author":"Seifer","year":"2024","journal-title":"Microsc. Microanal."},{"key":"sor5007_bb17","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1038\/s41524-022-00793-9","volume":"8","author":"Shi","year":"2022","journal-title":"npj Comput. Mater."},{"key":"sor5007_bb18","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1038\/nmeth.2842","volume":"11","author":"Wolf","year":"2014","journal-title":"Nat. Methods"},{"key":"sor5007_bb19","doi-asserted-by":"crossref","first-page":"e29929","DOI":"10.7554\/eLife.29929","volume":"6","author":"Wolf","year":"2017","journal-title":"eLife"},{"key":"sor5007_bb20","unstructured":"You, S., Varnavides, G., Khavnekar, S., Palatkin, N., Shao, S., Wu, M., Stroppa, D., Chernikova, D., Zhu, B., Egoavil, R., Vespucci, S., Ye, X., Schur, F. K. M., Spiecker, E. & Pelz, P. (2025). arXiv:2512.19460."},{"key":"sor5007_bb21","doi-asserted-by":"crossref","first-page":"2138","DOI":"10.1038\/s41592-025-02834-9","volume":"22","author":"Yu","year":"2025","journal-title":"Nat. Methods"}],"container-title":["Acta Crystallographica Section D Structural Biology"],"original-title":[],"link":[{"URL":"https:\/\/journals.iucr.org\/d\/issues\/2026\/10\/00\/sor5007\/sor5007.pdf","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.iucr.org\/d\/issues\/2026\/10\/00\/sor5007\/sor5007.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T09:19:37Z","timestamp":1792487977000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.iucr.org\/paper?S2059798326009630"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,23]]},"references-count":21,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2026,10]]}},"alternative-id":["S2059798326009630"],"URL":"https:\/\/doi.org\/10.1107\/s2059798326009630","relation":{"is-supplemented-by":[{"id-type":"uri","id":"https:\/\/github.com\/Pr4Et\/SavvyScan\/tree\/main\/Savvyscan%20on%20Red%20Pitaya","asserted-by":"subject"},{"id-type":"doi","id":"10.5281\/zenodo.20544863","asserted-by":"subject"}]},"ISSN":["2059-7983"],"issn-type":[{"value":"2059-7983","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9,23]]},"assertion":[{"value":"Acta Crystallographica Section D: Structural Biology","order":0,"name":"journal","label":"Publication","explanation":{"URL":"https:\/\/journals.iucr.org\/d"},"group":{"name":"general","label":"General"}},{"value":"research papers","order":1,"name":"content_type","label":"Content type","explanation":{"URL":"https:\/\/journals.iucr.org\/d\/services\/notesforauthors.html"},"group":{"name":"general","label":"General"}},{"value":"Available","URL":"https:\/\/scripts.iucr.org\/cgi-bin\/citedin?sor5007","order":2,"name":"article_metrics","label":"Article metrics","group":{"name":"general","label":"General"}},{"value":"Yes","order":0,"name":"peer_reviewed","label":"Peer reviewed","group":{"name":"peer_review","label":"Peer review"}},{"value":"Single blind","order":1,"name":"review_process","label":"Review process","group":{"name":"peer_review","label":"Peer review"}},{"value":"9 July 2026","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication history"}},{"value":"15 September 2026","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication history"}},{"value":"23 September 2026","order":2,"name":"published_online","label":"Published online","group":{"name":"publication_history","label":"Publication history"}},{"value":"This article has supporting information","name":"supplementary_materials","label":"Supplementary materials","explanation":{"URL":"https:\/\/scripts.iucr.org\/cgi-bin\/sendsup?sor5007"}},{"value":"\u00a9 2026 Seifer and Elbaum","order":0,"name":"copyright","label":"Copyright","explanation":{"URL":"https:\/\/journals.iucr.org\/services\/copyrightpolicy.html"},"group":{"name":"copyright_and_licencing","label":"Copyright and licencing"}},{"value":"Creative Commons Attribution (CC-BY)","order":1,"name":"license","label":"Licence","explanation":{"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/legalcode"},"group":{"name":"copyright_and_licencing","label":"Copyright and licencing"}}]}}