{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/post-acquisition-image-based-compensation-for","title":"Post-acquisition image based compensation for thickness variation in microscopy section series","arxiv_id":"1411.6970","date":"2014-11-25","proceeding":null,"authors":["Philipp Hanslovsky","John A. Bogovic","Stephan Saalfeld"],"abstract":"Serial section Microscopy is an established method for volumetric anatomy\nreconstruction. Section series imaged with Electron Microscopy are currently\nvital for the reconstruction of the synaptic connectivity of entire animal\nbrains such as that of Drosophila melanogaster. The process of removing\nultrathin layers from a solid block containing the specimen, however, is a\nfragile procedure and has limited precision with respect to section thickness.\nWe have developed a method to estimate the relative z-position of each\nindividual section as a function of signal change across the section series.\nFirst experiments show promising results on both serial section Transmission\nElectron Microscopy (ssTEM) data and Focused Ion Beam Scanning Electron\nMicroscopy (FIB-SEM) series. We made our solution available as Open Source\nplugins for the TrakEM2 software and the ImageJ distribution Fiji.","url_abs":"http://arxiv.org/abs/1411.6970v2","url_pdf":"http://arxiv.org/pdf/1411.6970v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"post-acquisition-image-based-compensation-for","repo_url":"https://github.com/saalfeldlab/em-thickness-estimation","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"post-acquisition-image-based-compensation-for","repo_url":"https://github.com/saalfeldlab/z-spacing","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[{"task_slug":"anatomy","task_name":"Anatomy"},{"task_slug":null,"task_name":"Position"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}