{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.bpr.2025.100211","article_type":"original","volume":5,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"OA_type":"gold","day":"11","scopus_import":"1","_id":"19795","publisher":"Elsevier","date_updated":"2025-06-10T07:38:14Z","ec_funded":1,"language":[{"iso":"eng"}],"status":"public","publication_status":"published","corr_author":"1","month":"06","quality_controlled":"1","abstract":[{"text":"Super-resolution microscopy often entails long acquisition times of minutes to hours. Since drifts during the acquisition adversely affect data quality, active sample stabilization is commonly used for some of these techniques to reach their full potential. Although drifts in the lateral plane can often be corrected after acquisition, this is not always possible or may come with drawbacks. Therefore, it is appealing to stabilize sample position in three dimensions (3D) during acquisition. Various schemes for active sample stabilization have been demonstrated previously, with some reaching sub-nanometer stability in 3D. Here, we present a scheme for active drift correction that delivers the nanometer-scale 3D stability demanded by state-of-the-art super-resolution techniques and is straightforward to implement compared to previous schemes capable of reaching this level of stabilization precision. Using a refined algorithm that can handle various types of reference structure, without sparse signal peaks being mandatory, we stabilized sample position to ∼1 nm in 3D using objective lenses both with high and low numerical aperture. Our implementation requires only the addition of a simple widefield imaging path and we provide an open-source control software with graphical user interface to facilitate easy adoption of the module. Finally, we demonstrate how this has the potential to enhance data collection for diffraction-limited and super-resolution imaging techniques using single-molecule localization microscopy and cryo-confocal imaging as showcases.","lang":"eng"}],"file":[{"checksum":"4018c833f25a3ad3b57e3577fed70334","file_id":"19802","file_name":"2025_BiophysicalReports_Vorlaufer.pdf","relation":"main_file","access_level":"open_access","file_size":7238179,"date_updated":"2025-06-10T07:24:46Z","success":1,"content_type":"application/pdf","creator":"dernst","date_created":"2025-06-10T07:24:46Z"}],"citation":{"ieee":"J. Vorlaufer <i>et al.</i>, “Image-based 3D active sample stabilization on the nanometer scale for optical microscopy,” <i>Biophysical Reports</i>, vol. 5, no. 2. Elsevier, 2025.","ama":"Vorlaufer J, Semenov N, Kreuzinger C, et al. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. <i>Biophysical Reports</i>. 2025;5(2). doi:<a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">10.1016/j.bpr.2025.100211</a>","apa":"Vorlaufer, J., Semenov, N., Kreuzinger, C., Javoor, M., Zens, B., Agudelo Duenas, N., … Danzl, J. G. (2025). Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. <i>Biophysical Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/10.1016/j.bpr.2025.100211</a>","ista":"Vorlaufer J, Semenov N, Kreuzinger C, Javoor M, Zens B, Agudelo Duenas N, Tavakoli M, Suplata M, Jahr W, Lyudchik J, Wartak A, Schur FK, Danzl JG. 2025. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. Biophysical Reports. 5(2), 100211.","short":"J. Vorlaufer, N. Semenov, C. Kreuzinger, M. Javoor, B. Zens, N. Agudelo Duenas, M. Tavakoli, M. Suplata, W. Jahr, J. Lyudchik, A. Wartak, F.K. Schur, J.G. Danzl, Biophysical Reports 5 (2025).","chicago":"Vorlaufer, Jakob, Nikolai Semenov, Caroline Kreuzinger, Manjunath Javoor, Bettina Zens, Nathalie Agudelo Duenas, Mojtaba Tavakoli, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” <i>Biophysical Reports</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">https://doi.org/10.1016/j.bpr.2025.100211</a>.","mla":"Vorlaufer, Jakob, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” <i>Biophysical Reports</i>, vol. 5, no. 2, 100211, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.bpr.2025.100211\">10.1016/j.bpr.2025.100211</a>."},"has_accepted_license":"1","department":[{"_id":"JoDa"},{"_id":"GradSch"},{"_id":"FlSc"},{"_id":"EM-Fac"}],"date_created":"2025-06-08T22:01:22Z","OA_place":"publisher","title":"Image-based 3D active sample stabilization on the nanometer scale for optical microscopy","project":[{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01","name":"CryoMinflux-guided in-situ molecular census and structure determination"},{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"},{"_id":"2668BFA0-B435-11E9-9278-68D0E5697425","grant_number":"LT00057","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration"}],"oa_version":"Published Version","oa":1,"date_published":"2025-06-11T00:00:00Z","DOAJ_listed":"1","file_date_updated":"2025-06-10T07:24:46Z","type":"journal_article","article_processing_charge":"Yes","issue":"2","intvolume":"         5","author":[{"full_name":"Vorlaufer, Jakob","first_name":"Jakob","last_name":"Vorlaufer","id":"937696FA-C996-11E9-8C7C-CF13E6697425"},{"full_name":"Semenov, Nikolai","last_name":"Semenov","first_name":"Nikolai","id":"e64d39c7-72ef-11ef-b75a-ee3046860d1b"},{"last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","full_name":"Kreuzinger, Caroline"},{"full_name":"Javoor, Manjunath","first_name":"Manjunath","last_name":"Javoor","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2"},{"orcid":"0000-0002-9561-1239","last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","full_name":"Zens, Bettina"},{"id":"40E7F008-F248-11E8-B48F-1D18A9856A87","first_name":"Nathalie","last_name":"Agudelo Duenas","full_name":"Agudelo Duenas, Nathalie"},{"full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854","last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","first_name":"Mojtaba"},{"full_name":"Suplata, Marek","first_name":"Marek","last_name":"Suplata","id":"EE8452B8-C26A-11E9-B157-E80CE6697425"},{"full_name":"Jahr, Wiebke","last_name":"Jahr","first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","first_name":"Julia","full_name":"Lyudchik, Julia"},{"first_name":"Andreas","last_name":"Wartak","id":"60aaa06c-3de5-11eb-9e53-baa88e955dcb","full_name":"Wartak, Andreas"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian Km","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian Km"},{"full_name":"Danzl, Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G"}],"publication_identifier":{"eissn":["2667-0747"]},"ddc":["570"],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"acknowledgement":"We acknowledge expert support by ISTA’s scientific service units, including the Miba Machine Shop, the Electron Microscopy Facility, and the Lab Support Facility. This work has been made possible in part by CZI grant DAF2021-234754 and grant DOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder DOI: https://doi.org/10.13039/100014989) (F.K.M.S. and J.G.D.). We further gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant DK W1232 (M.R.T. and J.G.D.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.L.); ISTA postdoctoral fellowship IST fellow (A.W.); and Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.).","article_number":"100211","year":"2025","publication":"Biophysical Reports"}