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. 2023 Oct 17;14:6543. doi: 10.1038/s41467-023-42085-w

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a A flow diagram of data processing with TomoBEAR. Blue boxes outline the steps that are performed fully automatically, orange boxes may require human intervention. The steps highlighted in magenta represent the functionality of live data processing. b, c an example of a.json configuration file that was used for processing the EMPIAR-10064 data set (results below). Panel B contains the “general” section and the steps for processing up to the refinement of gold fiducials. c contains modules for CTF estimation and correction, tomographic reconstruction, and template matching.