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. 2020 Nov 11;11:5716. doi: 10.1038/s41467-020-19513-2

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© The Author(s) 2020

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — Timeline depicting the parallel execution of the processes of the TranSPHIRE pipeline. Timings are based on a Tc holotoxin data set consisting of 2053 micrographs, each containing 36 particles on average, collected at a speed of 188 micrographs per hour (K2 super-resolution, 40 frames). TranSPHIRE ran on-the-fly up to the creation of an ab initio 3D reconstruction using default settings. Important milestones are denoted in black: a first 2D class averages produced after 1.4 h; b end of the feedback loop after 7.3 h; c ab initio 3D reconstruction after 9.1 h; and d final 3D reconstruction of the first batch of particles after 15.5 h. Due to the internal scheduling of modern operating systems, and because not every TranSPHIRE thread is always working to capacity, the number of available CPUs (12/24 hyperthreading) and assigned TranSPHIRE threads (45) is not identical, and does not limit the speed of the computations.