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. 2020 Nov 4;10:19027. doi: 10.1038/s41598-020-75835-7

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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 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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Schematic of OBCA workflow. Each plugin/script in the workflow generates output data that can be further analyzed by one of the other plugins/scripts in the flow. The ImageJ Colocalization Image Creator generates new images enhanced for semi-automatic OBCA. The ImageJ Colocalization Object Counter enables semi-automatic OBCA, and generates data files with counts and colocalization information in comma separated value (csv) format. The Excel macro summarizes, organizes and exports the data in combined csv data files. The MATLAB script reads the data files and generates an interactive 3D reconstruction. All four plugins/scripts can function as stand-alone tools, or combined as desired.