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. 2024 Oct 18;18:11779322241280431. doi: 10.1177/11779322241280431

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© The Author(s) 2024

This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (https://creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access page (https://us.sagepub.com/en-us/nam/open-access-at-sage).

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Figure 1. — Default workflow of detectCilia. 1. Image preparation: The original microscopy files are imported, and, if applicable, a maximum intensity z-stack projection is calculated. 2. Nuclei detection: The stained nuclei are segmented and counted using the mean area of a nucleus as an input parameter. 3. Cilia detection: Cilia are detected in the z-stack projection and every z-stack layer using the ratio of possible cilia pixels. Here, a primary cilium’s (expected) area is needed as an input parameter. 4. Cilia measurement: The information on all cilia (eg, lengths and heights) is collected, and the total lengths are calculated. The results are saved in a CSV file. (The images shown are sections of 190815_EV38_2_Collagen_ITSwithAsc+Dexa_63x_zstack_3.czi with enhanced brightness and contrast for better visualization.)