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. 2021 Mar 8;44(2):18. doi: 10.1140/epje/s10189-021-00031-y

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© The Author(s) 2021

Open AccessThis 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. 2 — CiliaQ output parameters. For each reconstructed cilium, CiliaQ determines a–e structural parameters and f–k intensity parameters for up to two user-defined intensity channels. a Ciliary surface and ciliary volume. b Ciliary length. c Ciliary orientation vector, the vector pointing from the base to the tip of the cilium. d Ciliary bending index, determined as the ratio of ciliary length and the length of the orientation vector. e Ciliary shape complexity index, determined as the ratio of the ciliary surface and the surface of a sphere containing the ciliary volume. f Average, minimum, maximum, and standard deviation of the fluorescence intensity values of ciliary voxels. g Fluorescence intensity profile along the ciliary centerline. h Average fluorescence intensity along the ciliary centerline. i Integrated fluorescence intensity on the ciliary centerline. j Colocalized ciliary volume compared to background, determined as the ciliary volume comprising voxels with fluorescence intensities above an intensity threshold that is calculated based on the general background intensity level in the image. k Colocalized ciliary length, determined as the ciliary length in the intensity profile with intensities above an intensity threshold that is calculated as described for I