A set of three ImageJ plugins to quantify ciliary shape, length, and fluorescence in 2D, 3D, and 4D images. Scroll down for information on how to use, cite, report ideas, issues, improve CiliaQ. Visit our CiliaQ wiki with Tutorials and a Q&A section or try out CiliaQ using an example image.

The ImageJ plugins are published along:

Jan N. Hansen, Sebastian Rassmann, Birthe Stueven, Nathalie Jurisch-Yaksi, Dagmar Wachten. CiliaQ: a simple, open-source software for automated quantification of ciliary morphology and fluorescence in 2D, 3D, and 4D images. Eur. Phys. J. E 44, 18 (2021). https://doi.org/10.1140/epje/s10189-021-00031-y

Included tools (ImageJ plugins)

• CiliaQ_Preparator: An ImageJ plugin to preprocess and segment images for CiliaQ analysis.
• CiliaQ_Editor: An ImageJ plugin to edit the segmented channel in images output by CiliaQ_Preparator before analysis with CiliaQ.
• CiliaQ: An ImageJ plugin to quantify the ciliary shape, length, and fluorescence in images that were pre-processed with CiliaQ_Preparator (and eventually edited with CiliaQ_Editor).

Tools for post-hoc analysis of the output data

See our R scripts for combining results produced with CiliaQ.

How to cite?

When using any of the CiliaQ plugins, please cite:

Jan N. Hansen, Sebastian Rassmann, Birthe Stueven, Nathalie Jurisch-Yaksi, Dagmar Wachten. CiliaQ: a simple, open-source software for automated quantification of ciliary morphology and fluorescence in 2D, 3D, and 4D images. Eur. Phys. J. E 44, 18 (2021). https://doi.org/10.1140/epje/s10189-021-00031-y

Copyright notice and contacts

Copyright (C) 2017-2024: Jan N. Hansen.

CiliaQ has been developed in the research group Biophysical Imaging, Institute of Innate Immunity, Bonn, Germany (https://www.iiibonn.de/dagmar-wachten-lab/dagmar-wachten-lab-science).

The project was mainly funded by the DFG priority program SPP 1726 "Microswimmers".

Contact: jan.hansen (at) uni-bonn.de

Using CiliaQ

Getting started

For information on hardware and software requirements and a guide on how to get CiliaQ running on your computer, please follow the installation instructions in the CiliaQ Wiki.

User Guide / Manual

A very detailed User Guide for the whole CiliaQ pipeline is available here as a PDF. Please also take a look at the tutorials, instructions, examples, and Q&As in the CiliaQ wiki.

How to stay up-to-date?

You want to be always up-to-date about CiliaQ and get news on CiliaQ (new features, updates, etc.)? Watch this repository on GitHub (see Watch button on upper right) or send an email with "Subscribe CiliaQ" to jan.hansen (at) uni-bonn.de.

Ideas? Missing functions? Issues? Bugs? Unclear in the User Guide?

Are you missing a function or a parameter in CiliaQ? Is an explanation missing in the User Guide? Are you encountering problems with CiliaQ?

Please let us know and report this by submitting an issue using the issue tracking systems for the github repositories or sending a message to jan.hansen (at) uni-bonn.de:

• For asking questions or proposing ideas, e-mail to jan.hansen (at) uni-bonn.de or use our discussions page: CiliaQ Discussions
• For general issues, CiliaQ, and User Guide: CiliaQ issue system
• For issues concerning CiliaQ_Preparator only: CiliaQ_Preparator issue system
• For issues concerning CiliaQ_Editor only: CiliaQ_Editor issue system

Source code

The source code for the individual ImageJ plugins and java tools is available at the respective repositories:

• CiliaQ_Preparator
• CiliaQ_Editor
• CiliaQ

Licenses

The three CiliaQ plugins are published under the GNU General Public License v3.0.

Some CiliaQ plugins include packages developed by others, for which different licenses may apply:

• The packages ciliaQ_skeleton_analysis and ciliaQ_skeletonize3D in CiliaQ have been derived from the plugins AnalyzeSkeleton_ and Skeletonize3D_, respectively (Both: GNU General Public License, http://www.gnu.org/licenses/gpl.txt, author: Ignacio Arganda-Carreras).
• The package ciliaQ_jnh.volumeViewer3D in CiliaQ represents a customised version of the code from Volume Viewer 2.0 (author: Kai Uwe Barthel, date: 01.12.2012). Customised variants of the code are marked by additional comments. The original code was retrieved from https://github.com/fiji/Volume_Viewer, which is published under the license "Public Domain" in the software project FIJI.
• The package ciliaQ_Prep_jnh.canny3d-thresholder in CiliaQ Preparator represents a customized version of the canny3d-thresholder (GNU General Public License v3.0, author: Sebastian Rassmann, GitHub repository: https://github.com/sRassmann/canny3d-thresholder).
• The package ciliaQ_jnh.stern_library.optimization in CiliaQ contains a copied version of the HungarianAlgorithm implementation by Kevin L. Stern (copyrighted 2012) that is used as permitted by the very permissive terms printed in the file. The original code was retrieved in August 2024 from https://github.com/KevinStern/software-and-algorithms/blob/master/src/main/java/blogspot/software_and_algorithms/stern_library/optimization/HungarianAlgorithm.java.

Some functions of CiliaQ Preparator (Hysteresis thresholding, Canny3D) require additional installation of the '3D ImageJ Suite' to your ImageJ / FIJI distribution. The '3D ImageJ Suite' is licensed via a GPL - for license details visit the main page of the '3D ImageJ Suite'.

Publications featuring an analysis based on CiliaQ

CiliaQ is used around the globe! Here are some published studies with CiliaQ analyses:

• Hansen, J.N., Kaiser, F., et al. 2020. Nanobody-directed targeting of optogenetic tools to study signaling in the primary cilium. eLife 9:e57907. https://doi.org/10.7554/eLife.57907

  • Contains CiliaQ analysis of biosensor measurements with 3D live microscopy .

• Arveseth, C.D., Happ, J.T., et al. 2021. Smoothened transduces hedgehog signals via activity-dependent sequestration of PKA catalytic subunits. PLOS Biology 19(4): e3001191. https://doi.org/10.1371/journal.pbio.3001191

• Sun, J., Shin, D.Y., Eiseman, M. et al. 2021. SLITRK5 is a negative regulator of hedgehog signaling in osteoblasts. Nat Commun 12, 4611. https://dx.doi.org/10.1038/s41467-021-24819-w

• Ancel, J., Belgacemi, R., Diabasana, Z., et al. 2021. Impaired Ciliary Beat Frequency and Ciliogenesis Alteration during Airway Epithelial Cell Differentiation in COPD. Diagnostics 11(9):1579. https://doi.org/10.3390/diagnostics11091579

• D’Gama, P.P., et al. 2021. Diversity and function of motile ciliated cell types within ependymal lineages of the zebrafish brain. Cell Rep. 37. https://dx.doi.org/10.1016/j.celrep.2021.109775

• Hansen, J.N., et al. 2022. A cAMP signalosome in primary cilia drives gene expression and kidney cyst formation. EMBO Rep. e54315. https://dx.doi.org/10.15252/embr.202154315

  • Contains CiliaQ analysis of lots of confocal 3D stacks to detect phosphorylated CREB1 in cilia and biosensor measurements with 3D live microscopy.

• Dewees, S.I., et al. 2022. Phylogenetic profiling and cellular analyses of ARL16 reveal roles in traffic of IFT140 and INPP5E. Mol. Biol. Cell 33(4):ar33. https://dx.doi.org/10.1091/mbc.E21-10-0509-T

• Sheu, S.H., et al. 2022. A serotonergic axon-cilium synapse drives nuclear signaling to alter chromatin accessibility. Cell. 185(18):3390-3407.e18. https://dx.doi.org/10.1016/j.cell.2022.07.026

• Happ, J.T., et al. 2022. A PKA inhibitor motif within SMOOTHENED controls Hedgehog signal transduction. Nat. Struct. Mol. Biol. 29, 990–999. https://dx.doi.org/10.1038/s41594-022-00838-z

• Cho, et al. 2022. Islet primary cilia motility controls insulin secretion. Science Advances.

• Tsekitsidou, E., et al. 2023. Calcineurin associates with centrosomes and regulates cilia length maintenance. J Cell Sci 136 (8): jcs260353. https://doi.org/10.1242/jcs.260353

• Teerikorpi, et al. 2025. Ciliary biology intersects autism and congenital heart disease. Development 152 (12): dev204295. https://doi.org/10.1242/dev.204295

• Nitoiu, A., et al. 2025. Defective IFT57 underlies a novel cause of Bardet-Biedl syndrome. Hum. Mol. Genet. Volume 34, Issue 13, 1 July 2025, Pages 1108–1122. https://doi.org/10.1093/hmg/ddaf058

• Corral-Serrano, J.C., 2025. A novel recurrent ARL3 variant c.209G > A p.(Gly70Glu) causes variable non-syndromic dominant retinal dystrophy with defective lipidated protein transport in human retinal stem cell models. Hum. Mol. Genet., Volume 34, Issue 9, 1 May 2025, Pages 821–834. https://doi.org/10.1093/hmg/ddaf029

• Lange et al., 2025. A conserved mechanism for the retrieval of polyubiquitinated proteins from cilia. Cell. https://doi.org/10.1016/j.cell.2025.07.043

• Rezi, C.K., et al., 2025. KIF13B controls ciliary protein content by promoting endocytic retrieval and suppressing release of large extracellular vesicles from cilia. Curr. Biol.. https://doi.org/10.1016/j.cub.2025.08.022.

• Hansen, J.N., et al., 2025. Intrinsic Diversity In Primary Cilia Revealed Through Spatial Proteomics. Cell (Accepted). Preprint: https://www.biorxiv.org/content/10.1101/2024.10.20.619273

  • Contains CiliaQ analysis revealing the protein localization of 715 different proteins in over 100,000 cilia to cluster and detect ciliary microdomains.

• Your paper to be featured here? Let me know!