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
See our R scripts for combining results produced with CiliaQ.
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 (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
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.
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.
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.
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:
The source code for the individual ImageJ plugins and java tools is available at the respective repositories:
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:
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'.