Home
WikiWelcome to the CiliaQ wiki! You are encountering problem with your own CiliaQ analysis or want to learn more about how to apply CiliaQ? See our Q&A section or follow one of our tutorials.
Please note that the CiliaQ wiki is a lively platform and more content and functions of the wiki will be realized.
We provide video tutorials on our CiliaQ YouTube Channel and written tutorials here in the Wiki. More tutorials will be developed soon - stay tuned!
- Installing the software and getting an overview about the CiliaQ workflow
- To install CiliaQ follow this guide
- Watch this video tutorial on YouTube
- Note: Since we generated the video, a new / better way to install the ImageJ 3D Suite has been become available. Please follow the guide for installing CiliaQ. The video tutorial, however, also introduces CiliaQ and thus, may still be helpful.
- CiliaQ Preparator - automatically segmenting cilia from background
- See the written tutorial (soon available)[
- Watch video tutorial on YouTube
- Extended tutorials:
- How to find good CiliaQ Preparator settings for your data set? Learn how you optimize CiliaQ Preparator settings to your image by following us while we search for good CiliaQ Preparator settings to obtain a good segmentation of cilia and background:
- CiliaQ Editor - editing segmentations
- See the written tutorial (soon available)
- Watch video tutorial on YouTube
- CiliaQ - detecting and quantifying cilia from the segmented image and visualizing results
- See the written tutorial
- Watch video tutorial on YouTube
- Understand the parameters and interpret the results with your own custom workflow or using CiliaQ Explorer
- Here we provide a written tutorial on the output parameters that you generate with CiliaQ, how to retrieve them from the output file, how they are calculated, and how they can be interpreted.
- Additionally, in 2025, we introduced CiliaQ Explorer, which can help you simply explore your results and perform quality control as well as statistics on them. For more details read Burgdorf et al., 2025 and see the CiliaQ Explorer github repository.
Try analyzing images with CiliaQ with our example data sets, providing images with instructions on how to analyze them.
We provide Questions & Answers for commonly asked questions to help you perform and optimize your CiliaQ analysis. If you want to submit additional questions of common interest, please let us know (e.g. by e-mail to: jan.hansen (at) uni-bonn.de).
Read this wikipost.
Read this related wikipost.
Read this related wikipost.
No, thanks to FIJI's inbuilt bioformats tool, CiliaQ can directly process raw microscopy files (e.g., .lif, .nd2, .czi) or .tif files. CiliaQ can process multi-channel, multi-z-plane (multi-slice), and/or multi-frame (time point) stacks and analyze cilium intensity across multiple channels in the image. It is optimal to run CiliaQ right on those raw files.
Read this wikipost
How to solve that the Plugin Installer throws a java.io.FileNotFoundException during installation of the CiliaQ plugins?
Read this wikipost
Read this wikipost
Most of my analyzed cilia show more than one branch - does this mean tracking of the cilia is incorrect?
Read this wikipost.
After CiliaQ analysis, some cilia are labeled with grey numbers in the 3D output file. For these cilia, no results appear in the output files. How can I retrieve the results for these cilia?
Read this wikipost.
Read this wikipost.
Read this wikipost.
Read this wikipost.
For some cilia, I obtain no cilium length value, with the # of found skeletons value equal to 0. Why? And how to fix it?
Read this wikipost (This answer also provides insight into how the cilium length is measured and why the cilium length measurements by CiliaQ may be a little bit shorter than manual measurements).
The detected ciliary objects (_RP_3D.tif file) are much wider and deformed compared to how I see the cilia in the image? Why?
Read this wikipost.
I am using non-confocal epifluorescence microscopy and get wrong length estimates. What could be the reason?
Read this related wikipost to see how to deal with off-focus blur in such images and set appropriate segmentation settings.
Read this related wikipost to see how to deal with off-focus blur in such images and set appropriate segmentation settings.
CiliaQ Preparator offers two segmentation styles:
Which one should I use when?
The advantage of using the option "Keep intensities above threshold" is useful to preserve intensity information in the mask that can be quantified by CiliaQ. To assess the output mask, you will however need to adjust the Look Up Table, since for the detected cilia the intensity information is kept in the mask (see Example how to do that).
Use the option creating a "binary image" if you don't need marker intensity measures, your background intensity level in the image is actually "0", or you use Leica microscopes with HyD detectors
If you don't need to read intensity information from the "reconstruction" / "marker" channel, you could use the "binary image" option, which makes it easier for you to scrutinize the mask generated by CiliaQ Preparator. Also, if your image background values are actually "0" (e.g., when using microscope's with noise-free detectors (e.g., Leica HyD detectors)), you should use the "binary image" option, since otherwise gaps in the marker staining may not be included in the mask if they have a zero intensity value.
How can I clean CiliaQ output data (e.g., delete false-positives such as mitotic spindles or cytokinetic bridges)?
Since Summer 2025, there is an additional plugin available that assists you in "cleaning" CiliaQ output files, i.e., removing false positives such as mitotic spindles or cytokinetic bridges in images resulting from stainings for acetylated tubulin as a cilia marker. The plugin was developed by the Pazour lab. Check out their publication for more details:
Jeffrey J Anuszczyk, Michael W Stuck, Thibaut Eguether, Gregory J Pazour. DeleteROI for Cleaning CiliaQ Output of Non-ciliary Contamination. MicroPubl Biol. 2025. Aug 14:2025. DOI: 10.17912/micropub.biology.001670
In 2025, we additionally introduced CiliaQ Explorer, a python based software to load CiliaQ output files, run automatic quality control, and create first overview plots and statistics. For more details see the STAR Protocols publication introducing CiliaQ Explorer:
Burgdorf D, Yüksel S, Sieckmann K, Hansen JN, Wachten D, Jurisch-Yaksi N. Protocol for measuring cilium length using 3D confocal fluorescence microscopy, CiliaQ software, and a quality control pipeline. STAR Protoc. 2025 Oct 8;6(4):104128. doi: 10.1016/j.xpro.2025.104128.