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Welcome 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.

Tutorials

We provide video tutorials on our CiliaQ YouTube Channel and written tutorials here in the Wiki. More tutorials will be developed soon - stay tuned!

The CiliaQ workflow in steps

1. 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.
2. 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:
       • Example 1: A 2D image acquired from cilia on cultured cells
       • Example 2: A 3D image acquired from cilia on cells in a tissue
       • Example 3: A 3D image acquired from cilia in cell culture whose intensity largely varied (high background signals, low signal to noise ratio)
3. CiliaQ Editor - editing segmentations
   • See the written tutorial (soon available)
   • Watch video tutorial on YouTube
4. CiliaQ - detecting and quantifying cilia from the segmented image and visualizing results
   • See the written tutorial
   • Watch video tutorial on YouTube
5. Understand the parameters and interpret the results
   • 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.

Learning CiliaQ analysis - run an example data set

Try analyzing images with CiliaQ with our example data sets, providing images with instructions on how to analyze them.

Q&A: Question And Answer

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).

Q&As for installations and troubleshooting technical errors

How to install a specific version of a CiliaQ plugin?

Read this wikipost

How to solve that the Plugin Installer throws a java.io.FileNotFoundException during installation of the CiliaQ plugins?

Read this wikipost

How to solve java.lang.NullPointerException in CiliaQ Preparator?

Read this wikipost

Q&As for improving and understanding analyses with CiliaQ

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.

How are the cilia numbered in the output txt-files?

Read this wikipost.

How and when could I use a manual threshold in CiliaQ Preparator?

Read this wikipost.

When I run CiliaQ on a 2D image I cannot see a single cilium in the output results files. Why?

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.

What should I consider when I analyze images from a non-confocal fluorescent microscope?

Read this related wikipost to see how to deal with off-focus blur in such images and set appropriate segmentation settings.