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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 are currently developing video tutorials and more written tutorials - stay tuned!

The CiliaQ workflow - running example data sets

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

How to find an appropriate segmentation method for my data sets?

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: Analysis of a 2D image acquired from cilia on cultured cells
• Example 2: Analysis of a 3D image acquired from cilia on cells in a tissue

Interpreting CiliaQ results / output parameters

Here we provide an overview about 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.

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 errors

• How to install a new version of a CiliaQ plugin?
• How to solve that the Plugin Installer throws a java.io.FileNotFoundException during installation of the CiliaQ plugins?

Q&As for CiliaQ

• Most of my analyzed cilia show more than one branch - does this mean tracking of the cilia is incorrect?
• 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?