Q&A: When I run CiliaQ on a 2D image, the results files are missing results. Why?

Answer provided on 4th of March 2023.

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By default CiliaQ is set to "additionally exclude cilia touching x or y or z borders". Since in a 2D image all objects "touch" the z borders as it has just one plane, CiliaQ by default will exclude all cilia from the results file. The results file then looks e.g. as follows:

To circumvent exclusion of all cilia make sure that you modify the settings of the CiliaQ plugin to "exclude cilia touching x or y borders" only:

In turn, you will obtain results for all cilia in the image (except for those touching x or y borders). Alternatively, if desired to not exclude cilia touching x or y borders either, you may also select "additionally exclude nothing" to obtain results in 2D images.

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Note that the Q&A that you just read is similar to the following Q&A, which you may also want to read:

• 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?