Q&A: After CiliaQ, results for cilia labeled grey in the 3D output images are not output. Why?
Question: "Once I have finished running my images through CiliaQ, some of the cilia turn out grey in the 3D output file and I cannot see results for their IDs in the text-files provided. Do you know of a way to make sure all of the cilia are recognised?"
Answer provided on 06th of August 2021.
This problem relates to the following setting in CiliaQ:
Exclude options provided in the CiliaQ settings dialog.
By default "additionally exclude ... cilia touching x or y or z borders" is selected. This means that all detected 3D objects that touch the x,y, or z borders of the stack are excluded in the output. The numbers appearing in white/grey in the output 3D files have been touching the stack borders and thus been excluded. The numbers appearing in green in the 3D image are those that do not touch x,y, or z borders and thus are also reported in the output txt files.
Example 3D output files from CiliaQ, showing ciliary masks / skeletons labeled with green and white / grey IDs. Green IDs refer to cilia that do not touch stack borders and white/grey IDs refer to cilia that touch the stack borders and thus, are excluded from results txt-files under default settings. For example, the cilium with ID 13 was excluded because it touches the y border of the image. The cilium with ID 1 was excluded because it touches the z border of the image.
Original image provided by (c) J.N.Hansen.
Side note: CiliaQ considers cilia as touching the z borders of the images if parts of the ciliary mask are lying in the first or last slice of the image stack.
Examplary ...CQP_ed.tif image created in the CiliaQ workflow. Only the channel revealing the ciliary segmentations (cyan) is displayed. The first slice image is displayed, showing that some ciliary masks are touching the z border (arrows). Original image provided by (c) J.N.Hansen.
If you want to retrieve results also for cilia that touch the z borders, you can select "additionally exclude... cilia touching x or y borders". Then also cilia touching z borders will be reported in the output files.