Q&A: How are the cilia numbered in the output txt files?
Answer provided by Lilian Fu, in July 2021.
You may find the labelling of detected cilia in the output images confusing at first glance but understanding how CiliaQ assigns number IDs to each cilium might help. Since we are working with stacks of images that create a three-dimensional space CiliaQ scans the images along the three axes. For each image slice, it will first look for ciliary objects along the x-, then the y- and finally the z-axis. The detected cilia are numbered in that order.
Extracted image from an examplary ..._CQ_RP.tif file.