The basal body detection does not always work, in particular for small cilia. This might be since the software searchers for basal body intensity within a radius of 3 micrometer around the ends of the skeleton. This radius could be reduced to better detect the correct basal body side in short cilia.
It would be useful to add a function for detecting the basal body based on a segmented channel or spot detection method and quantifying basal body parameters like the intensity in the different channels.
It could be also an option to add the basal body as the start of the ciliary intensity profile so that the transition zone would be mapped in the profile.
Some suggestions regarding basal bodies: