Primary cilia are hair-like sensory
organelles whose dimensions
and location vary with cell type and culture condition. Herein, we
employed scanning ion conductance microscopy (SICM) to visualize the
topography of primary cilia from different cell types. By combining
SICM with fluorescence imaging, we successfully distinguished between
surface cilia that project outward from the cell surface and subsurface
cilia that are trapped below it. The nanoscale structure of the ciliary
pocket, which cannot be easily identified using a confocal fluorescence
microscope, was observed in SICM images. Furthermore, we developed
a topographic reconstruction method using current-distance profiles
to evaluate the relationship between set point and topographic image
and found that a low set point is important for detecting the true
topography of a primary cilium using hopping mode SICM