What I wrote in my dissertation for how I quantified recovery after calcium switch assays: Percent recovery of junctional occludin/ZO-1 was measured by thresholding to the same percent of histogram, and the Skeletonize plug-in (Arganda-Carreras et al. 2010) was used to reduce signal to 1 pixel wide segments. Length of segments were measured, summed, and divided by total length of the cell junction to give percent recovery.
I only quantified the junctions between, in my case, two cells expressing the plasmid of interest.