Sometimes we might want to measure how far away spot-like structures are from an another structure. This could be distance of vesicles from the cell membrane or nucleus, or distance of cells from center of an organoid. There are likely other applications as well, but yours truly is a physicist and not a bioscientist. What is relevant that we can measure distances from smaller structures to other structures.  The more accurately the structures can be modeled in Imaris, the more accurate the estimation will be. Notably, exceedingly short distances are hard to quantify reliably so this method might not work well e.g. for interactions happening within the cell membrane where everything is squished together.   Also, the data should preferably be 3D data as Imaris handles that better than 2D data.

We have made a detailed Imaris manual for this method, allowing anyone to extract data from their images.