Nanoparticles are detected as spots based on the fluorescence signal above the threshold and their size using Imaris’ built-in spots detector. Bigger spots were fit with multiple nanoparticles based on the size. Surfaces are detected using Imaris’ built-in surface detector. Cell bodies are detected using Imaris’ built-in surface detector­­­­­. For each detected surface, a Euclidean distance map is computed. In the distance map, each pixel contains its distance to the nearest surface edge. Then, the average distance to the surface edge for each spot by measuring the mean intensity around the spot in the Euclidean distance map was computed. Negative values represent objects inside the surface and positive values outside the surface. Nanoparticle agglomerates were fitted with several nanoparticles based on the nanoparticle size.

To run this code you need an Imaris license with XTension enabeled. This matlab code was tested on matlab 2019a. https://github.com/BIOP/EasyXT