Elucidating how the nanometric structure of complex environments shapes the mesoscopic motion of the nano-objects within them is a fascinating but still open question. Due to a lack of knowledge of nanoscale details, diffusion properties are often described as anomalous. This applies to many systems, including the brain extracellular space that is the focus of this study. Its structure is indeed heterogeneous and tortuous, and ions, nutrients and signaling molecules diffuse in it for proper function of the brain.In recent years we have developed a strategy based on single-particle localization microscopy using SWIR emitting single-walled carbon nanotubes (SWCNTs) to decypher this brain compartment[1] but also pathological livers[2]. We now show that 3D tracking is essential to link the anomalous diffusion often observed at the macroscale to the local microscopic topologies of the edifices. We will present our recent results for the study of brain extracellular space [3], and other applicable structures including biophysical structures.