Single particle trajectories have revealed the dynamics of key channels and receptors at synapses, as they play a key role in shaping learning and memory. Statistical analysis coupled with stochastic modeling revealed the organization of subcellular compartments at a nanoscale resolution. We recently developed a model, analysis and the associated ImageJ software. This approach can be be applied to study diffusion and active motion. The biophysics properties can be extracted, leading often to high resolution heterogeneous mapping for the local protein distribution. In this workshop, I will present models and analysis of super-resolution trajectories as well as ImageJ plugin software. We will test it on neuronal membrane and also in sub-cellular networks such as the endoplasmic reticulum. We will present how the estimators are build and various fast algorithms to reconstruct potential wells and their geometrical organization. Reference: Parutto P, Heck J, Lu M, Kaminski C, Avezov E, Heine M, Holcman , High-throughput super-resolution single-particle trajectory analysis reconstructs organelle dynamics and membrane reorganization. D. Cell Rep Methods. 2022 Aug 22;2(8):100277. doi: 10.1016/j.crmeth.2022.100277