TrackPy is a Python package for particle tracking in 2D, 3D and higher dimensions. It can be used at a range of length scales and applied to image stacks recorded using both light microscopy and electron microscopy.
NanoJ is an open-source toolbox for super-resolution microscopy data analysis. It encompasses several essential processing steps; spatiotemporal alignment of raw data (NanoJ-Core), super-resolution image reconstruction (NanoJ-SRRF), image quality assessment (NanoJ-SQUIRREL), structural modelling (NanoJ-VirusMapper) and control of the sample environment (NanoJ-Fluidics).
TRABI (temporal, radial-aperture-based intensity estimation) is a free ImageJ macro used for 3D processing of 2D single molecule microscopy data. Through intensity estimation in different regions of the emission pattern of single fluorophores, a relative 3D position can be determined from 2D data with no adaptation to the microscope.