A lot of our microstructural work is performed in concert with microrheological measurements using microscopic observations of colloidal tracer particles moving within a complex fluid.
The analysis of these movies is easy these days, thanks to people who developed a number of open and freely available routines to ease the initial steps:
Particle tracking microrheology is performed by many folks using IDL: Particle tracking using IDL
or Matlab routines: The Matlab Particle Tracking Code Repository
but a more recent Python setup has found great use in our group: Trackpy: Fast, Flexible Particle-Tracking Toolkit
David Pine gives an excellent introduction to using Python, and iPython notebooks here: Introduction to Scientific Python