MeV proton and alpha (helium ion) particle beams can now be focused to 20nm spot sizes, and ion/matter simulations using the DEEP computer code show that these resolutions are maintained through the top micrometre or so of organic material. In addition, the energy deposition profiles of the transmitted ions are laterally constrained to a few nanometers from the initial ion path. This paves the way for high resolution structural imaging of relatively thick biological material, e.g. biological cells. Examples are shown of high resolution structural imaging of whole biological cells (MRC5) using on-axis scanning transmission ion microscopy (STIM). Nanoparticles have the ability to cross the cell membrane, and may therefore prove useful as drug delivery probes. We show that the combination of on-axis STIM for imaging the cell interior, and off-axis STIM for imaging gold nanoparticles with enhanced contrast within the cell, represents a powerful set of ion beam techniques for tracking gold nanoparticles in biological cells. Whole cell imaging at high spatial resolutions represents a new area for nuclear microprobes.