The typical process for creating ICCs in the lab involves ionisation of an elemental source, followed by confinement in an ion trap, where they are imaged via their fluorescence. Changing parameters such as the axial or radial confining potentials may lead to different observed geometries of the crystal, even if the number of ions does not change. 
For measurements involving highly charged ions, these are typically observed as "dark" areas in the fluorescence of the Coulomb crystal, due to their different energy levels.  This effect is also noticeable when ions in the Coulomb crystal appear to disappear, without changing the structure of the crystal, due to mixing with impurities in a non-ideal vacuum. 
Heating effects are also important in the characterisation of Coulomb crystals, since thermal motion can cause the image to blur. This may be stimulated by the cooling laser being slightly off-resonance, and so needs to be carefully monitored.