Pixel Imaging Mass Spectrometry is a new molecular imaging technique that relies on precision laser pulses to both align and strip molecules of their valence electrons thereby causing them to explode. By systematically collecting the fragments of the resulting coulomb explosion it is possible to reconstruct the structure of simple the parent molecules. For larger molecules the detailed simulation of the covariance maps reveals that they provide rich information about the parent molecular structure and fragmentation dynamics. However, due to the large number of fragment ions that are necessarily produced following Coulomb explosion of extended molecular structures and the correspondingly congested time-of-flight spectrum that results, alternative strategies are required to resolve structure of the parent molecule.

The underlying mathematical challenges of this problem that are unique to the pixel imaging mass spectrometer will be discussed, and a comparison of the forward model predictions with experimental data for the imaging of 3,5-dibromo-3',5'-difluoro-4'-cyanobiphenyl molecule will be presented. A brief survey of the established reconstruction methods for this type of problem will also be discussed.