X-ray free electron lasers present a brighter source of X-rays which opens up new techniques to protein crystallography. This includes time-resolved crystallography experiments, allowing us to probe very short time protein dynamics (on the order of tens of femtoseconds), and collecting higher resolution data on very small crystals which would not be achievable at a conventional synchrotron. However, the challenges facing free electron laser data processing are very different to synchrotron processing: namely that X-ray free electron lasers do not have any rotation of the crystal during data collection, and that all reflections are partially recorded. My DPhil has focused on a number of data processing problem which have been showcased in the software program cppxfel. Algorithms are being exported to other software suites.