  Modern Flash X-ray diffraction Imaging (FXI) acquires diffraction signals
from single biomolecules at a high repetition rate from X-ray Free Electron
Lasers (XFELs), easily obtaining millions of 2D diffraction patterns from a
single experiment. Due to the stochastic nature of FXI experiments and the
massive volumes of data, retrieving 3D electron densities from raw 2D
diffraction patterns is a challenging and time-consuming task.
  We propose a semi-automatic data analysis pipeline for FXI experiments, which
includes four steps: hit finding and preliminary filtering, pattern
classification, 3D Fourier reconstruction, and post analysis. We also include a
recently developed bootstrap methodology in the post-analysis step for
uncertainty analysis and quality control. To achieve the best possible
resolution, we further suggest using background subtraction, signal windowing,
and convex optimization techniques when retrieving the Fourier phases in the
post-analysis step.
  As an application example, we quantified the 3D electron structure of the
PR772 virus using the proposed data-analysis pipeline. The retrieved structure
was above the detector-edge resolution and clearly showed the
pseudo-icosahedral capsid of the PR772.
