a set of noisy diffraction patterns of mostly identical objects in random orientations with variable incident fluence were determined to produce a 3D intensity volume using the EMC algorithm [@Loh:2009]. The three dimensional diffraction volume was then phased using a background-aware phase retrieval algorithm to arrive at the real-space electron density using a combination of the Difference Map [@Elser:2003] and Error Reduction [@Fienup:1978] algorithms.

![Reconstruction of the virus electron density from measured diffraction snapshots is a two step process. First, the orientations of a set of noisy diffraction patterns of mostly identical objects in random orientations with variable incident fluence (top left) are determined to produce a 3D intensity volume (top right). The three dimensional diffraction volume is then phased using a background-aware phase retrieval algorithm to arrive at the real space electron density (bottom). The electron density is shown as both an isosurface plot and a slice through the center of the object.[]{data-label="fig:pipeline"}](SPI_Pipeline.pdf){width="\columnwidth"}

\[sec:merging\_steps\]Alignment: Determining the 3D reciprocal space intensity distribution
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Orientation determination, alignment and scaling of the diffraction patterns into a 3D diffraction volume was performed using the *Dragonfly* software [@Ayyer:2016]. Data was provided to *Dragonfly* in photon counts since the pnCCD detector used in this experiment 