database [@Maia:2012] as CXIDB 58.

The data set consists of frames with an average signal level of photons/frame. For a virus, the speckles were around 100 pixels wide. The pixels were therefore binned by a factor of 4 in both dimensions after photon conversion to reduce computational costs. Excluding bad pixels and the central speckle, where the detetor was often saturated, there were photons/frame on average. There were on average 22.2 photons/speckle at the detector corner.

Diffraction patterns were recorded at a repetition rate of 120 Hz, however only a small fraction of the X-ray pulses interacted with an object. These so-called “hits” included not only interactions with PR772 virus particles but also with water droplets, multi-particle clusters, and patterns with detector artifacts. Such spurious patterns need to be excluded from analysis. In [@Reddy:2017], Reddy et al describes the classification of the single particle patterns using various machine learning methods, with the data for this study based on the classification by manifold embedding [@Yoon:2011] to obtain a data set consisting of single virus diffraction patterns.

\[sec:recon\_steps\]Reconstruction procedure
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The PR772 virus electron density was reconstructed in a two-step process, illustrated in Fig. \[fig:pipeline\] and detailed below. First, the orientations of 