OnDA: online data analysis and feedback for serial X-ray imaging

Abstract

This article describes a free and open-source data analysis utility designed for fast online feedback during serial X-ray diffraction and scattering experiments: OnDA (online data analysis). Three complete real-time monitors for common types of serial X-ray imaging experiments are presented. These monitors are capable of providing the essential information required for quick decision making in the face of extreme rates of data collection. In addition, a set of modules, functions and algorithms that allow developers to modify the provided monitors or develop new ones are provided. The emphasis here is on simple, modular and scalable code that is based on open-source libraries and protocols. OnDA monitors have already proven to be invaluable tools in several experiments, especially for scoring and monitoring of diffraction data during serial crystallography experiments at both free-electron laser and synchrotron facilities. It is felt that in the future the kind of fast feedback that OnDA monitors provide will help researchers to deal with the expected very high throughput data flow at next-generation facilities such as the European X-ray free-electron laser.

Fast and accurate data collection for macromolecular crystallography using the JUNGFRAU detector

“…Researchers at the Paul Scherrer Institute are actively developing solutions to match the robustness and simplicity of operating HPC detectors. Such challenges are essentially the same for XFEL serial crystallography applications [39][40][41] .…”

Serial femtosecond X-ray diffraction of HIV-1 Gag MA-IP6 microcrystals at ambient temperature

“…Crystals were kept at 293 K before being introduced into the LCLS beam in a thin liquid jet using the coMESH injector ( Figure 3) at flow rates between 1-3 μ l/min. The sheath liquid contained the mother liquor, but added a 20% v/v of MPD, and was charged between 3-5 kV and flowrates varied between 1-3 μ l/min in order to maintain jet stability and maximize hit rate while monitoring with OnDa [39]. The 40 femtosecond X-rays pulses intercepted the continuous jet at 120 Hz, with a pulse energy between 2-3 mJ at a wavelength of 9.5 keV.…”

Processing serial crystallography data with CrystFEL: a step-by-step guide

“…For example, one file on disk might contain a single twodimensional image, or many two-dimensional images stacked together to form a three-dimensional array. The range of HDF5 layouts usable by CrystFEL has been described previously (White, Mariani et al, 2016) and includes the formats written by Cheetah (Barty et al, 2014), CASS (Foucar, 2016), OnDA (Mariani et al, 2016) and psocake (Shin et al, 2018), which all use their own layouts. The NeXus standard (Bernstein et al, 2014;Kö nnecke et al, 2015) is based on HDF5 and can also be used by CrystFEL.…”