Coping with high data collection rate for data storage and analysis… The ID29 challenge

Start Date
23-05-2022 14:00
End Date
23-05-2022 15:00
Hybrid webinar (Zoom & ESRF Auditorium)
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Coordinator contact(s)
Kimberley Robert

Scientific contact(s)
Nicolas Coquelle


"Coping with high data collection rate for data storage and analysis… The ID29 challenge"

Monday, May 23rd, 02:00PM

Presented by Nicolas Coquelle, ESRF


This is a hybrid webinar so you can either join via zoom (link below) or come to the auditorium. The places in the auditorium are limited so it will be based on first come, first served.


Please click here to join the webinar:
Webinar ID: 936 4979 3508
Passcode: 457121



Serial crystallography is a technique which emerged within the last decade with the advent of X-ray free electron lasers (XFELs). In such technique, a single diffraction pattern is recorded from a crystal, usually presented to the X-ray beam by the means of jets (Chapman et al., 2011; Boutet et al, 2012). Shortly after, such a serial approach was successfully implemented at different synchrotron sources (Gati et al., 2014; Stellato et al., 2014; Coquelle et al., 2015); and with the recent ESRF upgrade, the new ID29 beamline has been built to perform serial synchrotron experiments (SSX) with different specific sample environments. The photon flux characteristics of ID29, combined with the Jungfrau 4M detector, offers the possibility to collect data at higher rates (up to 1kHz). Data storage as well as live data analysis remains quite challenging at such pace. A lossy compression algorithm has therefore been developed at ESRF by Jerome Kieffer, building from signal separation implemented in pyFAI (Kieffer & Wright, 2013). A short description of the algorithm will be presented, and its use in a typical phasing test case will be discussed. Also, from this compression algorithm, a Bragg-peak finder has been derived and has been implemented into NanoPeakCell (Coquelle et al, 2015), which is currently used during SSX experiments for online visualization and live feedback at MX beamlines. A description of the current capabilities of NanoPeakCell and potential developments will be presented as well.



Boutet et al., High-resolution protein structure determination by serial femtosecond crystallography. Science 337, 362–364 (2012).
Chapman et al., Femtosecond X-ray protein nanocrystallography. Nature 470, 73–77 (2011).
Coquelle et al., Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams. Acta Crystallogr. D Biol. Crystallogr. 71, 1184–1196 (2015).
Gati et al., Serial crystallography on in vivo grown microcrystals using synchrotron radiation. IUCrJ 1, 87–94 (2014).
Kieffer, J. & Wright, J. (2013). pyFAI, a Python library for high performance azimuthal integration on GPU. Powder Diffraction, 28(S2), S339–S350.
Stellato et al., Room-temperature macromolecular serial crystallography using synchrotron radiation. IUCrJ 1, 204–212 (2014).