Data processing pipeline for serial femtosecond crystallography at SACLA.
A data processing pipeline for serial femtosecond crystallography at SACLA was developed, based onCheetah[Bartyet al.(2014).J. Appl. Cryst.47, 1118-1131] andCrystFEL[Whiteet al.(2016).J. Appl. Cryst.49, 680-689]. The original programs were adapted for data acquisition through the SACLA API, thread and inter-node parallelization, and efficient image handling. The pipeline consists of two stages: The first, online stage can analyse all images in real time, with a latency of less than a few seconds, to provide feedback on hit rate and detector saturation. The second, offline stage converts hit images into HDF5 files and runsCrystFELfor indexing and integration. The size of the filtered compressed output is comparable to that of a synchrotron data set. The pipeline enables real-time feedback and rapid structure solution during beamtime.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo , 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan.
Takanori
T
Nakane
Japan Synchrotron Radiation Research Institute , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan.
Yasumasa
Y
Joti
Japan Synchrotron Radiation Research Institute , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan.
Kensuke
K
Tono
Japan Synchrotron Radiation Research Institute , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan.
Makina
M
Yabashi
RIKEN SPring-8 Center , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.
Eriko
E
Nango
RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan; Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
So
S
Iwata
Department of Biological Sciences, Graduate School of Science, The University of Tokyo , 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan.
Ryuichiro
R
Ishitani
Department of Biological Sciences, Graduate School of Science, The University of Tokyo , 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan.
Osamu
O
Nureki
SACLA; parallelization; real-time processing; serial femtosecond crystallography; spot finding