Jungfraujoch/docs/EXTERNAL_TEST_DATA_STILLS.md

External test data: serial crystallography (XFEL stills)

The serial datasets of the still battery (tools/battery/still_battery.py, manifest tools/battery/still_manifest.json). Like the rotation sets on External test data, they were collected by other people, on detectors and in file formats we do not produce ourselves, and published for exactly this kind of reuse. All of them come from the Coherent X-ray Imaging Data Bank (CXIDB).

None of these data were collected by us. If you use any of them, cite the dataset DOI below and the paper of the entry.

Where the values come from

• Dataset DOI: the CXIDB entry's own DOI, resolved against DataCite before it was written down.
• Space group, cell, resolution and R-free are the values deposited with the PDB entry, read from the RCSB data API. Every entry is a dark or ground state refined against observed data; entries refined against extrapolated structure factors (the time points of a pump-probe series) are not used, because a merge of the measured images cannot be compared with them.
• Images are the frames in the files we use, counted in the files themselves.

Datasets

Set	CXIDB, dataset DOI	Facility / beamline	Detector, format	PDB	Space group, dmin (Å)	Paper
sacla243	243, 10.11577/17003933	SACLA BL2	MPCCD, 8 panels of 1024 x 512, 50 µm; Cheetah-SACLA HDF5	31JT	P 2 21 21, 1.63	Bibi, De Vrieze et al., J. Am. Chem. Soc. (2026)
sacla237	237, 10.11577/2999572	SACLA BL2	MPCCD; Cheetah-SACLA HDF5	9S06	P 21 21 21, 2.05	Rios-Santacruz et al., Nature (2026)
sacla236	236, 10.11577/3014306	SACLA BL2	MPCCD; Cheetah-SACLA HDF5	9V3D	P 43 21 2, 1.68	Kang et al., J. Appl. Cryst. (2026)
pal86	86, 10.11577/1502065	PAL-XFEL NCI	Rayonix MX225-HS, 1440 x 1440, 156 µm; Cheetah CXI	6IG7	P 61 2 2, 1.80	Park et al., Sci. Rep. (2019)
pal90	90, 10.11577/1511590	PAL-XFEL NCI	Rayonix MX225-HS; Cheetah CXI	6IRK	I 2 2 2, 1.75	Lee et al., Sci. Rep. (2019)
lcls222	222, 10.11577/2204603	LCLS MFX	Rayonix MX340-HS, 1920 x 1920, 177 µm; LCLS-I XTC	8TDQ	P 65 2 2, 1.65	Nguyen et al., J. Am. Chem. Soc. (2023)
lcls242_s, lcls242_t	242, 10.11577/3374214	LCLS MFX	Rayonix MX340-HS; LCLS-I XTC	9O4S (small cell), 9O4T (large cell)	P 1 21 1, 1.95	Wolff et al., bioRxiv (2026)
euxfel83	83, 10.11577/1464102	European XFEL SPB/SFX	AGIPD 1M, 16 x (512 x 128), 200 µm; Cheetah CXI	6GTH	P 32 2 1, 1.69	Wiedorn et al., Nat. Commun. (2018)
euxfel152	152, 10.11577/1660970	European XFEL SPB/SFX	AGIPD 1M; Cheetah CXI	6U57	I 2 3, 2.80	Echelmeier et al., Nat. Commun. (2020)
alvra103, alvra103_int16	103, 10.11577/1650020	SwissFEL Alvra	JUNGFRAU 16M, 75 µm; SwissFEL HDF5, float32 keV (converted)	6S0L	C 2 2 21, 2.65	Nass et al., IUCrJ (2020)
alvra213, alvra213_int16	213, 10.11577/2282689	SwissFEL Alvra	JUNGFRAU 4M, 75 µm; SwissFEL HDF5, float32 keV (converted)	8BKH (dark state)	P 1 21 1, 1.35	Barends et al., Nature (2024)

The files we use

Paths are relative to the still data root of the site config (tools/battery/README.md). CXIDB serves https://cxidb.org/data/<entry>/...; most of it accepts HTTP range requests, so a broken download resumes with curl -C -.

Set	Files	Images	Size
sacla243	sacla_243/raw_all/run*.h5: all 87 files of 243/Complete_dark/	52,151	198 GB
sacla237	sacla_237/raw/: the 18 files run130637-0 to run130642-2 of 237/SACLA_raw/2022Nov/dark_ref/ (the dark reference; the time points are not used)	10,792	48 GB
sacla236	sacla_236/raw/: the 18 files run157084-0 to run157089-2 of 236/Data/lyso01-apo-bigXtal/	16,083	67 GB
pal86	pal_86/raw/, pal_86/raw_more/: CXIDB_86_themolysin_{2..25}_SFX_Nam.cxi (file 1 is truncated on the server and cannot be opened)	49,193	111 GB
pal90	pal_90/raw/: CXIDB_90-GI_SFX-filter-r000{1,2}-c00.cxi	11,947	25 GB
lcls222	lcls_222/xtc/, lcls_222/xtc_more/: mfx/mfxlu5017/xtc/e1277-r0165-{s00-c00,s00-c01,s01-c00,s01-c01,s02-c00}.xtc (run 165, the substrate-bound state of 8TDQ)	8,534	72 GB
lcls242_*	lcls_242/xtc/, lcls_242/xtc_more/: xtc/mfxl1013721-r0256 to r0267 streams (the two crystal forms are in every run; each set keeps its own form)	~90,000	~700 GB
euxfel83	euxfel_83/raw/: XFEL-r0243-c00.cxi, XFEL-r0278-c00.cxi, XFEL-r0280-c00.cxi (Cheetah hits, from the entry's cheetah-calib-mar-v1/hdf5/ tree on the NERSC archive); euxfel_83/ref/agipd_mar18_v10.geom from the entry	2,790	4.7 GB
euxfel152	euxfel_152/raw/: runs r0108, 0110, 0112, 0114, 0115, 0116, 0118, 0123, 0125 extracted from XFEL2042-runs-cxi.tar (range requests on the tar members); euxfel_152/ref/kdo_embedded.geom, the geometry embedded in the header of the entry's KDO8PS.stream	3,801	5.7 GB
alvra103	swissfel_103/raw/: Raw_Files/2018-08-07/a2a/run{10..24}.JF06T32V01.h5; swissfel_103/ref/jf-16M.geom from the entry	~11,000	~750 GB
alvra213	swissfel_213/raw/march_dark_MbCO_II-March-06/data/dark/run_*.JF06T08V01.h5, from march/march_dark_MbCO_II-March-06.tar.gz (425 GB; download it to disk and extract, a streamed extraction does not survive a broken connection); swissfel_213/ref/mbco_march.geom from the JUNGFRAU geometry template of 2019-MARCH-SwissFEL-MbCO-supplement.tar.gz	~38,000	~430 GB

The _int16 sets. The SwissFEL files store converted JUNGFRAU data as uncompressed float32 keV, 68 MB (JF16M) or 17 MB (JF4M) a frame, which caps reading at about 74 or 295 frames/s at 5 GB/s. The _int16 sets are copies with the same layout in which /data/data holds whole photons (keV divided by the photon energy, rounded) as int16 with bitshuffle/LZ4, about 25 times smaller; rugnux reads them with --gain 1 and merges them to the same numbers. Make them with tools/battery/still/float32_to_int16.py <in.h5> <out.h5> <photon energy keV> (h5py and hdf5plugin), into swissfel_103/conv/ (4.57 keV) and swissfel_213/conv/ (12.037 keV), named <input>_int16.h5.

Not in the battery

• Time points of pump-probe series (e.g. the light data of CXIDB 237 and 213): every deposited time point was refined against extrapolated structure factors.
• Raw JUNGFRAU data (ADC values with gain bits that need pedestal and gain correction, e.g. LCLS CXIDB 189 and 214): only converted detector data are read.