leonarski_f
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* Rugnux: Several rotation sweeps of one crystal are merged as one dataset (`rugnux a_master.h5 b_master.h5`), on a common indexing and cell, with a non-isomorphous sweep left out and reported; `--sweeps separate` processes each sweep on its own. Bruker `.sfrm` frames and imgCIF files with a full goniometer axis chain are read. * Rugnux: More robust rotation processing - a retry with a more sensitive spot finder when no lattice is found, a self-consistent detector distance, long axes and doubled cells tested as hypotheses, a `-C` supercell multiple stepped down, and each ice ring merged, down-weighted or rejected on its own. * Rugnux: Serial stills are merged with a partiality-aware error model, reported as `ERROR_MODEL_A/B/C` with no ISa or R_merge/R_meas/R_pim; runs without `-S` have an overall intensity scale about 0.86-0.88 times that of earlier versions, with unchanged statistics. A second crystal form is left out of the merge and reported, the indexing ambiguity is resolved more reliably, and `--model` no longer influences processing. * Rugnux: The reported CC1/2 is the standard unweighted one, which can be lower than before on sweeps with weak frames; ISa comes with a 95% interval (`ISA_LOW`/`ISA_HIGH`). * Rugnux: Model refinement adds anisotropic/TLS, local NCS and twin refinement where R-free supports them; building waters and relabelling ions is now off by default (`--refine-solvent` turns it on). * NXmx: A detector of several modules is written as `module_0` ... `module_N` only, so DIALS reads each module as its own panel. * Other: JPEG previews use a bundled encoder (libjpeg-turbo no longer needed), Rugnux prints how to cite it, and the release archives contain the HTML documentation. Reviewed-on: #92 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
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Publications
How to cite
Rugnux — if you find Rugnux useful, please cite:
F. Leonarski and M. Wang, "Rugnux: from diffraction images to structure at synchrotrons and XFELs in one program" (2026), bioRxiv doi:10.64898/2026.10.24.761522.
Jungfraujoch — the primary citation is:
F. Leonarski, M. Brückner, C. Lopez-Cuenca, A. Mozzanica, H.-C. Stadler, Z. Matěj, A. Castellane, B. Mesnet, J. Wojdyla, B. Schmitt and M. Wang, "Jungfraujoch: hardware-accelerated data-acquisition system for kilohertz pixel-array X-ray detectors" (2023), J. Synchrotron Rad. 30, 227-234 doi:10.1107/S1600577522010268.
Work that relies on real-time serial crystallography, live indexing feedback or the system's full data rate should also cite:
J. Duan, H.-C. Stadler, J. Nan, Z. Matěj, G. Gotthard, F. Dworkowski, M. Bjelčić, O. Aurelius, A. Mozzanica, S. Grimm, M. Burian, T. Ursby, M. Wang and F. Leonarski, "Jungfraujoch: 38 GB s⁻¹ real-time serial crystallography – data acquisition and live indexing feedback" (2026), J. Appl. Cryst. 59, 1668-1677 doi:10.1107/S1600576726008083.
Data collected with Jungfraujoch and processed with Rugnux in the broker (Rugnux live mode) come out
of both programs, and the files jfjoch_writer writes from them name both: please cite both.
Rugnux
- F. Leonarski and M. Wang, "Rugnux: from diffraction images to structure at synchrotrons and XFELs in one program" (2026), bioRxiv doi:10.64898/2026.10.24.761522.
Jungfraujoch
- J. Duan, H.-C. Stadler, J. Nan, Z. Matěj, G. Gotthard, F. Dworkowski, M. Bjelčić, O. Aurelius, A. Mozzanica, S. Grimm, M. Burian, T. Ursby, M. Wang and F. Leonarski, "Jungfraujoch: 38 GB s⁻¹ real-time serial crystallography – data acquisition and live indexing feedback" (2026), J. Appl. Cryst. 59, 1668-1677 doi:10.1107/S1600576726008083 — the system at its full data rate, with live indexing feedback during serial data collection.
- P. Gasparotto, L. Barba, H.-C. Stadler, G. Assmann, H. Mendonça, A. W. Ashton, M. Janousch, F. Leonarski and B. Béjar, "TORO Indexer: a PyTorch-based indexing algorithm for kilohertz serial crystallography" (2024), J. Appl. Cryst. 57, 931-944 doi:10.1107/S1600576724003182 — the GPU indexing algorithm behind Jungfraujoch's real-time indexing.
- F. Leonarski, J. Nan, Z. Matěj, Q. Bertrand, A. Furrer, I. Gorgisyan, M. Bjelčić, M. Kepa, H. Glover, V. Hinger, T. Eriksson, A. Cehovin, M. Eguiraun, P. Gasparotto, A. Mozzanica, T. Weinert, A. Gonzalez, J. Standfuss, M. Wang, T. Ursby and F. Dworkowski, "Kilohertz serial crystallography with the JUNGFRAU detector at a fourth-generation synchrotron source" (2023), IUCrJ 10, 729-737 doi:10.1107/S2052252523008618 — serial crystallography at 2 kHz with a JUNGFRAU 4M and Jungfraujoch at the BioMAX beamline of MAX IV.
- F. Leonarski, M. Brückner, C. Lopez-Cuenca, A. Mozzanica, H.-C. Stadler, Z. Matěj, A. Castellane, B. Mesnet, J. Wojdyla, B. Schmitt and M. Wang, "Jungfraujoch: hardware-accelerated data-acquisition system for kilohertz pixel-array X-ray detectors" (2023), J. Synchrotron Rad. 30, 227-234 doi:10.1107/S1600577522010268 — the primary citation: the FPGA-accelerated acquisition system.
- F. Leonarski, A. Mozzanica, M. Brückner, C. Lopez-Cuenca, S. Redford, L. Sala, A. Babic, H. Billich, O. Bunk, B. Schmitt and M. Wang, "JUNGFRAU detector for brighter x-ray sources: Solutions for IT and data science challenges in macromolecular crystallography" (2020), Struct. Dyn. 7, 014305 doi:10.1063/1.5143480 — the data handling problem of the JUNGFRAU detector that Jungfraujoch was designed to solve.