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docs: credit the L test, FFT indexing, TORO, Niggli, peakfinder8 and SparseCCL

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Six methods the pages name or describe carried no citation: Padilla & Yeates
(the L test), Steller, Bolotovsky & Rossmann (the projection/FFT autoindexing
MOSFLM implements), TORO (what ffbidx implements), Krivy & Gruber and the
ITA lattice-character table (the reduction and Bravais assignment), Cheetah's
peakfinder8 (the per-ring background statistics of the adaptive finder) and
Hennequin et al.'s SparseCCL (already credited to traccc, now also to its
authors). Each gets its ACKNOWLEDGEMENT.md paragraph, a References entry in
CPU_DATA_ANALYSIS.md, and a one-line credit at the algorithm. The
Sheriff & Hendrickson / Popov & Bourenkov entry is re-scoped so each claim
sits on the paper that supports it - P&B 2003 is titled, and credited for the
sigma-aware anisotropy estimation its statistic modelling contains, not for
the tensor and its constraints. All DOIs verified against the publishers;
the SparseCCL DOI resolves to IEEE document 9049184 (IEEE blocks content
scraping, so verified by the resolved document id plus two independent
sources).

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
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@@ -19,7 +19,10 @@ experiments" (2025), [arXiv:2505.22822](https://arxiv.org/abs/2505.22822);
[traccc](https://github.com/acts-project/traccc). The CPU spot extractor adapts its SparseCCL source,
and the CUDA spot extractor follows the design of its GPU counterpart - a backward-neighbour graph
over a sorted hit list, resolved by a parallel union-find. traccc is MPL-2.0; see
[THIRD_PARTY_NOTICES.md](THIRD_PARTY_NOTICES.md).
[THIRD_PARTY_NOTICES.md](THIRD_PARTY_NOTICES.md). The SparseCCL algorithm itself is A. Hennequin,
B. Couturier, V. V. Gligorov and L. Lacassagne, "SparseCCL: Connected Components Labeling and
Analysis for sparse images" (2019), DASIP 2019, 65-70
[doi:10.1109/DASIP48288.2019.9049184](https://doi.org/10.1109/DASIP48288.2019.9049184).
This software uses Viridis, Magma and Inferno colormaps from Matplotlib under its BSD-compatible license
@@ -129,7 +132,12 @@ crystallography" (2023), Acta Cryst. D79, 449-461
**[MOSFLM](https://www.mrc-lmb.cam.ac.uk/mosflm/)** — the Rossmann FFT autoindexing algorithm and
post-refinement practice, including which parameters are safe to refine per image and which must be
refined over a wedge. A. G. W. Leslie and H. R. Powell, "Processing diffraction data with MOSFLM"
refined over a wedge. The autoindexing algorithm itself — projecting the reciprocal-space points
onto many directions and Fourier-transforming the 1D projection histograms — is I. Steller,
R. Bolotovsky and M. G. Rossmann, "An algorithm for automatic indexing of oscillation images using
Fourier analysis" (1997), J. Appl. Cryst. 30, 1036-1040
[doi:10.1107/S0021889897008777](https://doi.org/10.1107/S0021889897008777); MOSFLM is the
implementation whose practice is followed. A. G. W. Leslie and H. R. Powell, "Processing diffraction data with MOSFLM"
(2007), in *Evolving Methods for Macromolecular Crystallography*, NATO Science Series II, vol. 245,
41-51 [doi:10.1007/978-1-4020-6316-9_4](https://doi.org/10.1007/978-1-4020-6316-9_4);
T. G. G. Battye, L. Kontogiannis, O. Johnson, H. R. Powell and A. G. W. Leslie, "iMOSFLM: a new
@@ -144,12 +152,33 @@ region, the serial/stills processing model, and the per-frame indexing acceptanc
(`indexing_peak_check()` in `peaks.c`). T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass,
A. Barty and H. N. Chapman, "CrystFEL: a software suite for snapshot serial crystallography" (2012),
J. Appl. Cryst. 45, 335-341 [doi:10.1107/S0021889812002312](https://doi.org/10.1107/S0021889812002312).
The self-calibrating spot finder's per-resolution-ring background statistics, with the Bragg peaks
excluded by iterated clipping, follow Cheetah's peakfinder8: A. Barty, R. A. Kirian,
F. R. N. C. Maia, M. Hantke, C. H. Yoon, T. A. White and H. N. Chapman, "Cheetah: software for
high-throughput reduction and analysis of serial femtosecond X-ray diffraction data" (2014),
J. Appl. Cryst. 47, 1118-1131
[doi:10.1107/S1600576714007626](https://doi.org/10.1107/S1600576714007626).
**[fast-feedback-indexer](https://github.com/paulscherrerinstitute/fast-feedback-indexer)** — the
known-cell indexer for serial stills (`-X ffbidx`) is PSI's fast-feedback-indexer library, linked at
build time (BSD-3-Clause; see [THIRD_PARTY_NOTICES.md](THIRD_PARTY_NOTICES.md)), which implements
the TORO algorithm: 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](https://doi.org/10.1107/S1600576724003182).
**[GEMMI](https://github.com/project-gemmi/gemmi)** — symmetry operations, unit-cell and
structure-factor machinery, and MTZ / XDS_ASCII I/O. Vendored in `gemmi_gph/`, so it also carries a
licence obligation. M. Wojdyr, "GEMMI: A library for structural biology" (2022), J. Open Source
Softw. 7, 4200 [doi:10.21105/joss.04200](https://doi.org/10.21105/joss.04200).
**Křivý & Gruber's Niggli reduction, and the lattice-character table** — the reduction that puts
every candidate cell in a comparable form is I. Křivý and B. Gruber, "A unified algorithm for
determining the reduced (Niggli) cell" (1976), Acta Cryst. A32, 297-298
[doi:10.1107/S0567739476000636](https://doi.org/10.1107/S0567739476000636), used through GEMMI's
implementation; the table of lattice characters that maps a reduced cell to Bravais lattices and
centrings follows International Tables for Crystallography Vol. A, Table 9.2.5.1.
**Grosse-Kunstleve, Sauter & Adams's numerically stable cell reduction** - the magnitude-scaled
tolerance that decides the sign of a structurally-zero scalar product, and with it the Niggli type a
reduced cell is presented in. R. W. Grosse-Kunstleve, N. K. Sauter and P. D. Adams, "Numerically
@@ -176,6 +205,13 @@ Röttger and co-workers'. K. Röttger, A. Endriss, J. Ihringer, S. Doyle and W.
constants and thermal expansion of H2O and D2O ice Ih between 10 and 265 K" (1994), Acta Cryst. B50,
644-648 [doi:10.1107/S0108768194004933](https://doi.org/10.1107/S0108768194004933).
**The twinning L test** is Padilla and Yeates's: pairing each acentric reflection with a
symmetry-independent neighbour and reading the first and second moments of
L = (I1−I2)/(I1+I2) against their untwinned and perfect-twin values. J. E. Padilla and
T. O. Yeates, "A statistic for local intensity differences: robustness to anisotropy and
pseudo-centering and utility for detecting twinning" (2003), Acta Cryst. D59, 1124-1130
[doi:10.1107/S0907444903007947](https://doi.org/10.1107/S0907444903007947).
**Diffraction anisotropy** — the description of the overall fall-off by a single anisotropic
displacement tensor, its symmetry constraints, and the fact that only its deviatoric part is
determined (the isotropic part being degenerate with the overall scale) are Sheriff and Hendrickson's.