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href="python_client/docs/DefaultApi.html#config-select-detector-get" class=md-nav__link ><strong>config_select_detector_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-select-detector-put" class=md-nav__link ><strong>config_select_detector_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-spot-finding-get" class=md-nav__link ><strong>config_spot_finding_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-spot-finding-put" class=md-nav__link ><strong>config_spot_finding_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-user-mask-get" class=md-nav__link ><strong>config_user_mask_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-user-mask-put" class=md-nav__link ><strong>config_user_mask_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-user-mask-tiff-get" class=md-nav__link ><strong>config_user_mask_tiff_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-user-mask-tiff-put" class=md-nav__link ><strong>config_user_mask_tiff_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-zeromq-metadata-get" class=md-nav__link ><strong>config_zeromq_metadata_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-zeromq-metadata-put" class=md-nav__link ><strong>config_zeromq_metadata_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-zeromq-preview-get" class=md-nav__link ><strong>config_zeromq_preview_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-zeromq-preview-put" class=md-nav__link ><strong>config_zeromq_preview_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#deactivate-post" class=md-nav__link ><strong>deactivate_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#detector-status-get" class=md-nav__link ><strong>detector_status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#fpga-status-get" class=md-nav__link ><strong>fpga_status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-clear-post" class=md-nav__link ><strong>image_buffer_clear_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-image-cbor-get" class=md-nav__link ><strong>image_buffer_image_cbor_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-image-jpeg-get" class=md-nav__link ><strong>image_buffer_image_jpeg_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-image-tiff-get" class=md-nav__link ><strong>image_buffer_image_tiff_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-start-cbor-get" class=md-nav__link ><strong>image_buffer_start_cbor_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-status-get" class=md-nav__link ><strong>image_buffer_status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-pusher-status-get" class=md-nav__link ><strong>image_pusher_status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#initialize-post" class=md-nav__link ><strong>initialize_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#pedestal-post" class=md-nav__link ><strong>pedestal_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#preview-pedestal-tiff-get" class=md-nav__link ><strong>preview_pedestal_tiff_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#preview-plot-bin-get" class=md-nav__link ><strong>preview_plot_bin_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#preview-plot-get" class=md-nav__link ><strong>preview_plot_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#result-scan-get" class=md-nav__link ><strong>result_scan_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#start-post" class=md-nav__link ><strong>start_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#statistics-calibration-get" class=md-nav__link ><strong>statistics_calibration_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#statistics-data-collection-get" class=md-nav__link ><strong>statistics_data_collection_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#statistics-get" class=md-nav__link ><strong>statistics_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#status-get" class=md-nav__link ><strong>status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#trigger-post" class=md-nav__link ><strong>trigger_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#version-get" class=md-nav__link ><strong>version_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#wait-till-done-post" class=md-nav__link ><strong>wait_till_done_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#wait-until-running-post" class=md-nav__link ><strong>wait_until_running_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#xfel-event-code-get" class=md-nav__link ><strong>xfel_event_code_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#xfel-pulse-id-get" class=md-nav__link ><strong>xfel_pulse_id_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/AzimIntSettings.html" class=md-nav__link >AzimIntSettings</a> <li class=md-nav__item > <a href="python_client/docs/BraggIntegrationSettings.html" class=md-nav__link >BraggIntegrationSettings</a> <li class=md-nav__item > <a href="python_client/docs/BrokerStatus.html" class=md-nav__link >BrokerStatus</a> <li class=md-nav__item > <a href="python_client/docs/CalibrationStatisticsInner.html" class=md-nav__link >CalibrationStatisticsInner</a> <li class=md-nav__item > <a href="python_client/docs/DarkMaskSettings.html" class=md-nav__link >DarkMaskSettings</a> <li class=md-nav__item > <a href="python_client/docs/DatasetSettings.html" class=md-nav__link >DatasetSettings</a> <li class=md-nav__item > <a href="python_client/docs/DatasetSettingsSmargon.html" class=md-nav__link >DatasetSettingsSmargon</a> <li class=md-nav__item > 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><strong>config_bragg_integration_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-dark-mask-get" class=md-nav__link ><strong>config_dark_mask_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-dark-mask-put" class=md-nav__link ><strong>config_dark_mask_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-detector-get" class=md-nav__link ><strong>config_detector_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-detector-put" class=md-nav__link ><strong>config_detector_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-file-writer-get" class=md-nav__link ><strong>config_file_writer_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-file-writer-put" class=md-nav__link ><strong>config_file_writer_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-image-format-conversion-post" class=md-nav__link ><strong>config_image_format_conversion_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-image-format-get" class=md-nav__link ><strong>config_image_format_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-image-format-put" class=md-nav__link ><strong>config_image_format_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-image-format-raw-post" class=md-nav__link ><strong>config_image_format_raw_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-indexing-get" class=md-nav__link ><strong>config_indexing_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-indexing-put" class=md-nav__link ><strong>config_indexing_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-instrument-get" class=md-nav__link ><strong>config_instrument_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-instrument-put" class=md-nav__link ><strong>config_instrument_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-internal-generator-image-put" class=md-nav__link ><strong>config_internal_generator_image_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-internal-generator-image-tiff-put" class=md-nav__link ><strong>config_internal_generator_image_tiff_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-mask-get" class=md-nav__link ><strong>config_mask_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-mask-tiff-get" class=md-nav__link ><strong>config_mask_tiff_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-roi-get" class=md-nav__link ><strong>config_roi_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-roi-put" class=md-nav__link ><strong>config_roi_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-select-detector-get" class=md-nav__link ><strong>config_select_detector_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-select-detector-put" class=md-nav__link ><strong>config_select_detector_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-spot-finding-get" class=md-nav__link ><strong>config_spot_finding_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-spot-finding-put" class=md-nav__link ><strong>config_spot_finding_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-user-mask-get" class=md-nav__link ><strong>config_user_mask_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-user-mask-put" class=md-nav__link ><strong>config_user_mask_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-user-mask-tiff-get" class=md-nav__link ><strong>config_user_mask_tiff_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-user-mask-tiff-put" class=md-nav__link ><strong>config_user_mask_tiff_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-zeromq-metadata-get" class=md-nav__link ><strong>config_zeromq_metadata_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-zeromq-metadata-put" class=md-nav__link ><strong>config_zeromq_metadata_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-zeromq-preview-get" class=md-nav__link ><strong>config_zeromq_preview_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-zeromq-preview-put" class=md-nav__link ><strong>config_zeromq_preview_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#deactivate-post" class=md-nav__link ><strong>deactivate_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#detector-status-get" class=md-nav__link ><strong>detector_status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#fpga-status-get" class=md-nav__link ><strong>fpga_status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-clear-post" class=md-nav__link ><strong>image_buffer_clear_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-image-cbor-get" class=md-nav__link ><strong>image_buffer_image_cbor_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-image-jpeg-get" class=md-nav__link ><strong>image_buffer_image_jpeg_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-image-tiff-get" class=md-nav__link ><strong>image_buffer_image_tiff_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-start-cbor-get" class=md-nav__link ><strong>image_buffer_start_cbor_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-status-get" class=md-nav__link ><strong>image_buffer_status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-pusher-status-get" class=md-nav__link ><strong>image_pusher_status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#initialize-post" class=md-nav__link ><strong>initialize_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#pedestal-post" class=md-nav__link ><strong>pedestal_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#preview-pedestal-tiff-get" class=md-nav__link ><strong>preview_pedestal_tiff_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#preview-plot-bin-get" class=md-nav__link ><strong>preview_plot_bin_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#preview-plot-get" class=md-nav__link ><strong>preview_plot_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#result-scan-get" class=md-nav__link ><strong>result_scan_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#start-post" class=md-nav__link ><strong>start_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#statistics-calibration-get" class=md-nav__link ><strong>statistics_calibration_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#statistics-data-collection-get" class=md-nav__link ><strong>statistics_data_collection_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#statistics-get" class=md-nav__link ><strong>statistics_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#status-get" class=md-nav__link ><strong>status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#trigger-post" class=md-nav__link ><strong>trigger_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#version-get" class=md-nav__link ><strong>version_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#wait-till-done-post" class=md-nav__link ><strong>wait_till_done_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#wait-until-running-post" class=md-nav__link ><strong>wait_until_running_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#xfel-event-code-get" class=md-nav__link ><strong>xfel_event_code_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#xfel-pulse-id-get" class=md-nav__link ><strong>xfel_pulse_id_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/Detector.html" class=md-nav__link >Detector</a> <li class=md-nav__item > <a href="python_client/docs/DetectorList.html" class=md-nav__link >DetectorList</a> <li class=md-nav__item > <a href="python_client/docs/DetectorListElement.html" class=md-nav__link >DetectorListElement</a> <li class=md-nav__item > <a href="python_client/docs/DetectorModule.html" class=md-nav__link >DetectorModule</a> <li class=md-nav__item > <a href="python_client/docs/DetectorModuleDirection.html" class=md-nav__link >DetectorModuleDirection</a> <li class=md-nav__item > <a href="python_client/docs/DetectorPowerState.html" class=md-nav__link >DetectorPowerState</a> <li class=md-nav__item > <a href="python_client/docs/DetectorSelection.html" class=md-nav__link >DetectorSelection</a> <li class=md-nav__item > <a href="python_client/docs/DetectorSettings.html" class=md-nav__link >DetectorSettings</a> <li class=md-nav__item > <a href="python_client/docs/DetectorState.html" class=md-nav__link >DetectorState</a> <li class=md-nav__item > <a href="python_client/docs/DetectorStatus.html" class=md-nav__link >DetectorStatus</a> <li class=md-nav__item > <a href="python_client/docs/DetectorTiming.html" class=md-nav__link >DetectorTiming</a> <li class=md-nav__item > <a href="python_client/docs/DetectorType.html" class=md-nav__link >DetectorType</a> <li class=md-nav__item > <a href="python_client/docs/ErrorMessage.html" class=md-nav__link >ErrorMessage</a> <li class=md-nav__item > <a 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class=md-nav__link >ImagePusherType</a> <li class=md-nav__item > <a href="python_client/docs/IndexingAlgorithm.html" class=md-nav__link >IndexingAlgorithm</a> <li class=md-nav__item > <a href="python_client/docs/IndexingSettings.html" class=md-nav__link >IndexingSettings</a> <li class=md-nav__item > <a href="python_client/docs/InstrumentMetadata.html" class=md-nav__link >InstrumentMetadata</a> <li class=md-nav__item > <a href="python_client/docs/IntegrationModel.html" class=md-nav__link >IntegrationModel</a> <li class=md-nav__item > <a href="python_client/docs/JfjochSettings.html" class=md-nav__link >JfjochSettings</a> <li class=md-nav__item > <a href="python_client/docs/JfjochStatistics.html" class=md-nav__link >JfjochStatistics</a> <li class=md-nav__item > <a href="python_client/docs/MeasurementStatistics.html" class=md-nav__link >MeasurementStatistics</a> <li class=md-nav__item > <a href="python_client/docs/PcieDevicesInner.html" class=md-nav__link >PcieDevicesInner</a> <li 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href="python_client/docs/RoiCircleList.html" class=md-nav__link >RoiCircleList</a> <li class=md-nav__item > <a href="python_client/docs/RoiDefinitions.html" class=md-nav__link >RoiDefinitions</a> <li class=md-nav__item > <a href="python_client/docs/RotationAxis.html" class=md-nav__link >RotationAxis</a> <li class=md-nav__item > <a href="python_client/docs/ScanResult.html" class=md-nav__link >ScanResult</a> <li class=md-nav__item > <a href="python_client/docs/ScanResultImagesInner.html" class=md-nav__link >ScanResultImagesInner</a> <li class=md-nav__item > <a href="python_client/docs/SpotFindingSettings.html" class=md-nav__link >SpotFindingSettings</a> <li class=md-nav__item > <a href="python_client/docs/StandardDetectorGeometry.html" class=md-nav__link >StandardDetectorGeometry</a> <li class=md-nav__item > <a href="python_client/docs/TcpSettings.html" class=md-nav__link >TcpSettings</a> <li class=md-nav__item > <a href="python_client/docs/UnitCell.html" class=md-nav__link >UnitCell</a> <li class=md-nav__item > <a href="python_client/docs/ZeromqMetadataSettings.html" class=md-nav__link >ZeromqMetadataSettings</a> <li class=md-nav__item > <a href="python_client/docs/ZeromqPreviewSettings.html" class=md-nav__link >ZeromqPreviewSettings</a> <li class=md-nav__item > <a href="python_client/docs/ZeromqSettings.html" class=md-nav__link >ZeromqSettings</a> </ul> </nav> </div> </div> </div> <div class="md-sidebar md-sidebar--secondary" data-md-component=toc > <div class=md-sidebar__scrollwrap > <div class=md-sidebar__inner > <nav class="md-nav md-nav--secondary"> <ul class=md-nav__list data-md-scrollfix=""> </ul> </nav> </div> </div> </div> <div class=md-content > <article class="md-content__inner md-typeset" role=main > <section class="tex2jax_ignore mathjax_ignore" id=acknowledgements > <h1 id=acknowledgement--page-root >Acknowledgements<a class=headerlink href="#acknowledgement--page-root" title="Link to this heading">¶</a></h1> <p>Citation: F. Leonarski, M. Bruckner, C. Lopez-Cuenca, A. Mozzanica, H.-C. Stadler, Z. Matej, 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 <a class="reference external" href="https://doi.org/10.1107/S1600577522010268">doi:10.1107/S1600577522010268</a>.</p> <p>The project is supported by :</p> <ul class=simple > <li><p>Innosuisse via Innovation Project “NextGenDCU high data rate acquisition system for X-ray detectors in structural biology applications” (101.535.1 IP-ENG; Apr 2023 - Sep 2025).</p> <li><p>ETH Domain via Open Research Data Contribute project (Jan - Dec 2023)</p> <li><p>AMD University Program with donation of licenses of Ethernet IP cores and Vivado software</p> </ul> <p>Decoding bitshuffle+LZ4 images on the GPU, rather than decompressing them on the host and uploading the result, follows Jon Wright (ESRF): “Experiences with GPU decompression for bitshuffle + LZ4 data”, HDF5 User Group meeting (2021), and <a class="reference external" href="https://github.com/jonwright/bslz4decoders">bslz4decoders</a>. The CUDA kernels in Jungfraujoch are its own, but the approach is his.</p> <p>Spot extraction groups strong pixels into spots with the sparse connected-component labelling of the ACTS traccc project: P. Gessinger, H. M. Gray, A. Krasznahorkay, C. Leggett, J. Niermann, A. Salzburger, S. N. Swatman and B. Yeo, “traccc: GPU track reconstruction library for HEP experiments” (2025), <a class="reference external" href="https://arxiv.org/abs/2505.22822">arXiv:2505.22822</a>; <a class="reference external" href="https://github.com/acts-project/traccc">traccc</a>. 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 <a class="reference internal" href=THIRD_PARTY_NOTICES.html ><span class="std std-doc">THIRD_PARTY_NOTICES.md</span></a>.</p> <p>This software uses Viridis, Magma and Inferno colormaps from Matplotlib under its BSD-compatible license</p> <section id=crystallographic-methods-adopted-from-other-packages > <h2 id=crystallographic-methods-adopted-from-other-packages >Crystallographic methods adopted from other packages<a class=headerlink href="#crystallographic-methods-adopted-from-other-packages" title="Link to this heading">¶</a></h2> <p>The analysis pipeline reimplements methods first published, and in most cases first implemented, by other crystallographic software. The code below is Jungfraujoch’s own; the methods are theirs, and are acknowledged here. Where a package’s source was consulted this is said explicitly. None of these packages is linked or vendored, with the single exception of GEMMI (see <a class="reference internal" href=THIRD_PARTY_NOTICES.html ><span class="std std-doc">THIRD_PARTY_NOTICES.md</span></a>).</p> <p><strong><a class="reference external" href="https://xds.mr.mpg.de/">XDS</a></strong> — rotation geometry and notation, the reciprocal Lorentz and partiality treatment, the maximum-likelihood mosaicity estimate, the <code class="docutils literal notranslate"><span class=pre >MINPK</span></code> criterion for rejecting a reflection whose predicted profile is not cleanly its own, the intensity-based test for a centred lattice, and the scaling correction surfaces indexed by image number and detector region. W. Kabsch, “XDS” (2010), Acta Cryst. D66, 125-132 <a class="reference external" href="https://doi.org/10.1107/S0907444909047337">doi:10.1107/S0907444909047337</a>; W. Kabsch, “Integration, scaling, space-group assignment and post-refinement” (2010), Acta Cryst. D66, 133-144 <a class="reference external" href="https://doi.org/10.1107/S0907444909047374">doi:10.1107/S0907444909047374</a>.</p> <p><strong>Profile fitting</strong> with reweighted, de-biased variances is the Kabsch/Otwinowski iteration, from the second XDS paper above and from Z. Otwinowski and W. Minor, “Processing of X-ray diffraction data collected in oscillation mode” (1997), Methods Enzymol. 276, 307-326 <a class="reference external" href="https://doi.org/10.1016/S0076-6879%2897%2976066-X">doi:10.1016/S0076-6879(97)76066-X</a>.</p> <p><strong><a class="reference external" href="https://dials.github.io/">DIALS</a></strong> — the resolution cutoff from the CC1/2 fall-off, per-observation outlier rejection at merge, the scaling error model, and the treatment of a reflection whose background is contaminated. Its published behaviour, and in places its source, settled several choices here. G. Winter, D. G. Waterman, J. M. Parkhurst et al., “DIALS: implementation and evaluation of a new integration package” (2018), Acta Cryst. D74, 85-97 <a class="reference external" href="https://doi.org/10.1107/S2059798317017235">doi:10.1107/S2059798317017235</a>; D. G. Waterman, G. Winter, R. J. Gildea et al., “Diffraction-geometry refinement in the DIALS framework” (2016), Acta Cryst. D72, 558-575 <a class="reference external" href="https://doi.org/10.1107/S2059798316002187">doi:10.1107/S2059798316002187</a>; J. Beilsten-Edmands, G. Winter, R. Gildea et al., “Scaling diffraction data in the DIALS software package: algorithms and new approaches for multi-crystal scaling” (2020), Acta Cryst. D76, 385-399 <a class="reference external" href="https://doi.org/10.1107/S2059798320003198">doi:10.1107/S2059798320003198</a>; J. M. Parkhurst, G. Winter, D. G. Waterman et al., “Robust background modelling in DIALS” (2016), J. Appl. Cryst. 49, 1912-1921 <a class="reference external" href="https://doi.org/10.1107/S1600576716013595">doi:10.1107/S1600576716013595</a>.</p> <p><strong><a class="reference external" href="https://www.ccp4.ac.uk/">POINTLESS</a></strong> (CCP4) — the space-group search. Stage A scores each candidate rotation operator by the correlation of I(h) with I(Rh) on <strong>resolution-normalised</strong> intensities (E²), as POINTLESS does — both arms of a symmetry pair sit at the same |s|, so on raw intensities the resolution fall-off is variance shared between them and lifts a false operator’s correlation as much as a true one’s; the screw-axis test scores a predicted-absent class against the rest of its own axial row rather than against a global mean or a fixed cut, and lets confidence fall away with the number of axial reflections instead of refusing below a count. P. Evans, “Scaling and assessment of data quality” (2006), Acta Cryst. D62, 72-82 <a class="reference external" href="https://doi.org/10.1107/S0907444905036693">doi:10.1107/S0907444905036693</a>; P. R. Evans, “An introduction to data reduction: space-group determination, scaling and intensity statistics” (2011), Acta Cryst. D67, 282-292 <a class="reference external" href="https://doi.org/10.1107/S090744491003982X">doi:10.1107/S090744491003982X</a>; P. R. Evans and G. N. Murshudov, “How good are my data and what is the resolution?” (2013), Acta Cryst. D69, 1204-1214 <a class="reference external" href="https://doi.org/10.1107/S0907444913000061">doi:10.1107/S0907444913000061</a>; J. Agirre, M. Atanasova, H. Bagdonas et al., “The CCP4 suite: integrative software for macromolecular crystallography” (2023), Acta Cryst. D79, 449-461 <a class="reference external" href="https://doi.org/10.1107/S2059798323003595">doi:10.1107/S2059798323003595</a>.</p> <p><strong><a class="reference external" href="https://www.mrc-lmb.cam.ac.uk/mosflm/">MOSFLM</a></strong> — 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” (2007), in <em>Evolving Methods for Macromolecular Crystallography</em>, NATO Science Series II, vol. 245, 41-51 <a class="reference external" href="https://doi.org/10.1007/978-1-4020-6316-9_4">doi:10.1007/978-1-4020-6316-9_4</a>; T. G. G. Battye, L. Kontogiannis, O. Johnson, H. R. Powell and A. G. W. Leslie, “iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM” (2011), Acta Cryst. D67, 271-281 <a class="reference external" href="https://doi.org/10.1107/S0907444910048675">doi:10.1107/S0907444910048675</a>; H. R. Powell, T. G. G. Battye, L. Kontogiannis, O. Johnson and A. G. W. Leslie, “Integrating macromolecular X-ray diffraction data with the graphical user interface iMosflm” (2017), Nat. Protoc. 12, 1310-1325 <a class="reference external" href="https://doi.org/10.1038/nprot.2017.037">doi:10.1038/nprot.2017.037</a>.</p> <p><strong><a class="reference external" href="https://www.desy.de/~twhite/crystfel/">CrystFEL</a></strong> — spot finding, the three-ring integration region, the serial/stills processing model, and the per-frame indexing acceptance test (<code class="docutils literal notranslate"><span class=pre >indexing_peak_check()</span></code> in <code class="docutils literal notranslate"><span class=pre >peaks.c</span></code>). 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 <a class="reference external" href="https://doi.org/10.1107/S0021889812002312">doi:10.1107/S0021889812002312</a>.</p> <p><strong><a class="reference external" href="https://github.com/project-gemmi/gemmi">GEMMI</a></strong> — symmetry operations, unit-cell and structure-factor machinery, and MTZ / XDS_ASCII I/O. Vendored in <code class="docutils literal notranslate"><span class=pre >gemmi_gph/</span></code>, so it also carries a licence obligation. M. Wojdyr, “GEMMI: A library for structural biology” (2022), J. Open Source Softw. 7, 4200 <a class="reference external" href="https://doi.org/10.21105/joss.04200">doi:10.21105/joss.04200</a>.</p> <p><strong>Hexagonal-ice ring positions</strong> — the eleven measured ring <span class="math notranslate nohighlight">\(d\)</span> spacings the ice-ring score, the ice-ring flagging and the ice calibrant are all built on are taken from the measurements of, not enumerated from a cell. D. W. Moreau, H. Atakisi and R. E. Thorne, “Ice in biomolecular cryocrystallography” (2021), Acta Cryst. D77, 540-554 <a class="reference external" href="https://doi.org/10.1107/S2059798321001170">doi:10.1107/S2059798321001170</a>.</p> <p><strong>Diffraction anisotropy</strong> — 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. The estimator fits that tensor to the observed intensity distribution, taking sigma(I) into account, in the sense of Popov and Bourenkov. The directional diffraction limits - <I/sigma(I)> in a cone about each principal direction, and the reporting of the anisotropic deltaB as the range of the principal components - follow AIMLESS. rugnux reports these; it corrects no intensity and removes no reflection on a directional criterion. S. Sheriff and W. A. Hendrickson, “Description of overall anisotropy in diffraction from macromolecular crystals” (1987), Acta Cryst. A43, 118-121 <a class="reference external" href="https://doi.org/10.1107/S010876738709977X">doi:10.1107/S010876738709977X</a>; A. N. Popov and G. P. Bourenkov, “Choice of data-collection parameters based on statistic modelling” (2003), Acta Cryst. D59, 1145-1153 <a class="reference external" href="https://doi.org/10.1107/S0907444903008163">doi:10.1107/S0907444903008163</a>; P. R. Evans and G. N. Murshudov, “How good are my data and what is the resolution?” (2013), Acta Cryst. D69, 1204-1214 <a class="reference external" href="https://doi.org/10.1107/S0907444913000061">doi:10.1107/S0907444913000061</a>.</p> <p><strong><a class="reference external" href="https://doi.org/10.1107/S0021889811041768">ANODE</a></strong> — reading the anomalous difference map at the atoms of a supplied model and reporting the strongest sites by name, instead of searching the map for blobs. The map itself is the textbook anomalous difference Fourier; what is taken from ANODE is that reading: A. Thorn and G. M. Sheldrick, “ANODE: anomalous and heavy-atom density calculation” (2011), J. Appl. Cryst. 44, 1285-1287 <a class="reference external" href="https://doi.org/10.1107/S0021889811041768">doi:10.1107/S0021889811041768</a>.</p> <p><strong>Data-quality statistics</strong> follow the established conventions rather than any one program: R_meas and R_pim, CC1/2 and CC*, and the reporting of I/sigma(I). K. Diederichs and P. A. Karplus, “Improved R-factors for diffraction data analysis in macromolecular crystallography” (1997), Nat. Struct. Biol. 4, 269-275 <a class="reference external" href="https://doi.org/10.1038/nsb0497-269">doi:10.1038/nsb0497-269</a>; P. A. Karplus and K. Diederichs, “Linking crystallographic model and data quality” (2012), Science 336, 1030-1033 <a class="reference external" href="https://doi.org/10.1126/science.1218231">doi:10.1126/science.1218231</a>; K. Diederichs and P. A. Karplus, “Better models by discarding data?” (2013), Acta Cryst. D69, 1215-1222 <a class="reference external" href="https://doi.org/10.1107/S0907444913001121">doi:10.1107/S0907444913001121</a>.</p> <p><strong>Uncertainty conventions</strong> follow the IUCr Commission on Crystallographic Nomenclature: D. Schwarzenbach, S. C. Abrahams, H. D. Flack et al., “Statistical descriptors in crystallography: Report of the IUCr Subcommittee on Statistical Descriptors” (1989), Acta Cryst. A45, 63-75 <a class="reference external" href="https://doi.org/10.1107/S0108767388009596">doi:10.1107/S0108767388009596</a>; D. Schwarzenbach, S. C. Abrahams, H. D. Flack, E. Prince and A. J. C. Wilson, “Statistical descriptors in crystallography. II. Report of a Working Group on Expression of Uncertainty in Measurement” (1995), Acta Cryst. A51, 565-569 <a class="reference external" href="https://doi.org/10.1107/S0108767395002340">doi:10.1107/S0108767395002340</a>.</p> </section> </section> </article> </div> </div> </main> </div> <footer class=md-footer > <div class=md-footer-nav > <nav class="md-footer-nav__inner md-grid"> <a href=index.html title="PSI Jungfraujoch" class="md-flex md-footer-nav__link md-footer-nav__link--prev" rel=prev > <div class="md-flex__cell md-flex__cell--shrink"> <i class="md-icon md-icon--arrow-back md-footer-nav__button"></i> </div> <div class="md-flex__cell md-flex__cell--stretch md-footer-nav__title"> <span class=md-flex__ellipsis > <span class=md-footer-nav__direction > "Previous" </span> PSI Jungfraujoch </span> </div> </a> <a href=LICENSE.html title=License class="md-flex md-footer-nav__link md-footer-nav__link--next" rel=next > <div class="md-flex__cell md-flex__cell--stretch md-footer-nav__title"><span class=md-flex__ellipsis > <span class=md-footer-nav__direction > "Next" </span> License </span> </div> <div class="md-flex__cell md-flex__cell--shrink"><i class="md-icon md-icon--arrow-forward md-footer-nav__button"></i> </div> </a> </nav> </div> <div class="md-footer-meta md-typeset"> <div class="md-footer-meta__inner md-grid"> <div class=md-footer-copyright > <div class=md-footer-copyright__highlight > © Copyright 2024, Paul Scherrer Institute. </div> Created using <a href="http://www.sphinx-doc.org/">Sphinx</a> 8.1.3. and <a href="https://github.com/bashtage/sphinx-material/">Material for Sphinx</a> </div> </div> </div> </footer> <script src="_static/javascripts/application.js"></script> <script>app.initialize({version: "1.0.4", url: {base: ".."}})</script> |