Scientists at European XFEL conduct experiments that generate very large and complex datasets. The subsequent data analysis is challenging as scientists must combine their domain expertise with facility- and software-specific knowledge scattered across documentation, tools, and support channels. To address this problem, we designed and evaluated an agentic AI system tailored to the scientists' needs and integrated with the high-performance computing environment of European XFEL. Using a design science research approach, we conducted a rapid literature review, a systematic evaluation of 16 AI tools, multiple interviews, a focus group, and a user study with experts at European XFEL to develop and evaluate two prototypes. Our study identifies key knowledge challenges in scientific data analysis, derives requirements for an AI agent that supports knowledge retrieval and source code generation, and proposes design recommendations for a specialized system adaptable to the evolving AI tool landscape. These findings provide guidance for developing maintainable AI support in highly specialized scientific environments.

Structure determination of, e.g., single molecules is a key application of X-ray free-electron lasers (XFELs) and 4 th generation synchrotron sources, particularly using the coherent and pulsed X-ray radiation from XFELs. Scientific interest focuses on understanding the physical, biological, and chemical properties of samples at the nanometer scale. The X-rays from XFELs enable Coherent X-ray Diffraction Imaging (CXDI), where coherent X-rays irradiate a sample, and a far-field diffraction pattern is captured by an imaging detector. By the nature of the underlying physics, the resolution, at which the molecular structure of a sample can be probed with the CXDI technique, is limited by the wavelength of the X-ray radiation and the exposure time if a detector can record the diffraction pattern up to very large scattering angles. The resolution that can be achieved under real experimental conditions, depends strongly on additional parameters. The Shannon pixel size, linked to the detector resolution, the coherent dose that can be deposited in the sample without changing its structure, the image contrast, and the signal-to-noise ratio of the detected scattered radiation at high q , i.e., at high scattering angles 2Θ, have a strong influence on the resolution. The signal-to-noise ratio at high q defines the “effective” maximum solid angle in a specific experiment setup at which a detector can efficiently detect a signal and in consequence determines the achievable resolution. The image contrast defines how well bright image features can be distinguished from dark ones. We present the preliminary results of our study on the influence of the point spread function on the signal-to-noise ratio, image contrast, position resolution, and achievable sample resolution for different pixel sizes.

The European X-ray Free Electron Laser is a research facility located close to Hamburg, offering X-ray pulses with ultra-high brilliance and femtosecond duration at megahertz repetition rates. The detection systems necessary to unlock the full scientific potential made possible by this machine poses considerable challenges both in terms of data volume and rate, as well as the interpretation of their recorded signal. To provide optimal data quality, expert and detector-specific knowledge not easily accessible to external facility users is essential, and its implementation must cope with the generated volumes. We therefore aim to perform these preparatory processing steps and offer users a dataset suitable for further analysis as the primary data product. This work describes the machinery and workflows providing this data to users in an automatic, configurable and reproducible manner, both online during the experiment, and offline for scientific analysis afterward on the way to publication.

The European X-ray Free Electron Laser (European XFEL) is a cutting-edge user facility that generates per second up to 27,000 ultra-short, spatially coherent X-ray pulses within an energy range of 0.26 to more than 20 keV. Specialized instrumentation, including various 2D X-ray detectors capable of handling the unique time structure of the beam, is required. The one-megapixel AGIPD (AGIPD1M) detectors, developed for the European XFEL by the AGIPD Consortium, are the primary detectors used for user experiments at the SPB/SFX and MID instruments. The first AGIPD1M detector was installed at SPB/SFX when the facility began operation in 2017, and the second one was installed at MID in November 2018. The AGIPD detector systems require a dedicated infrastructure, well-defined safety systems, and high-level control procedures to ensure stable and safe operation. As of now, the AGIPD1M detectors installed at the SPB/SFX and MID experimental end stations are fully integrated into the European XFEL environment, including mechanical integration, vacuum, power, control, data acquisition, and data processing systems. Specific high-level procedures allow facilitated detector control, and dedicated interlock systems based on Programmable Logic Controllers ensure detector safety in case of power, vacuum, or cooling failure. The first 6 years of operation have clearly demonstrated that the AGIPD1M detectors provide high-quality scientific results. The collected data, along with additional dedicated studies, have also enabled the identification and quantification of issues related to detector performance, ensuring stable operation. Characterization and calibration of detectors are among the most critical and challenging aspects of operation due to their complex nature. A methodology has been developed to enable detector characterization and data correction, both in near real-time (online) and offline mode. The calibration process optimizes detector performance and ensures the highest quality of experimental results. Overall, the experience gained from integrating and operating the AGIPD detectors at the European XFEL, along with the developed methodology for detector characterization and calibration, provides valuable insights for the development of next-generation detectors for Free Electron Laser X-ray sources.

The European XFEL is a megahertz repetition-rate facility producing extremely bright and coherent pulses of a few tens of femtoseconds duration. The amount of data generated in the context of user experiments can exceed hundreds of gigabits per second, resulting in tens of petabytes stored every year. These rates and volumes pose significant challenges both for facilities and users thereof. In fact, if unaddressed, extraction and interpretation of scientific content will be hindered, and investment and operational costs will quickly become unsustainable. In this article, we outline challenges and solutions in data reduction.

Time-resolved X-ray absorption spectroscopy (tr-XAS) has been shown to be a versatile measurement technique for investigating non-equilibrium dynamics. Novel X-ray free electron laser (XFEL) facilities like the European XFEL offer increased repetition rates for stroboscopic XAS experiments through a burst operation mode, which enables measurements with up to 4.5 MHz. These higher repetition rates lead to higher data acquisition rates but can also introduce long-lived excitations that persist and thus build up during each burst. Here, we report on such long-lived effects in Ni and NiO thin film samples that were measured at the European XFEL. We disentangle the long-lived excitations from the initial pump-induced change and perform a detailed modelling-based analysis of how they modify transient X-ray spectra. As a result, we link the long-lived effects in Ni to a local temperature increase, as well as the effects in NiO to excited charge carrier trapping through polaron formation. In addition, we present possible correction methods, as well as discuss ways in which the effects of these long-lived excitations could be minimized for future time-resolved X-ray absorption spectroscopy measurements.

The European XFEL is a research facility that delivers extremely bright and short coherent X-ray pulses of tunable energy at MHz repetition rate, providing unprecedented capabilities to conduct scientific research across multiple domains. Among the suite of deployed detectors, several ePix100 modules, belonging to the family of ePix detectors developed at SLAC, are used. These charge-integrating hybrid pixel detectors offer single-photon resolution for energies above 2 keV and a dynamic range of 100 photons at 8 keV. Their low noise, small pixel size, compact dimensions, maneuverability and vacuum compatibility make them an attractive choice for some of the hard X-ray instruments at the European XFEL for imaging, spectroscopy, and scattering experiments. The European XFEL is committed to providing users with completely corrected detector data. To achieve this goal, periodic calibration procedures are conducted to generate calibration constants that allow the conversion of raw detector output into physically meaningful information through a series of successive data correction steps. In this work, an overview of the ePix100 calibration procedures and correction algorithms will be provided, with a focus on particularly relevant processes for this detector, such as common mode noise and charge sharing correction.

Femtosecond transient soft X-ray absorption spectroscopy (XAS) is a very promising technique that can be employed at X-ray free-electron lasers (FELs) to investigate out-of-equilibrium dynamics for material and energy research. Here, a dedicated setup for soft X-rays available at the Spectroscopy and Coherent Scattering (SCS) instrument at the European X-ray Free-Electron Laser (European XFEL) is presented. It consists of a beam-splitting off-axis zone plate (BOZ) used in transmission to create three copies of the incoming beam, which are used to measure the transmitted intensity through the excited and unexcited sample, as well as to monitor the incoming intensity. Since these three intensity signals are detected shot by shot and simultaneously, this setup allows normalized shot-by-shot analysis of the transmission. For photon detection, an imaging detector capable of recording up to 800 images at 4.5 MHz frame rate during the FEL burst is employed, and allows a photon-shot-noise-limited sensitivity to be approached. The setup and its capabilities are reviewed as well as the online and offline analysis tools provided to users.

The complex electronic structure of metallic ferromagnets is determined by a balance between exchange interaction, electron hopping leading to band formation, and local Coulomb repulsion. The interplay between the respective terms of the Hamiltonian is of fundamental interest, since it produces most, if not all, of the exotic phenomena observed in the solid state. By combining high energy and temporal resolution in femtosecond time-resolved X-ray absorption spectroscopy with ab initio time-dependent density functional theory we analyze the electronic structure in fcc Ni on the time scale of these interactions in a pump-probe experiment. We distinguish transient broadening and energy shifts in the absorption spectra, which we demonstrate to be caused by electron repopulation and correlation-induced modifications of the electronic structure, respectively. Importantly, the theoretical description of this experimental result hence requires to take the local Coulomb interaction into account, revealing a temporal interplay between band formation, exchange interaction, and Coulomb repulsion.

The advent of X-ray free-electron lasers (XFELs) has revolutionized fundamental science, from atomic to condensed matter physics, from chemistry to biology, giving researchers access to X-rays with unprecedented brightness, coherence and pulse duration. All XFEL facilities built until recently provided X-ray pulses at a relatively low repetition rate, with limited data statistics. Here, results from the first megahertz-repetition-rate X-ray scattering experiments at the Spectroscopy and Coherent Scattering (SCS) instrument of the European XFEL are presented. The experimental capabilities that the SCS instrument offers, resulting from the operation at megahertz repetition rates and the availability of the novel DSSC 2D imaging detector, are illustrated. Time-resolved magnetic X-ray scattering and holographic imaging experiments in solid state samples were chosen as representative, providing an ideal test-bed for operation at megahertz rates. Our results are relevant and applicable to any other non-destructive XFEL experiments in the soft X-ray range.

At the European XFEL, two undulator systems for hard and one for soft X-rays have been successfully put into operation [1]. The SASE3 soft X-ray undulator system generates linearly polarized radiation in the horizontal plane. One of the requirements for extending the radiation characteristics is the ability to obtain different polarization modes. These include both right and left circular, elliptical polarization, or linear polarization at an arbitrary angle. For this purpose, a system consisting of four APPLE X helical undulators developed at the Paul Scherrer Institute (PSI) is used [2, 3]. This paper presents the design parameters of the SASE3 undulator system after modifying it with the helical afterburner. It also describes the methods and the design solutions different from those used at PSI. The status and schedule of the project are introduced. PROJECT IMPLEMENTATION CONCEPT The SASE3 undulator system consists of 21 planar U68 variable-gap undulators, each 5 m long with a period of 68 mm. Depending on the energy of the electron beam (8.5 GeV 17.5 GeV), this system can generate radiation in the range from 0.24 keV to 4.6 keV. The purpose of modifying the SASE3 beamline is to enable the generation of soft X-rays with desired polarization. At European XFEL it was decided to use the method of obtaining a high degree of circular polarization using a reverse undulator tapering [4]. The essence of the idea is to use a micro bunched electron beam after a system of planar undulators and direct it into a system of helical undulators tuned to the resonant frequency, where it will emit powerful coherent radiation with controlled polarization. To achieve a high degree of, for instance, circular polarization, it is necessary to suppress or cut off the linear polarization generated by the planar undulators. Specifically, for this purpose, it is proposed to use the planar undulators in reverse tapering mode. In this mode, the bunching factor is approximately the same as for nontapered undulators, but the radiation power decreases by orders of magnitude. The results of a numerical 3D simulation using the FAST code [5] show that, for example, at a wavelength of 1.5 nm (0.83 keV), using the last 11 planar undulator cells with a total length of 55 meters, in the 2.1% reverse taper mode, the linearly polarized power reaches a value of 0.4 GW, while the bunching factor increases continuously. The power of circularly polarized radiation generated by a 10 m long helical undulator, located directly behind the system of linear undulators, increases very rapidly and reaches up to 155 GW. Hence, the degree of circular polarization reaches a value of ~99.9%. Similar results were obtained using a numerical three-dimensional SIMPLEX simulation [6]. Table 1 shows the simulation results for four wavelengths considering a helical afterburner of eightor twelve-meters composition length [7]. Table 1: Radiation Power, Generated by the Helical Afterburner at Circular and Linear Polarization Photon Energy Planar Undulators Helical afterburner length

The first DSSC 1-Mpixel camera became available at the European XFEL (EuXFEL) in the Hamburg area in February 2019. It was successfully tested, installed, and commissioned at the Spectroscopy and Coherent Scattering Instrument. DSSC is a high-speed, large-area, 2-D imaging detector system optimized for photon science applications in the energy range between 0.25 and 6 keV. The camera is based on direct conversion Si sensors and is composed of $1024 \times 1024$ pixels of hexagonal shape with a side length of $136~\mu \text{m}$ . The 256 application-specific integrated circuits (ASICs) provide full parallel readout, comprising analog filtering, digitization, and in-pixel data storage. In order to cope with the demanding X-ray pulse time structure of the EuXFEL, the DSSC provides a peak frame rate of 4.5 MHz. The first Mpixel camera is equipped with miniaturized silicon drift detector (MiniSDD) pixel arrays. The intrinsic response of the pixels and the linear readout limit the dynamic range but allow one to achieve noise values of about 60 electrons r.m.s. at the highest frame rate. The challenge of providing high-dynamic range (~104 photons/pixel/pulse) and single-photon detection simultaneously requires a nonlinear system front end, which will be obtained with the DEPFET active pixel technology foreseen for the advanced version of the camera. This technology will provide lower noise and a nonlinear response at the sensor level. This article describes the architecture of the whole detector system together with the main experimental results achieved up to now.

The ePix detector family provides multiple variants of hybrid pixel detectors to support a wide range of applications at free electron laser (FEL) facilities. The ePix detectors are by design versatile and easily re-configurable camera systems with common mechanical, electrical and data acquisition interfaces. Operation of detectors at FEL sources providing high brilliance, high repetition rate and ultra-short X-ray pulses poses a high risk of radiation damage to exposed detector components, such as the sensor and the readout Application Specific Integrated Circuit (ASIC). Knowledge about radiation-induced damage is important for understanding its influence on the quality of scientific data and the lifetime of the detector. We present the results of a systematic study of the influence of radiation-induced damage on the performance and lifetime of an ePix100a detector module using a direct attenuated beam of the European X-ray Free Electron Laser Facility (European XFEL) at 9 keV photon energy and average power of 10 μW. An area of 20 pixels×20 pixels was irradiated with an average photon flux of ≈ 7× 109 photons/s to a dose of approximately (760± 65) kGy at the location of the Si/SiO2 interfaces in the sensor. A dose dependent increase in both offset and noise of the ePix100a detector have been observed originating from an increase of the sensor leakage current. Moreover, we observed an effect directly after irradiation resulting in the saturation of individual pixels by their dark current. Changes in gain are evaluated one and half hours post-irradiation and suggest damage to occur also on the ASIC level. Based on the obtained results, thresholds for beam parameters are deduced and the detector lifetime is estimated with respect to the requirements to the data quality in order to satisfy the scientific standards defined by the experiments. We conclude the detector can withstand a beam with an energy up to 1 μJ at a photon energy of 9 keV impacting on an area of 1 mm2. The detector can be used without significant degradation of its performance for several years if the incident photon beam intensities do not exceed the detector's dynamic range by at least three orders of magnitude. Our results provide valuable input for the operation of the ePix100a detector at FEL facilities and the design of future detector technology.

The X-ray free-electron lasers that became available during the last decade, like the European XFEL (EuXFEL), place high demands on their instrumentation. Especially at low photon energies below 1 keV, detectors with high sensitivity, and consequently low noise and high quantum efficiency, are required to enable facility users to fully exploit the scientific potential of the photon source. A 1-Megapixel pnCCD detector with a 1024 × 1024 pixel format has been installed and commissioned for imaging applications at the Nano-Sized Quantum System (NQS) station of the Small Quantum System (SQS) instrument at EuXFEL. The instrument is currently operating in the energy range between 0.5 and 3 keV and the NQS station is designed for investigations of the interaction of intense FEL pulses with clusters, nano-particles and small bio-molecules, by combining photo-ion and photo-electron spectroscopy with coherent diffraction imaging techniques. The core of the imaging detector is a pn-type charge coupled device (pnCCD) with a pixel pitch of 75 µm × 75 µm. Depending on the experimental scenario, the pnCCD enables imaging of single photons thanks to its very low electronic noise of 3 e− and high quantum efficiency. Here an overview on the EuXFEL pnCCD detector and the results from the commissioning and first user operation at the SQS experiment in June 2019 are presented. The detailed descriptions of the detector design and capabilities, its implementation at EuXFEL both mechanically and from the controls side as well as important data correction steps aim to provide useful background for users planning and analyzing experiments at EuXFEL and may serve as a benchmark for comparing and planning future endstations at other FELs.

The European XFEL is a hard X-ray free-electron laser (FEL) based on a high-electron-energy superconducting linear accelerator. The superconducting technology allows for the acceleration of many electron bunches within one radio-frequency pulse of the accelerating voltage and, in turn, for the generation of a large number of hard X-ray pulses. We report on the performance of the European XFEL accelerator with up to 5,000 electron bunches per second and demonstrating a full energy of 17.5 GeV. Feedback mechanisms enable stabilization of the electron beam delivery at the FEL undulator in space and time. The measured FEL gain curve at 9.3 keV is in good agreement with predictions for saturated FEL radiation. Hard X-ray lasing was achieved between 7 keV and 14 keV with pulse energies of up to 2.0 mJ. Using the high repetition rate, an FEL beam with 6 W average power was created. The first operation of the European X-ray free-electron laser facility accelerator based on superconducting technology is reported. The maximum electron energy is 17.5 GeV. A laser average power of 6 W is achieved at a photon energy of 9.3 keV.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal suspension into the path of the XFEL, wasting a vast amount of sample due to the pulsed nature of all current XFEL sources. The European XFEL (EuXFEL) delivers femtosecond (fs) X-ray pulses in trains spaced 100 ms apart whereas pulses within trains are currently separated by 889 ns. Therefore, continuous sample delivery via fast jets wastes >99% of sample. Here, we introduce a microfluidic device delivering crystal laden droplets segmented with an immiscible oil reducing sample waste and demonstrate droplet injection at the EuXFEL compatible with high pressure liquid delivery of an SFX experiment. While achieving ~60% reduction in sample waste, we determine the structure of the enzyme 3-deoxy-D-manno-octulosonate-8-phosphate synthase from microcrystals delivered in droplets revealing distinct structural features not previously reported.