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The rapid growth of large-scale spatial gene expression data demands efficient and reliable computational tools to extract major trends of gene expression in their native spatial context. Here, we used stability-driven unsupervised learning (i.e., staNMF) to identify principal patterns (PPs) of 3D gene expression profiles and understand spatial gene distribution and anatomical localization at the whole mouse brain level. Our subsequent spatial correlation analysis systematically compared the PPs to known anatomical regions and ontology from the Allen Mouse Brain Atlas using spatial neighborhoods. We demonstrate that our stable and spatially coherent PPs, whose linear combinations accurately approximate the spatial gene data, are highly correlated with combinations of expert-annotated brain regions. These PPs yield a brain ontology based purely on spatial gene expression. Our PP identification approach outperforms principal component analysis and typical clustering algorithms on the same task. Moreover, we show that the stable PPs reveal marked regional imbalance of brainwide genetic architecture, leading to region-specific marker genes and gene coexpression networks. Our findings highlight the advantages of stability-driven machine learning for plausible biological discovery from dense spatial gene expression data, streamlining tasks that are infeasible by conventional manual approaches., Competing Interests: Competing interests statement:The authors declare no competing interest.

Improving the scalability of tissue imaging throughput with bright, coherent X-rays requires identifying and mitigating artifacts resulting from the interactions between X-rays and matter. At synchrotron sources, long-term imaging of soft tissues in solution can result in gas bubble formation or cavitation, which dramatically compromises image quality and integrity of the samples. By combining in-line phase-contrast imaging with gas chromatography in real time, we were able to track the onset and evolution of high-energy X-ray-induced gas bubbles in ethanol-embedded soft tissue samples for tens of minutes (two to three times the typical scan times). We demonstrate quantitatively that vacuum degassing of the sample during preparation can significantly delay bubble formation, offering up to a twofold improvement in dose tolerance, depending on the tissue type. However, once nucleated, bubble growth is faster in degassed than undegassed samples, indicating their distinct metastable states at bubble onset. Gas chromatography analysis shows increased solvent vaporization concurrent with bubble formation, yet the quantities of dissolved gasses remain unchanged. By coupling features extracted from the radiographs with computational analysis of bubble characteristics, we uncover dose-controlled kinetics and nucleation site-specific growth. These hallmark signatures provide quantitative constraints on the driving mechanisms of bubble formation and growth. Overall, the observations highlight bubble formation as a critical yet often overlooked hurdle in upscaling X-ray imaging for biological tissues and soft materials and we offer an empirical foundation for their understanding and imaging protocol optimization. More importantly, our approaches establish a top-down scheme to decipher the complex, multiscale radiation-matter interactions in these applications., (open access.)

Atomically thin layered van der Waals heterostructures feature exotic and emergent optoelectronic properties. With growing interest in these novel quantum materials, the microscopic understanding of fundamental interfacial coupling mechanisms is of capital importance. Here, using multidimensional photoemission spectroscopy, we provide a layer- and momentum-resolved view on ultrafast interlayer electron and energy transfer in a monolayer-WSe 2 /graphene heterostructure. Depending on the nature of the optically prepared state, we find the different dominating transfer mechanisms: while electron injection from graphene to WSe 2 is observed after photoexcitation of quasi-free hot carriers in the graphene layer, we establish an interfacial Meitner-Auger energy transfer process following the excitation of excitons in WSe 2 . By analysing the time-energy-momentum distributions of excited-state carriers with a rate-equation model, we distinguish these two types of interfacial dynamics and identify the ultrafast conversion of excitons in WSe 2 to valence band transitions in graphene. Microscopic calculations find interfacial dipole-monopole coupling underlying the Meitner-Auger energy transfer to dominate over conventional Förster- and Dexter-type interactions, in agreement with the experimental observations. The energy transfer mechanism revealed here might enable new hot-carrier-based device concepts with van der Waals heterostructures., (© 2023. Springer Nature Limited.)

Singlet fission 1-13 may boost photovoltaic efficiency 14-16 by transforming a singlet exciton into two triplet excitons and thereby doubling the number of excited charge carriers. The primary step of singlet fission is the ultrafast creation of the correlated triplet pair 17 . Whereas several mechanisms have been proposed to explain this step, none has emerged as a consensus. The challenge lies in tracking the transient excitonic states. Here we use time- and angle-resolved photoemission spectroscopy to observe the primary step of singlet fission in crystalline pentacene. Our results indicate a charge-transfer mediated mechanism with a hybridization of Frenkel and charge-transfer states in the lowest bright singlet exciton. We gained intimate knowledge about the localization and the orbital character of the exciton wave functions recorded in momentum maps. This allowed us to directly compare the localization of singlet and bitriplet excitons and decompose energetically overlapping states on the basis of their orbital character. Orbital- and localization-resolved many-body dynamics promise deep insights into the mechanics governing molecular systems 18-20 and topological materials 21-23 ., (© 2023. The Author(s).)

Hybrid plasmonic devices involve a nanostructured metal supporting localized surface plasmons to amplify light-matter interaction, and a non-plasmonic material to functionalize charge excitations. Application-relevant epitaxial heterostructures, however, give rise to ballistic ultrafast dynamics that challenge the conventional semiclassical understanding of unidirectional nanometal-to-substrate energy transfer. Epitaxial Au nanoislands are studied on WSe 2 with time- and angle-resolved photoemission spectroscopy and femtosecond electron diffraction: this combination of techniques resolves material, energy, and momentum of charge-carriers and phonons excited in the heterostructure. A strong non-linear plasmon-exciton interaction that transfers the energy of sub-bandgap photons very efficiently to the semiconductor is observed, leaving the metal cold until non-radiative exciton recombination heats the nanoparticles on hundreds of femtoseconds timescales. The results resolve a multi-directional energy exchange on timescales shorter than the electronic thermalization of the nanometal. Electron-phonon coupling and diffusive charge-transfer determine the subsequent energy flow. This complex dynamics opens perspectives for optoelectronic and photocatalytic applications, while providing a constraining experimental testbed for state-of-the-art modelling., (© 2023 The Authors. Advanced Materials published by Wiley-VCH GmbH.)

The electronic band structure and crystal structure are the two complementary identifiers of solid-state materials. Although convenient instruments and reconstruction algorithms have made large, empirical, crystal structure databases possible, extracting the quasiparticle dispersion (closely related to band structure) from photoemission band mapping data is currently limited by the available computational methods. To cope with the growing size and scale of photoemission data, here we develop a pipeline including probabilistic machine learning and the associated data processing, optimization and evaluation methods for band-structure reconstruction, leveraging theoretical calculations. The pipeline reconstructs all 14 valence bands of a semiconductor and shows excellent performance on benchmarks and other materials datasets. The reconstruction uncovers previously inaccessible momentum-space structural information on both global and local scales, while realizing a path towards integration with materials science databases. Our approach illustrates the potential of combining machine learning and domain knowledge for scalable feature extraction in multidimensional data., (© 2022. The Author(s).)

Technological advancements in X-ray imaging using bright and coherent synchrotron sources now allows the decoupling of sample size and resolution while maintaining high sensitivity to the microstructures of soft, partially dehydrated tissues. The continuous developments in multiscale X-ray imaging resulted in hierarchical phase-contrast tomography, a comprehensive approach to address the challenge of organ-scale (up to tens of centimeters) soft tissue imaging with resolution and sensitivity down to the cellular level. Using this technique, we imaged ex vivo an entire human left lung at an isotropic voxel size of 25.08 μm along with local zooms down to 6.05-6.5 μm and 2.45-2.5 μm in voxel size. The high tissue contrast offered by the fourth-generation synchrotron source at the European Synchrotron Radiation Facility reveals the complex multiscale anatomical constitution of the human lung from the macroscopic (centimeter) down to the microscopic (micrometer) scale. The dataset provides comprehensive organ-scale 3D information of the secondary pulmonary lobules and delineates the microstructure of lung nodules with unprecedented detail., (© 2022. The Author(s).)

Fermi surface is at the heart of our understanding of metals and strongly correlated many-body systems. An abrupt change in the Fermi surface topology, also called Lifshitz transition, can lead to the emergence of fascinating phenomena like colossal magnetoresistance and superconductivity. While Lifshitz transitions have been demonstrated for a broad range of materials by equilibrium tuning of macroscopic parameters such as strain, doping, pressure, and temperature, a nonequilibrium dynamical route toward ultrafast modification of the Fermi surface topology has not been experimentally demonstrated. Combining time-resolved multidimensional photoemission spectroscopy with state-of-the-art TDDFT+ U simulations, we introduce a scheme for driving an ultrafast Lifshitz transition in the correlated type-II Weyl semimetal T d -MoTe 2 We demonstrate that this nonequilibrium topological electronic transition finds its microscopic origin in the dynamical modification of the effective electronic correlations. These results shed light on a previously unexplored ultrafast scheme for controlling the Fermi surface topology in correlated quantum materials., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).)

Upscaling X-ray nanoimaging to macroscopic specimens has the potential for providing insights across multiple length scales, but its feasibility has long been an open question. By combining the imaging requirements and existing proof-of-principle examples in large-specimen preparation, data acquisition and reconstruction algorithms, the authors provide imaging time estimates for howX-ray nanoimaging can be scaled to macroscopic specimens. To arrive at this estimate, a phase contrast imaging model that includes plural scattering effects is used to calculate the required exposure and corresponding radiation dose. The coherent X-ray flux anticipated from upcoming diffraction-limited light sources is then considered. This imaging time estimation is in particular applied to the case of the connectomes of whole mouse brains. To image the connectome of the whole mouse brain, electron microscopy connectomics might require years, whereas optimized X-ray microscopy connectomics could reduce this to one week. Furthermore, this analysis points to challenges that need to be overcome (such as increased X-ray detector frame rate) and opportunities that advances in artificial-intelligence-based 'smart' scanning might provide. While the technical advances required are daunting, it is shown that X-ray microscopy is indeed potentially applicable to nanoimaging of millimetre- or even centimetre-size specimens., (© Ming Du et al. 2021.)

Characterization of the electronic band structure of solid state materials is routinely performed using photoemission spectroscopy. Recent advancements in short-wavelength light sources and electron detectors give rise to multidimensional photoemission spectroscopy, allowing parallel measurements of the electron spectral function simultaneously in energy, two momentum components and additional physical parameters with single-event detection capability. Efficient processing of the photoelectron event streams at a rate of up to tens of megabytes per second will enable rapid band mapping for materials characterization. We describe an open-source workflow that allows user interaction with billion-count single-electron events in photoemission band mapping experiments, compatible with beamlines at 3 rd and 4 rd generation light sources and table-top laser-based setups. The workflow offers an end-to-end recipe from distributed operations on single-event data to structured formats for downstream scientific tasks and storage to materials science database integration. Both the workflow and processed data can be archived for reuse, providing the infrastructure for documenting the provenance and lineage of photoemission data for future high-throughput experiments.

Time-of-flight-based momentum microscopy has a growing presence in photoemission studies, as it enables parallel energy- and momentum-resolved acquisition of the full photoelectron distribution. Here, we report table-top extreme ultraviolet time- and angle-resolved photoemission spectroscopy (trARPES) featuring both a hemispherical analyzer and a momentum microscope within the same setup. We present a systematic comparison of the two detection schemes and quantify experimentally relevant parameters, including pump- and probe-induced space-charge effects, detection efficiency, photoelectron count rates, and depth of focus. We highlight the advantages and limitations of both instruments based on exemplary trARPES measurements of bulk WSe 2 . Our analysis demonstrates the complementary nature of the two spectrometers for time-resolved ARPES experiments. Their combination in a single experimental apparatus allows us to address a broad range of scientific questions with trARPES.

Time-resolved soft-x-ray photoemission spectroscopy is used to simultaneously measure the ultrafast dynamics of core-level spectral functions and excited states upon excitation of excitons in WSe_{2}. We present a many-body approximation for the Green's function, which excellently describes the transient core-hole spectral function. The relative dynamics of excited-state signal and core levels clearly show a delayed core-hole renormalization due to screening by excited quasifree carriers resulting from an excitonic Mott transition. These findings establish time-resolved core-level photoelectron spectroscopy as a sensitive probe of subtle electronic many-body interactions and ultrafast electronic phase transitions.

Lead-halide perovskite (LHP) semiconductors are emergent optoelectronic materials with outstanding transport properties which are not yet fully understood. We find signatures of large polaron formation in the electronic structure of the inorganic LHP CsPbBr_{3} by means of angle-resolved photoelectron spectroscopy. The experimental valence band dispersion shows a hole effective mass of 0.26±0.02 m_{e}, 50% heavier than the bare mass m_{0}=0.17 m_{e} predicted by density functional theory. Calculations of the electron-phonon coupling indicate that phonon dressing of the carriers mainly occurs via distortions of the Pb-Br bond with a Fröhlich coupling parameter α=1.81. A good agreement with our experimental data is obtained within the Feynman polaron model, validating a viable theoretical method to predict the carrier effective mass of LHPs ab initio.

Time-resolved photoemission with ultrafast pump and probe pulses is an emerging technique with wide application potential. Real-time recording of nonequilibrium electronic processes, transient states in chemical reactions, or the interplay of electronic and structural dynamics offers fascinating opportunities for future research. Combining valence-band and core-level spectroscopy with photoelectron diffraction for electronic, chemical, and structural analyses requires few 10 fs soft X-ray pulses with some 10 meV spectral resolution, which are currently available at high repetition rate free-electron lasers. We have constructed and optimized a versatile setup commissioned at FLASH/PG2 that combines free-electron laser capabilities together with a multidimensional recording scheme for photoemission studies. We use a full-field imaging momentum microscope with time-of-flight energy recording as the detector for mapping of 3D band structures in (k x , k y , E) parameter space with unprecedented efficiency. Our instrument can image full surface Brillouin zones with up to 7 Å -1 diameter in a binding-energy range of several eV, resolving about 2.5 × 10 5 data voxels simultaneously. Using the ultrafast excited state dynamics in the van der Waals semiconductor WSe 2 measured at photon energies of 36.5 eV and 109.5 eV, we demonstrate an experimental energy resolution of 130 meV, a momentum resolution of 0.06 Å -1 , and a system response function of 150 fs.

Image symmetrization is an effective strategy to correct symmetry distortion in experimental data for which symmetry is essential in the subsequent analysis. In the process, a coordinate transform, the symmetrization transform, is required to undo the distortion. The transform may be determined by image registration (i.e. alignment) with symmetry constraints imposed in the registration target and in the iterative parameter tuning, which we call symmetry-guided registration. An example use case of image symmetrization is found in electronic band structure mapping by multidimensional photoemission spectroscopy, which employs a 3D time-of-flight detector to measure electrons sorted into the momentum (k x , k y ) and energy (E) coordinates. In reality, imperfect instrument design, sample geometry and experimental settings cause distortion of the photoelectron trajectories and, therefore, the symmetry in the measured band structure, which hinders the full understanding and use of the volumetric band mapping datasets. We demonstrate that symmetry-guided registration can correct the symmetry distortion in the momentum-resolved photoemission patterns. Using proposed symmetry metrics, we show quantitatively that the iterative approach to symmetrization outperforms its non-iterative counterpart in the restored symmetry of the outcome while preserving the average shape of the photoemission pattern. Our approach is generalizable to distortion corrections in different types of symmetries and should also find applications in other experimental methods that produce images with similar features., (Copyright © 2019. Published by Elsevier B.V.)