Significance: X-ray fluorescence microscopy provides unparalleled sensitivity for measuring the distribution of trace elements in many-micrometer-thick specimens, whereas ptychography offers a path to the imaging of weakly fluorescing biological ultrastructure at beyond-focusing-optic resolution. We demonstrate here for the first time, to our knowledge, the combination of fluorescence and ptychography for imaging frozen-hydrated specimens at cryogenic temperatures, with excellent structural and chemical preservation. This combined approach will have significant impact on studies of the intracellular localization of nanocomposites with attached therapeutic or diagnostic agents, help elucidate the roles of trace metals in cell development, and further the study of diseases where trace metal misregulation is suspected (including neurodegenerative diseases).

Focussed Ion Beam (FIB) milling is a mainstay of nano-scale machining. By manipulating a tightly focussed beam of energetic ions, often gallium (Ga⁺), FIB can sculpt nanostructures via localised sputtering. This ability to cut solid matter on the nano-scale revolutionised sample preparation across the life, earth and materials sciences. Despite its widespread usage, detailed understanding of the FIB-induced structural damage, intrinsic to the technique, remains elusive. Here we examine the defects caused by FIB in initially pristine objects. Using Bragg Coherent X-ray Diffraction Imaging (BCDI), we are able to spatially-resolve the full lattice strain tensor in FIB-milled gold nano-crystals. We find that every use of FIB causes large lattice distortions. Even very low ion doses, typical of FIB imaging and previously thought negligible, have a dramatic effect. Our results are consistent with a damage microstructure dominated by vacancies, highlighting the importance of free-surfaces in determining which defects are retained. At larger ion fluences, used during FIB-milling, we observe an extended dislocation network that causes stresses far beyond the bulk tensile strength of gold. These observations provide new fundamental insight into the nature of the damage created and the defects that lead to a surprisingly inhomogeneous morphology.

Ptychography is a coherent diffraction imaging (CDI) method for extended objects in which diffraction patterns are acquired sequentially from overlapping coherent illumination spots. The object’s complex transmission function can be reconstructed from those diffraction patterns at a spatial resolution limited only by the scattering strength of the object and the detector geometry. Most experiments to date have positioned the illumination spots on the sample using a move-settle-measure sequence in which the move and settle steps can take longer to complete than the measure step. We describe here the use of a continuous “fly-scan” mode for ptychographic data collection in which the sample is moved continuously, so that the experiment resembles one of integrating the diffraction patterns from multiple probe positions. This allows one to use multiple probe mode reconstruction methods to obtain an image of the object and also of the illumination function. We show in simulations, and in x-ray imaging experiments, some of the characteristics of fly-scan ptychography, including a factor of 25 reduction in the data acquisition time. This approach will become increasingly important as brighter x-ray sources are developed, such as diffraction limited storage rings.

Combining spatially resolved x-ray Laue diffraction with atomic-scale simulations, we observe how ion-irradiated tungsten undergoes a series of nonlinear structural transformations with increasing radiation exposure. Nanoscale defect-induced deformations accumulating above 0.02 displacements per atom (dpa) lead to highly fluctuating strains at $\sim 0.1\mathrm{dpa}$, collapsing into a driven quasisteady structural state above $\sim 1\mathrm{dpa}$. The driven asymptotic state is characterized by finely dispersed vacancy defects coexisting with an extended dislocation network and exhibits positive volumetric swelling, due to the creation of new crystallographic planes through self-interstitial coalescence, but negative lattice strain.

Lattice defects play a key role in determining the properties of crystalline materials. Probing the three-dimensional (3D) lattice strains that govern their interactions remains a challenge. Bragg coherent diffraction imaging (BCDI) allows strain to be measured with nanoscale 3D resolution. However, it is currently limited to materials that form microcrystals. Here we introduce a technique that allows the manufacture of BCDI samples from bulk materials. Using tungsten as an example, we show that focused ion-beam machining can be used to extract, from macroscopic crystals, micron-sized BCDI samples containing specific preselected defects. To interpret the experimental data, we develop a displacement-gradient-based analysis for multireflection BCDI. This allows accurate recovery of the full lattice strain tensor from samples containing multiple dislocations. These capabilities open the door to BCDI as a microscopy tool for studying complex real-world materials.