Electron tomography data were collected at the National Center for Electron Microscopy. For TEM experiments, a Titan 60-300 equipped with a HAADF detector (Gatan, Pleasanton, CA) and four windowless silicon drift EDS detectors (FEI Super-X) were used with a solid angle of 0.7 srad. The microscope operated in scanning transmission electron microscopy (STEM) mode at 200 kV with an electron beam current of ~550 pA for STEM-EDS maps and ~40 pA for HAADF-STEM imaging. A typical total dose for the complete tomography series was ~1300 e2, and a typical total dose for an EDS map was ~1100 e2. EDS data were collected as a tilt series of scanned spectrum images, which measured emitted x-rays from regions probed by the electron beam. The images were drift-corrected over ~120 s, assuming a time-dependent linear drift model at different tilt angles.

HAADF-STEM scans and probes local structural information by collecting electrons scattered onto the HAADF detector. All tilt series of projection images were typically acquired between −64° and 72°, with a linear tilt step of 2°. The tilt range was limited by the shadowing of the sample holder (Hummingbird, Lacey, WA). HAADF-STEM images were acquired with a convergence semi-angle of 10 mrad at a detector inner semi-angle of 63 mrad and outer semi-angle of 305 mrad. Image size was 1024 × 1024 pixels with a pixel size of 4.67 nm. Each projection image was binned by 3 to have a pixel size of 14.01 nm. We carefully checked the integrity of the samples before and after taking tomographic tilt series using zero-degree projections and before and after EDS mapping. We observed no visible sample damage.

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