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STXM and ptychography data acquisition
This protocol is extracted from research article:
Multimodal x-ray and electron microscopy of the Allende meteorite

Procedure

STXM and x-ray ptychography data were recorded at beamline 7.0.1 in the Advanced Light Source (ALS) (6, 7)—the Coherent Scattering and Microscopy (COSMIC) beamline—at the Lawrence Berkeley National Laboratory (LBNL). COSMIC provides monochromatic soft x-rays with energies ranging from 250 to 2500 eV, spanning the carbon and sulfur K-edges, and is optimized for spectromicroscopy of elements commonly found in mineral samples, including Fe, Ni, Mg, and Al. X-rays were focused using a Fresnel zone plate with a 45-nm outer zone width to give a total coherent flux of approximately 109 photons/s at the sample position. The sample substrate TEM grid was mounted onto a standard FEI CompuStage sample manipulator derived from an FEI CM200 series TEM and secured with a Hummingbird 3-mm half-grid tip. The use of a TEM-compatible sample holder was a crucial enabling technology that permitted seamless sample transfer between the x-ray and electron microscopes. Other commercially available TEM sample holders designed for tomography, cryo-tomography, and in situ experiments can also fit into the chamber environment. Once mounted, the sample chamber was pumped down to 1 × 10−6 torr. Diffraction data were recorded with a fast charge-coupled device camera developed by LBNL with the following specifications: 50 frames/s, 15-bit dynamic range with a 12-bit analog-to-digital converter, and 1 megapixel. Images were acquired without a beamstop.

STXM data were recorded with 10-ms dwell time using an 80 × 80 square scan grid that proceeded with 40-nm steps to cover a 3.2-μm by 3.2-μm field of view. XAS data can be collected using either point spectra at a single location, a line scan along a direction, or an image stack over a sequence of photon energies. We first performed a line energy scan to determine the correct absorption edge for the elements and then collected image stacks with energies varying across the absorption edge. Complete STXM-XAS image stacks using the above parameters were recorded at the Fe L3-edge (707 eV), Ni L2/3-edge (865/848 eV), Mg K-edge (1302 eV), and Al K-edge (1551 eV). Energy scan steps increased with 1-eV steps from 15 eV below the edge, then changed to 0.25-eV steps within ±5 eV of absorption resonance, followed by 1-eV steps to 15 eV above the edge. STXM energy stacks of each element took 30 to 60 min to record.

Ptychography data were recorded using double-exposure mode with 15/150-ms dwell times to enhance dynamic range and scanned in an 80 × 80 square grid with 35-nm steps to cover a 2.8-μm × 2.8-μm field of view. The resulting pixel size was 8 nm/pixel. Each ptychography image comprised 6400 diffraction patterns of 128 × 128 pixels. The total dose (Dp) deposited on the meteorite grain was estimated as $Dp=(PtA)(μρ)E$, where the fluence $(PtA)$ for 100-ms exposure is 6.46 × 1010 photons/μm2, μ is the linear absorption coefficient, ρ is the average density of minerals, and μ/ρ was estimated to be 10 cm2 g−1 with the average photon energy (E) at 1100 eV. The dose per projection was estimated to be 1.1 × 107 gray, which was within the tolerable dose for imaging at the resolution presented in this work (33). To compare absorption contrast differences for each element, ptychography images at both 5 eV below and directly on resonance were collected at the Fe L3-edge, Ni L2/3-edge, Mg K-edge, and Al K-edge. Phase retrieval of complex images was initially performed at COSMIC using the distributed graphics processing unit (GPU)–based ptychographic solver SHARP (34). To further improve reconstruction quality and to remove artifacts due to the rectilinear scanning grid, final ptychographic images presented in our results were refined using a parallel ptychography reconstruction algorithm (35, 36), with an update condition derived from the hybrid projection-reflection algorithm (3740). Each reconstruction ran for 5000 iterations, where the probe was updated continuously after the fifth iteration.

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