3D electron diffraction benchmark for thickness-dependent dynamical effects

This repository contains the complete experimental diffraction data, data-reduction outputs, structure-refinement files, and analysis scripts associated with the corresponding publication on thickness-dependent three-dimensional electron diffraction (3D ED) measurements of pure-silica zeolites with LTA and STW topologies. Four focused-ion-beam-milled lamellae of different thicknesses were prepared from a single crystal of each zeolite. The approximate thicknesses determined from SEM imaging are 100, 200, 350, and 600 nm for LTA and 100, 130, 210, and 350 nm for STW. For each zeolite, all four lamellae share the same parent crystal and crystallographic orientation, forming a controlled thickness series. The 3D ED datasets were collected on a Thermo Fisher Scientific Themis Z microscope operated at 300 kV and equipped with a Timepix Cheetah hybrid-pixel detector. Data were acquired over an approximately −45° to +45° tilt range at a rotation speed of 0.3° s⁻¹ and an exposure time of 0.01 s per frame, corresponding to 0.03° per raw frame. Four consecutive raw frames were merged into effective 0.12° frames for data processing. The repository is organized into four ZIP archives: datasets.zip contains the original and merged diffraction images for all eight datasets. Raw data are provided as 16-bit, 512 × 512 pixel TIFF images, together with a comment.txt file describing the data-collection strategy and a measurement_metadata.json file containing experimental parameters. Merged data are provided as 16-bit, 512 × 512 pixel IMG files with relevant acquisition information stored in the image headers. The datasets are: LTA_t1: approximately 100 nm, 3,033 raw TIFF frames and 758 merged IMG frames LTA_t2: approximately 200 nm, 3,032 raw TIFF frames and 758 merged IMG frames LTA_t3: approximately 350 nm, 3,041 raw TIFF frames and 760 merged IMG frames LTA_t4: approximately 600 nm, 3,028 raw TIFF frames and 757 merged IMG frames STW_t1: approximately 100 nm, 3,025 raw TIFF frames and 757 merged IMG frames STW_t2: approximately 130 nm, 3,025 raw TIFF frames and 757 merged IMG frames STW_t3: approximately 210 nm, 3,026 raw TIFF frames and 757 merged IMG frames STW_t4: approximately 350 nm, 3,026 raw TIFF frames and 757 merged IMG frames data_reductions.zip contains the complete XDS input and output files for each LTA and STW dataset. Separate XDS_CONV_MERGED and XDS_CONV_UNMERGED directories contain the XDSCONV input and output files used to generate merged and unmerged reflection-intensity files. The merged files contain symmetry-averaged intensities, whereas the unmerged files retain individual measurements of symmetry-equivalent reflections. refinements.zip contains SHELXT/SHELXL structure-solution and refinement files for all datasets. Separate directories are provided for refinements based on merged intensities and for evaluations performed against unmerged intensities. Structural parameters were refined against merged data; the resulting models were subsequently held fixed while residual values were evaluated against the corresponding unmerged data. scripts.zip contains the Python scripts used for post-processing and analysis: accuracies.py calculate_Rint_Rsigma.py filter_XDSASCII.py README.md requirements.txt For comparison across the four thicknesses of each zeolite, the reflection files were post-processed to retain only reflections present in all four datasets of the corresponding thickness series. Reflection files are plain-text files containing the reciprocal-space indices h, k, and l, followed by the reflection intensity and its error-corrected standard uncertainty.