STEM SerialED: achieving high-resolution data for ab initio structure determination of beam-sensitive nanocrystalline materials
Bibliographic record
Abstract
Serial electron diffraction (SerialED), which applies a snapshot data acquisition strategy on each crystal, was introduced to tackle the problem of radiation damage in the structure determination of beam-sensitive materials by three-dimensional electron diffraction (3D ED). The snapshot data acquisition in SerialED can be realized both in transmission and scanning transmission electron microscopes (TEM/STEM). However, the current SerialED workflow based on STEM setups requires special external devices and software, which brings challenges for its broader adoption. Here, we present a simplified experimental implementation of STEM-based SerialED on Thermo Fisher Scientific STEMs using common proprietary software interfaced through Python scripts to automate data collection. Specifically, we utilize TEM Imaging and Analysis (TIA) scripting and TEM scripting to access the STEM functionalities of the microscope, and DigitalMicrograph (DM) scripting to control the camera for snapshot data acquisition. Data analysis adapts the existing workflow using the software CrystFEL developed for serial X-ray crystallography. Our workflow for SerialED can be used on any Gatan or Thermo Fisher Scientific camera. We apply this workflow to collect high-resolution STEM SerialED data from two aluminosilicate zeolites, Zeolite Y and ZSM-25, and demonstrate, for the first time, ab initio structure determination through direct methods using the STEM SerialED data. Zeolite Y is relatively stable under the electron beam, and SerialED data extend to 0.60 Å. We show that the structural model obtained using SerialED data merged from 358 crystals is nearly identical to that using continuous rotation electron diffraction (cRED) data from one crystal. This demonstrates that accurate structures can be obtained from SerialED. Zeolite ZSM-25 is very beam-sensitive and has a complex structure. We show that SerialED greatly improves data resolution of ZSM-25, compared to serial rotation electron diffraction (SerialRED), from 1.50 Å to 0.90 Å. This allows for the first time the use of standard phasing methods such as direct methods for ab initio structure determination of ZSM-25.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.005 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".