doi: 10.1038/s43586-022-00107-9; Article citation ID:
1038/s43586-022-00095-w
PrimeView
Machine learning in scanning transmission
electron microscopy
Results
STEM data are often recorded on vendor
software platforms, which enable
visualization of data in real time, but are
often closed-source black box methods.
STEM can be used on its own or in
combination with other methods such as
electron energy loss (EEL) spectroscopy
(EELS) and energy-dispersive X-ray
spectroscopy to obtain a wealth of
information from the same sample.
These higher-dimension STEM datasets
require more data analysis and processing:
time-series movies may require drift
correction, tomographic tilt series
need software to reconstruct 3D sample
volumes and spectroscopic datasets
require comparison to known samples or
first-principle calculations. These analyses
are simplified using machine learning
approaches, including deep neural
networks, multivariate statistical methods
and Bayesian optimization, among others.
Machine learning is also useful in handling
the large datasets that are increasingly
being produced using STEM.
Reproducibility and data
deposition
When reporting STEM data, the most
important experimental parameters
include accelerating voltage of the
microscope, convergence angle of the
probe, step size between adjacent probe
positions, dwell time and an estimate
of the beam current in the STEM probe.
Specific imaging modalities require
additional metadata. STEM benefits from
the digitization of data, which improves
data analysis and sharing, both in the raw
format and after processing. Researchers
should make data available in open source
file formats (ASCII, CSV or hdf5) with all
the information needed to understand
and reproduce the findings. Data
repositories exist, but the commonly used
ones do not prescribe which metadata to
include, nor do they specify data format.
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(2022) 2:12 For the Primer, visit doi: 10.
Experimentation
STEM is closely related to
conventional transmission
microscopy and scanning
electron microscopy.
Conventional
detectors
Projector lenses transfer the
electrons transmitted through
the sample to the detector or
an EEL spectrometer.
Projector lenses
Sample
A beam of electrons is
extracted from a source and
accelerated to a high energy.
Condenser lenses shape and
demagnify the beam before it
is converged onto the sample
by an objective lens to form a
probe.
Source
Scanning transmission electron microscopy (STEM)
involves seeing atoms by scanning a small electron beam
probe across a thin sample. STEM enables the imaging of
structures with picometre-level precision. This Primer
focuses on the interface between machine learning and
STEM in the analysis of increasingly complex datasets.
Applications
Because STEM enables the analysis of
Spectrometer atomic bond lengths and angles measured
at the single-atom level, it is particularly
useful in materials science and chemistry.
EELS data
When the signal is recorded using high-
angle annular dark-field (HAADF) mode,
STEM can be used to map ferroelectric
When a beam electron excites a sample electron to a phenomena, measure grain boundaries
higher-energy state, the corresponding loss of energy and interfaces, examine heavy atoms on
can be measured with EELS, allowing the study of core- 2D substrates, probe epitaxial growth of
loss, plasmon and optical transitions in materials. nanocrystals, monitor chemical reactions
in situ and determine the structure of
solids at an atomic scale.
The intensity measured
by the detectors is based
on the number of Image data Limitations and
electrons transmitted optimizations
and forms images as a
function of probe Despite major advances in STEM,
position. instrument operation has remained
unchanged. Stabilization tuning and
Electron focusing of the microscope is a generally
beam manual and time-consuming process, and
depends on predefined tuning routines
and operator intuition. The development
of machine learning has led to automation
and autonomous experiments in STEM,
where the microscope automatically
chooses optimal imaging parameters
and identifies the region of interest in the
sample.
Outlook
Attaining the full promise of machine
Machine learning in STEM requires open software
learning architecture both to allow control of the
microscope operation and to customize
experiments. Universal and flexible
workflows for sample preparation,
Condenser lenses imaging and data analysis are needed
to improve the reproducibility of STEM
experiments but also to facilitate the
Electron beam adoption of machine learning in the
automation of STEM. Finally, extracting
accurate physical information from STEM
data will revolutionize our understanding
of condensed matter physics and
chemistry on an atomic level.
Written by Dominique Morneau; designed by Alex Whitworth
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