Literature
Metals, alloys, oxides > 10^5Zeolites Zeolites1,000 - 5,000 MOFs, COFs, hybrid perovskites several to 100
Applications
Operando 4D-STEM — ML-assisted 4D-STEM and electrochemical liquid-cell TEM for Cu nanostructures (2022) doi
Reviews
Differentiable Imaging: Progress, Challenges, and Outlook (2025) doi
Electron ptychography (2025) doi
Spectral SNR as dose-aware metric for STEM phase retrieval (2025) doi
Nature Computational microscopy with CDI and ptychography (2025) doi
Phase imaging methods in the STEM (2025) doi
What electron ptychography can and can’t do yet (2025) doi
Introduction to electron ptychography for materials scientists (2024) doi
Iterative phase retrieval algorithms for STEM (2023) doi
Machine learning in STEM (2022) doi
4D-STEM ptychography for electron-beam-sensitive materials (2022) doi
4D-STEM from scanning nanodiffraction to ptychography and beyond (2019) doi
Reconstruction
Ptychography with ML
Improving iterative reconstructions with generative neural networks (2025) doi
Deep learning enhancements of 4D-STEM reconstruction (2025) doi
Accelerating iterative ptychography with integrated neural network (2025) doi
Self-supervised machine learning framework for high-throughput electron microscopy (2025) doi
Improving Multislice Electron Ptychography with a Generative Prior (2025) doi
Deep generative priors for robust and efficient electron ptychograph (2025) doi
Deep Learning Enhancements of 4DSTEM Ptychographic Reconstruction (2025) doi
AI-enabled high-resolution scanning coherent diffraction imaging (2020) doi
Deep learning at the edge enables real-time streaming imaging (2023) doi
DirectPtycho
Differentiable programming and optimization
Electron ptychography via differentiable programming (2025) doi
Accelerating reconstructions using spectral initializations (2021) doi
Low-dose and beam-sensitive imaging
Benchmarking methods for low-dose imaging of beam-sensitive materials (2025) doi
Improving low-dose performance of aberration correction in single sideband (2025) doi
Stability at low electron dose (2025) doi
Low-dose cryo-electron ptychography of proteins at sub-nanometer resolution (2024) doi
Parallel electron ptychography for 3D imaging of extreme dose-sensitive samples (2024) doi
4D-STEM for electron-beam-sensitive materials (2022) doi
Low-dose phase retrieval of biological specimens using cryo-electron ptychography (2020) doi
Aberrations and microscope corrections
Aberration measurement and consistency among algorithms (2025) doi
Programmable beam control for EELS and ptychography (2025) doi
High-resolution and atomic-scale imaging
Sub-ångström resolution ptychography in a scanning electron microscope at 20 keV (2025) doi
Electron ptychography reveals correlated lattice vibrations at atomic resolution (2025) doi
Science Achieving sub-0.5 Å resolution in uncorrected electron microscope (2024) doi
Sub-nanometer depth resolution with tilt-coupled multislice (2025) doi
Electron ptychography of 2D materials to deep sub-ångström resolution (2021) doi
Science Atomic-resolution limits set by lattice vibrations (2021) doi
Science Pushing the limits of electron ptychography (2018) doi
Tomography
Uncovering 3D structure of upconverting core-shell nanoparticles with multislice (2024) doi
Determining depth-dependent atomic composition of nanoparticles (2024) doi
Sub-nanometer depth resolution with tilt-coupled multislice (2025) doi
Ptychographic transmission microscopy in 3D using multi-slice approach (2012) doi
Solving complex nanostructures with ptychographic atomic electron tomography (2023) doi
Multi-slice ptychographic tomography for soft tissue imaging (2023) doi
Nature Ptychographic X-ray computed tomography at the nanoscale (2010) doi
Iterative joint ptychography-tomography with total variation regularization (2019) doi
CTorch — PyTorch-compatible GPU-accelerated auto-differentiable projector toolbox (2025) doi
End-to-end atomic electron tomography reconstruction and alignment using deep learning (2025) doi
Low-dose 4D-STEM tomography for beam-sensitive nanocomposites (2023) doi
Joint deep learning model to recover information and reduce missing-wedge artifacts (2019) doi
Observing crystal nucleation in four dimensions using atomic electron tomography (2019) doi
Science Atomic electron tomography for 3D structures without crystals (2016) doi
3D coordinates of individual atoms in materials revealed by electron tomography (2015) doi
Multislice Electron Tomography Using Four-Dimensional Scanning Transmission Electron Microscopy (2023) doi
Electron ptychographic microscopy for 3D imaging (2017) doi
Nature Electron tomography at 2.4 ångström resolution (2012) doi
Multidimensional ptychography and 4D-STEM (2023) doi
Effect of dynamical scattering on single-plane phase retrieval (2023) doi
Quantifying phase magnitudes of open-source focused-probe 4D-STEM ptychography reconstructions (2025) doi
Phase retrieval framework for direct reconstruction (2022) doi
Ptychographic reconstruction with object initialization (2022) doi
PtychoShelves versatile high-level framework for ptychographic data analysis (2020) doi
Phase reconstruction using fast binary 4D STEM data (2020) doi
Towards optimized illumination for high-resolution ptychography (2019) doi
Subsampled STEM-ptychography (2018) doi
Further improvements to the ptychographical iterative engine (2017) doi
X-ray ptychography with extended depth of field (2016) doi
A computational framework for ptychographic reconstructions (2016) doi
Alternating projection, ptychographic imaging and phase synchronization (2016) doi
X-ray near-field ptychography for optically thick specimens (2015) doi
Ptychographic microscope for 3D imaging (2014) doi
Phase tomography from X-ray coherent diffractive imaging projections (2014) doi
Nature Reconstructing state mixtures from diffraction measurements (2013) doi
Maximum-likelihood refinement for coherent diffractive imaging (2012) doi
Ptychographic coherent diffractive imaging of weakly scattering specimens (2010) doi
Quantitative biological imaging by ptychographic X-ray diffraction microscopy (2010) doi
An improved ptychographical phase retrieval algorithm for diffractive imaging (2009) doi
Probe retrieval in ptychographic coherent diffractive imaging (2009) doi
Science High-resolution scanning X-ray diffraction microscopy (2008) doi
A phase retrieval algorithm for shifting illumination (2004) doi
Movable aperture lensless transmission microscopy (2004) doi
Parallel and GPU computing
Scalable and accurate multi-GPU-based image reconstruction (2022) doi
Parallel ptychographic reconstruction (2014) doi
Historical foundations
Extending X-ray crystallography methodology to non-crystalline specimens (1999) doi
Multi-angle precession electron diffraction (MAPED)
Multi-angle precession electron diffraction (MAPED) for 4D-STEM precession (2025) doi
Sequential tilting 4D-STEM for improved momentum-resolved STEM field mapping (2025)
SSB/WDD/tcBF
Live iterative ptychography (2024) doi
Improving the low-dose performance of aberration correction in single sideband ptychography (2025) doi
Live processing of momentum-resolved STEM data for first moment imaging and ptychography (2021) doi
Wigner Distribution Deconvolution Adaptation for Live Ptychography Reconstruction (2023) doi
Relaxing direct ptychography sampling requirements via parallax imaging insights (2025) doi
Tilt-corrected BF-STEM (2025) doi
Data streaming
Streaming large-scale microscopy data to supercomputing facility (2025) doi
Accelerating ptychography workflows with NVIDIA Holoscan at Diamond Light Source (2023) doi
GPU-accelerated template matching for orientation mapping in 4D-STEM (2022) doi
Real-time integration center of mass (riCOM) reconstruction for 4D STEM (2022) doi
Real-time interactive 4D-STEM phase-contrast imaging from electron event representation data (2021) doi
Real-time integration center of mass (riCOM) reconstruction for 4D-STEM (2021) doi
RDMA data transfer and GPU acceleration for high-throughput online processing (2020) doi
Streaming multi-GPU implementation of image simulation algorithms for STEM (2017) doi
The scattering of electrons by atoms and crystals (1957) doi
Nature 3D imaging of dislocations in a nanoparticle at atomic resolution (2013) doi
Strain mapping
Drift correction
Predictive drift correction of multi-frame STEM (2025) doi
Scanning distortion correction in STEM images (2018) doi
Correcting nonlinear drift distortion from image pairs with orthogonal scan directions (2016) doi
Correction of nonlinear lateral distortions of scanning probe microscopy images (2014) doi
Simulations
Advanced imaging techniques
Event-driven
Denoise
Unsupervised deep denoising for four-dimensional scanning transmission electron microscopy doi
Self-supervised machine learning framework for high-throughput electron microscopy (2025) doi
Denoising atomic resolution 4D scanning transmission electron microscopy data with tensor singular value decomposition (2020) doi
Cryogenic 4D-STEM
Cryogenic 4D-STEM analysis of amorphous-crystalline polymer blend (2022) doi
Cryo-EM
3D model of purple membrane obtained by electron microscopy (1975) doi
Ultrafast TEM
Orientation mapping
Automated Crystal Orientation Mapping in py4DSTEM using Sparse Correlation Matching (2024) doi
Strategies for fast and reliable 4D-STEM orientation and phase mapping of nanomaterials and devices (2024) doi
In situ nanometer-resolution strain and orientation mapping for gas-solid reactions via precession-assisted four-dimensional scanning transmission electron microscopy (2025) doi
Deep learning
Deep image prior (2017) doi
GPU computing
Early general purpose GPU computing (2003–2007)
CUDA era (2008–2012)
Deep learning and GPU acceleration (2012–2018)
Surveys and architectural perspectives (2013–2019)
Molecular dynamics and biophysics
Astrophysics and cosmology
Computational finance
Quantum chemistry and computational chemistry
WebGPU
Real-time cloth simulation using WebGPU (2025) doi
Books
Electron microscopy
Transmission Electron Microscopy: A Textbook for Materials Science, Williams and Carter (2009)
Principles of Electron Optics: Applied Geometrical Optics, Hawkes and Kasper (1989)
Optics
Principles of Optics, Born and Wolf (1959)
CUDA
Programming Massively Parallel Processors: A Hands-on Approach, Hwu, Kirk, Kajj (2010)
Software
Ptychography
Year |
Software |
Algorithms |
Institution |
GPU |
C++ kernel |
PyTorch |
Multi-slice |
Mixed probe |
|---|---|---|---|---|---|---|---|---|
ePIE, AD |
ANL |
✓ |
- |
✓ |
✓ |
✓ |
||
AD |
Cornell |
✓ |
- |
✓ |
✓ |
✓ |
||
ePIE, LSQML, AD |
MIT |
✓ |
- |
- |
✓ |
✓ |
||
Pretrained NN |
ORNL |
✓ |
- |
✓ |
- |
- |
||
ePIE family |
TU Delft |
✓ |
- |
- |
✓ |
✓ |
||
PINN |
SLAC |
✓ |
- |
- |
- |
- |
||
CG |
DESY |
✓ |
✓ |
- |
- |
- |
||
Pretrained NN |
ANL |
✓ |
- |
✓ |
- |
- |
||
ePIE, LSQML |
ANL |
✓ |
- |
- |
✓ |
✓ |
||
ePIE, DM, LSQML |
ANL |
✓ |
✓ |
- |
✓ |
- |
||
SSB, WDD, DM, RAAR, GD |
LBNL |
✓ |
- |
- |
✓ |
✓ |
||
AD |
ANL |
✓ |
- |
- |
✓ |
- |
||
SSB |
DESY |
✓ |
- |
- |
- |
- |
||
NN |
ANL |
✓ |
- |
✓ |
- |
- |
||
PIE |
DTU |
✓ |
- |
- |
✓ |
- |
||
ER, RAAR, DM, ML |
ESRF |
✓ |
- |
- |
- |
✓ |
||
ePIE, DM, LSQML |
PSI |
✓ |
- |
- |
✓ |
✓ |
||
AD |
ANL |
- |
- |
- |
- |
- |
||
2018 |
DM |
BNL |
- |
- |
- |
- |
- |
|
DM, RAAR, ePIE, ML |
Multiple |
✓ |
✓ |
- |
✓ |
✓ |
||
SHARP |
GPU-based |
LBNL |
✓ |
✓ |
- |
- |
- |
Algorithm abbreviations: SSB (Single Sideband), WDD (Wigner Distribution Deconvolution), DM (Difference Map), RAAR (Relaxed Averaged Alternating Reflections), ePIE (extended Ptychographic Iterative Engine), ML (Maximum Likelihood), AD (Automatic Differentiation), GD (Gradient Descent), ER (Error Reduction), PIE (Ptychographic Iterative Engine), LSQML (Least Squares Maximum Likelihood), NN (Neural Network), CNN (Convolutional Neural Network), CG (Conjugate Gradient), PINN (Physics-Informed Neural Network)
Institution abbreviations: ANL (Argonne National Laboratory), Cornell (Cornell University), MIT (Massachusetts Institute of Technology), ORNL (Oak Ridge National Laboratory), LLNL (Lawrence Livermore National Laboratory), TU Delft (Delft University of Technology), SLAC (SLAC National Accelerator Laboratory), DESY (Deutsches Elektronen-Synchrotron), LBNL (Lawrence Berkeley National Laboratory), DTU (Technical University of Denmark), ESRF (European Synchrotron Radiation Facility), PSI (Paul Scherrer Institute), BNL (Brookhaven National Laboratory), Diamond (Diamond Light Source)
History
Dates from Dr. Yougi Liao’s Practical Electron Microscopy and Database (2006) book
1897 – J. J. Thomson discovers the electron.
1924 – Louis de Broglie determines the wave-like behavior of electrons.
1931 – Knoll & Ruska build the first electron microscope.
1939 – von Borries & Ruska build a practical EM with 10 nm resolution.
1986 – Nobel Prize in Physics awarded for the design of the first electron microscope to Ruska. Nobel lecture.
2017 – Nobel Prize in Chemistry awarded for cryo-electron microscopy, developed by Jacques Dubochet, Joachim Frank, and Richard Henderson.