Literature

Reviews

Ptychography and phase retrieval

Nature Computational microscopy with CDI and ptychography (2025) doi
Electron ptychography (2025) doi
What electron ptychography can and can’t do yet (2025) doi
Phase imaging methods in the STEM (2025) doi
Introduction to electron ptychography for materials scientists (2024) doi
Iterative phase retrieval algorithms for STEM (2023) doi
4D-STEM from scanning nanodiffraction to ptychography and beyond (2019) doi

Imaging and machine learning

Differentiable Imaging: Progress, Challenges, and Outlook (2025) doi
Spectral SNR as dose-aware metric for STEM phase retrieval (2025) doi
Machine learning in STEM (2022) doi

Reconstruction algorithms

Iterative and classical methods

Quantifying phase magnitudes of open-source focused-probe 4D-STEM ptychography reconstructions (2025) doi
Multidimensional ptychography and 4D-STEM (2023) doi
Effect of dynamical scattering on single-plane phase retrieval (2023) doi
Ptychographic reconstruction with object initialization (2022) doi
Phase retrieval framework for direct reconstruction (2022) doi
Accelerating reconstructions using spectral initializations (2021) 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
Quantitative biological imaging by ptychographic X-ray diffraction microscopy (2010) doi
Ptychographic coherent diffractive imaging of weakly scattering specimens (2010) doi
Probe retrieval in ptychographic coherent diffractive imaging (2009) doi
An improved ptychographical phase retrieval algorithm for diffractive imaging (2009) doi
Science High-resolution scanning X-ray diffraction microscopy (2008) doi
Movable aperture lensless transmission microscopy (2004) doi
A phase retrieval algorithm for shifting illumination (2004) doi
Extending X-ray crystallography methodology to non-crystalline specimens (1999) doi

Direct methods (SSB and WDD)

Tilt-corrected BF-STEM (2025) doi
Relaxing direct ptychography sampling requirements via parallax imaging insights (2025) doi
Improving the low-dose performance of aberration correction in single sideband ptychography (2025) doi
Live iterative ptychography (2024) doi
Wigner Distribution Deconvolution Adaptation for Live Ptychography Reconstruction (2023) doi
Live processing of momentum-resolved STEM data for first moment imaging and ptychography (2021) doi

ML and backpropagation methods

Self-supervised machine learning framework for high-throughput electron microscopy (2025) doi
Improving Multislice Electron Ptychography with a Generative Prior (2025) doi
Improving iterative reconstructions with generative neural networks (2025) doi
Accelerating iterative ptychography with integrated neural network (2025) doi
Deep learning enhancements of 4D-STEM reconstruction (2025) doi
Electron ptychography via differentiable programming (2025) doi
Deep learning at the edge enables real-time streaming imaging (2023) doi
AI-enabled high-resolution scanning coherent diffraction imaging (2020) doi

Tomography and 3D imaging

Sub-nanometer depth resolution with tilt-coupled multislice (2025) doi
End-to-end atomic electron tomography reconstruction and alignment using deep learning (2025) doi
CTorch — PyTorch-compatible GPU-accelerated auto-differentiable projector toolbox (2025) doi
Uncovering 3D structure of upconverting core-shell nanoparticles with multislice (2024) doi
Determining depth-dependent atomic composition of nanoparticles (2024) doi
Solving complex nanostructures with ptychographic atomic electron tomography (2023) doi
Low-dose 4D-STEM tomography for beam-sensitive nanocomposites (2023) doi
Multi-slice ptychographic tomography for soft tissue imaging (2023) doi
Multislice Electron Tomography Using 4D-STEM (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
Iterative joint ptychography-tomography with total variation regularization (2019) doi
Electron ptychographic microscopy for 3D imaging (2017) 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
Ptychographic transmission microscopy in 3D using multi-slice approach (2012) doi
Nature Electron tomography at 2.4 ångström resolution (2012) doi
Nature Ptychographic X-ray computed tomography at the nanoscale (2010) doi

Advanced imaging techniques

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
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

Low-dose and beam-sensitive imaging

Stability at low electron dose (2025) doi
Improving low-dose performance of aberration correction in single sideband (2025) doi
Benchmarking methods for low-dose imaging of beam-sensitive materials (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

Denoising

A novel adaptive noise model selection framework for blind denoising of Scanning Electron Microscopy images (2025) doi
Noise Distribution Adaptive Self-Supervised Image Denoising using Tweedie Distribution and Score Matching doi
Self-supervised denoising method for single neutron image based on the S2S-NR network doi
SDF: A self-supervised denoiser framework for X-Ray computed tomography (2025) doi
Non-local Denoising for 4D STEM Orientation Mapping (2025) doi
Self-supervised machine learning framework for high-throughput EM (2025) doi
Unsupervised deep denoising for 4D-STEM (2025) doi
Denoising of 4D-STEM Dataset using Pix2Pix GAN Algorithm and Artifact Reduction Strategy (2024) doi
Cluster-Based Filtering Technique for Denoising 4D-STEM Dataset (2024) doi
Denoising 4D STEM datasets with PCA (2024) doi
Self-supervised denoising of grating-based phase-contrast computed tomography (2024) doi
Weak signal extraction enabled by deep neural network denoising of diffraction data (2024) doi
Diffraction denoising using self-supervised learning (2024) doi
Disentangling multiple scattering with deep learning: application to strain mapping from electron diffraction patterns (2022) doi
Deep learning-based noise filtering toward millisecond order imaging by using scanning transmission electron microscopy (2022) doi
Denoising low-intensity diffraction signals using 𝑘-space deep learning: Applications to phase recovery (2021) doi
Denoising atomic resolution 4D-STEM data with tensor singular value decomposition (2020) doi

Event-driven imaging

Event-driven acquisition and processing framework for 4D-STEM (2025) doi
Science Event-responsive scanning transmission electron microscopy (2024) doi
Event driven 4D STEM acquisition with a Timepix3 detector (2022) doi

Cryo-EM and low-temperature imaging

Cryogenic 4D-STEM analysis of amorphous-crystalline polymer blend (2022) doi
3D model of purple membrane obtained by electron microscopy (1975) doi

Ultrafast and time-resolved imaging

Laser-driven ultrafast transmission electron microscopy (2025) doi
Coherently amplified ultrafast imaging using free-electron interferometer (2024) doi
Science Imaging of transient structures using nanosecond in situ TEM (2008) doi

Orientation mapping

In situ nanometer-resolution strain and orientation mapping for gas-solid reactions via precession-assisted 4D-STEM (2025) doi
Strategies for fast and reliable 4D-STEM orientation and phase mapping of nanomaterials and devices (2024) doi
Automated Crystal Orientation Mapping in py4DSTEM using Sparse Correlation Matching (2024) doi

Multi-angle precession electron diffraction

Multi-angle precession electron diffraction (MAPED) for 4D-STEM precession (2025) doi
Sequential tilting 4D-STEM for improved momentum-resolved STEM field mapping (2025)

Deep learning architectures

Deep image prior (2017) doi

Aberrations

Rapid aberration measurement with pixelated detectors 2015 https://doi.org/10.1111/jmi.12372 Aberration measurement using the Ronchigram contrast transfer function 2010 Coherent interference in convergent-beam electron diffraction and shadow imaging (1979) https://doi.org/10.1016/S0304-3991(79)80021-2 Practical autoalignment of transmission electron microscopes (1992) https://doi.org/10.1016/0304-3991(92)90052-L

Data streaming and real-time processing

Streaming large-scale microscopy data to supercomputing facility (2025) doi
Accelerating ptychography workflows with NVIDIA Holoscan at Diamond Light Source (2023) doi
Real-time integration center of mass (riCOM) reconstruction for 4D STEM (2022) doi
GPU-accelerated template matching for orientation mapping in 4D-STEM (2022) doi
Real-time integration center of mass (riCOM) reconstruction for 4D-STEM (2021) doi
Real-time interactive 4D-STEM phase-contrast imaging from electron event representation data (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

Strain mapping

Strain relief mechanisms in the growth of GaN/Ga2O3 heterostructures investigated via 4D-STEM (2025) doi
Accurate measurement of strain at interfaces in 4D-STEM (2021) doi
Gatan 4D-STEM strain mapping link

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

Prismatic 2.0 — simulation software for STEM and HRTEM (2021) doi
Fast algorithm for STEM imaging and 4D-STEM diffraction simulations (2021) doi
Fast image simulation algorithm for STEM (2017) doi, abTEM API

Applications

Materials characterization

Nature 3D imaging of dislocations in a nanoparticle at atomic resolution (2013) doi
The scattering of electrons by atoms and crystals (1957) doi

GPU computing

Early general purpose GPU computing (2003–2007)

N-body simulations on GPUs (2007) doi
Scan primitives for GPU computing (2007) doi
Survey of general-purpose computation on graphics hardware (2007) doi
GPGPU scientific computing (2005) link
Brook for GPUs — stream computing on graphics hardware (2004) doi

CUDA era (2008–2012)

GPGPU processing in CUDA architecture (2012) doi
ImageNet classification with deep convolutional neural networks (2012) doi
Acceleration of option pricing technique on graphics processing units (2012) doi
LAMMPS — general-purpose molecular dynamics simulations on GPU (2010) doi
GAMER — GPU-accelerated adaptive mesh refinement code for astrophysics (2009) doi
GPGPU general-purpose computation on graphics hardware (2008) doi
GPU computing (2008) doi
General-purpose molecular dynamics simulations fully on GPU (2008) doi

Deep learning and GPU acceleration (2012–2018)

Highly scalable deep learning training with mixed precision (2018) doi
GAMER-2 — GPU-accelerated adaptive mesh refinement code (2018) doi
GPU option pricing (2015) doi
FireCaffe — near-linear acceleration of deep neural network training on compute clusters (2015) doi
The Q Continuum Simulation (2014) doi
GPU accelerated implementation of density functional theory calculations (2014) doi
Parallel ptychographic reconstruction (2014) doi

Surveys and architectural perspectives (2013–2019)

Survey of architectural approaches for improving GPGPU (2019) doi
H-AMR — GPU-accelerated GRMHD code for exascale computing with 3D adaptive mesh refinement (2019) doi
Survey on GPU computing for large-scale data analytics (2018) doi
Brief history and introduction to GPGPU (2013) doi

Molecular dynamics and biophysics

Transformational role of GPU computing and deep learning in drug discovery (2022) doi
Classical molecular dynamics on graphics processing unit (2020) doi
Quantum chemistry on graphics processing units (2010) doi

Computational finance

Parallelization and acceleration of dynamic option pricing (2025) doi

Parallel and scalable computing

Scalable and accurate multi-GPU-based image reconstruction (2022) doi

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

CUDA by Example: An Introduction to General-Purpose GPU Programming, Sanders and Kandrot (2010)
Programming Massively Parallel Processors: A Hands-on Approach, Hwu, Kirk, Kajj (2010)
CUDA C Programming

Software

Ptychography

Ptychography software packages (DRAFT)
Year	Software	Algorithms	Institution	GPU	C++ kernel	PyTorch	Multi-slice	Mixed probe
2025	Pty-Chi	ePIE, AD	ANL	✓	-	✓	✓	✓
2025	PtyRAD	AD	Cornell	✓	-	✓	✓	✓
2025	phaser	ePIE, LSQML, AD	MIT	✓	-	-	✓	✓
2024	PtychoFormer	Pretrained NN	ORNL	✓	-	✓	-	-
2023	PtyLab	ePIE family	TU Delft	✓	-	-	✓	✓
2023	PtychoPINN	PINN	SLAC	✓	-	-	-	-
2022	PtyGer	CG	DESY	✓	✓	-	-	-
2023	Airpi	Pretrained NN	ANL	✓	-	✓	-	-
2022	Tike	ePIE, LSQML	ANL	✓	-	-	✓	✓
2021	Ptychopy	ePIE, DM, LSQML	ANL	✓	✓	-	✓	-
2021	py4DSTEM	SSB, WDD, DM, RAAR, GD	LBNL	✓	-	-	✓	✓
2021	Adorym	AD	ANL	✓	-	-	✓	-
2021	Ptychography 4.0	SSB	DESY	✓	-	-	-	-
2021	PtychoNN	NN	ANL	✓	-	✓	-	-
2020	abTEM	PIE	DTU	✓	-	-	✓	-
2020	PyNX	ER, RAAR, DM, ML	ESRF	✓	-	-	-	✓
2020	PtychoShelves	ePIE, DM, LSQML	PSI	✓	-	-	✓	✓
2019	ptychoSampling	AD	ANL	-	-	-	-	-
2018	NSLS-II (Ptycho-gui)	DM	BNL	-	-	-	-	-
2016	PtyPy	DM, RAAR, ePIE, ML	Multiple	✓	✓	-	✓	✓
2016	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.