.. _literature: .. rst-class:: full-width 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 `_ - :green:`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 `_ - :red:`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 `_ - :red:`Science` Atomic-resolution limits set by lattice vibrations (2021) `doi `_ - :red:`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 `_ - :green:`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 `_ - :red:`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 `_ - :green:`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 `_ - :green:`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 `_ - :red:`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 `_ - :green:`Nature` 3D imaging of dislocations in a nanoparticle at atomic resolution (2013) `doi `_ Strain mapping -------------- - Strain relief mechanisms in the growth of GaN/Ga2O3 heterostructures investigated via 4D-STEM (2025) `` - 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 `_ Advanced imaging techniques --------------------------- Event-driven ^^^^^^^^^^^^^ - Event-driven acquisition and processing framework for 4D-STEM (2025) `doi `_ - :red:`Science` Event-responsive scanning transmission electron microscopy (2024) `doi `_ - Event driven 4D STEM acquisition with a Timepix3 detector (2022) `doi `_ 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 ^^^^^^^^^^^^^ - Laser-driven ultrafast transmission electron microscopy (2025) `doi `_ - Coherently amplified ultrafast imaging using free-electron interferometer (2024) `doi `_ - :red:`Science` Imaging of transient structures using nanosecond in situ TEM (2008) `doi `_ 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) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - N-body simulations on GPUs (2007) `doi `_ - Survey of general-purpose computation on graphics hardware (2007) `doi `_ - Scan primitives for GPU computing (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 `_ - GPGPU general-purpose computation on graphics hardware (2008) `doi `_ - GPU computing (2008) `doi `_ Deep learning and GPU acceleration (2012–2018) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Highly scalable deep learning training with mixed precision (2018) `doi `_ - **FireCaffe** — near-linear acceleration of deep neural network training on compute clusters (2015) `doi `_ - ImageNet classification with deep convolutional neural networks (2012) `doi `_ Surveys and architectural perspectives (2013–2019) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Survey of architectural approaches for improving GPGPU (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 `_ - **LAMMPS** — general-purpose molecular dynamics simulations on GPU (2010) `doi `_ - General-purpose molecular dynamics simulations fully on GPU (2008) `doi `_ Astrophysics and cosmology ^^^^^^^^^^^^^^^^^^^^^^^^^^^ - **H-AMR** — GPU-accelerated GRMHD code for exascale computing with 3D adaptive mesh refinement (2019) `doi `_ - **GAMER-2** — GPU-accelerated adaptive mesh refinement code (2018) `doi `_ - The Q Continuum Simulation (2014) `doi `_ - **GAMER** — GPU-accelerated adaptive mesh refinement code for astrophysics (2009) `doi `_ Computational finance ^^^^^^^^^^^^^^^^^^^^^ - Parallelization and acceleration of dynamic option pricing (2025) `doi `_ - GPU option pricing (2015) `doi `_ - Acceleration of option pricing technique on graphics processing units (2012) `doi `_ Quantum chemistry and computational chemistry ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - GPU accelerated implementation of density functional theory calculations (2014) `doi `_ - Quantum chemistry on graphics processing units (2010) `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 ^^^^ - Programming Massively Parallel Processors: A Hands-on Approach, Hwu, Kirk, Kajj (2010) Software -------- Ptychography ^^^^^^^^^^^^^ .. list-table:: Ptychography software packages (DRAFT) :header-rows: 1 :widths: 4 4 4 4 4 4 4 4 4 * - 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. .. bibliography:: refs.bib :style: plain