Resources

Welcome to the PtyRAD resources hub!

Here you will find official publications, educational materials, and related community tools to help you master electron ptychography and the PtyRAD software.

Official Publications & Documentation

• PtyRAD GitHub Repo: The official GitHub repo of PtyRAD.

• PtyRAD Documentation: The complete, up-to-date guide to installing, configuring, and using the software.

• PtyRAD Journal Paper: The official peer-reviewed publication (Microscopy and Microanalysis).

• PtyRAD arXiv Preprint: The open-access preprint of the core paper.

• Paper Zenodo Archive: Preserved datasets, scripts, and reproducible code releases associated with the publication (29.5 GB).

• PtyRAD Paper Repo: Same with Paper Zenodo Archive, but strips off the datasets and files so it’s only the code and notebooks.

Tutorials & Educational Materials

• PtyRAD Official YouTube Channel: Video tutorials, workshop recordings, and code walkthroughs.

• PtyRAD Beta Test Materials (Cornell Box): A curated collection containing raw demo data, tutorial recordings, and presentation slides.

• Algorithms & Code Structure of PtychoShelves (Blog): A deep dive written by myself detailing the algorithms and code structure of PtychoShelves and fold_slice.

• fold_slice Tutorial Slides (Argonne Box): Educational slides compiled by Dr. Yi Jiang covering the mechanics of the fold_slice algorithm.

Community & Ecosystem

• py4D-browser-transform: A plugin for py4D-browser that provides utility functions for transforming the datacube, currently including flipping, transposing, permuting axes.

  

• ptycho-packages: A GitHub repository tracking and listing other available ptychography software packages across the scientific community.

  Selected list:

  Year	Reference	Supported Algorithms	Language	Notes
  2025	PtyRAD (Lee 2025)	AD	Python	PyTorch-based AD package for electron and x-ray ptychography.
  2025	phaser (Gilgenbach 2025)	ePIE, LSQML, AD	Python	Jax-based package with AD and conventional algos with different backends like cupy and pytorch (experimental)
  2025	pty-chi (Du 2025)	ePIE family, DM, LSQML, AD, BH	Python	PyTorch-based ptychography engine (use Ptychodus for preprocessing)
  2025	ptyrodactyl	AD	Python	Jax-based AD for electron and optical ptychography
  2025	quantem	AD, direct ptycho	Python	Developing full suite of electron microscopy methods
  2023	PtyLab (Loetgering 2023)	ePIE family	MATLAB, Python, Julia	Fourier & conventional ptychography; mPIE, zPIE, aPIE, pcPIE, e3PIE.
  2021	fold_slice (Chen 2021)	ePIE, DM, LSQML	MATLAB	Modified PtychoShelves for electron ptychography.
  2021	py4DSTEM (Savitzky 2021, Varvanides 2023)	SSB, WDD, DM, RAAR, GD	Python	Full 4D-STEM toolbox beyond ptychography.
  2021	Adorym (Du 2021)	AD	Python	HPC AD framework for 2D/3D ptychography, CDI, holography, tomography.
  2020	PtychoShelves (Wakonig 2020)	ePIE, DM, LSQML	MATLAB	MATLAB-based GPU-accelerated engines for mixed state multislice. X-ray focused.
  2016	PtyPy (Enders 2016)	DM, RAAR, ePIE, ML	Python	Supports on-the-fly reconstructions; mixed probe and object.