# 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**](https://github.com/chiahao3/ptyrad): The official GitHub repo of PtyRAD. * [**PtyRAD Documentation**](https://ptyrad.readthedocs.io/en/latest/index.html): The complete, up-to-date guide to installing, configuring, and using the software. * [**PtyRAD Journal Paper**](https://academic.oup.com/mam/article/doi/10.1093/mam/ozaf070/8222545?utm_source=authortollfreelink&utm_campaign=mam&utm_medium=email&guestAccessKey=e9e13516-273a-4e46-bec4-7488e9001d7d): The official peer-reviewed publication (Microscopy and Microanalysis). * [**PtyRAD arXiv Preprint**](https://arxiv.org/abs/2505.07814): The open-access preprint of the core paper. * [**Paper Zenodo Archive**](https://doi.org/10.5281/zenodo.15392805): Preserved datasets, scripts, and reproducible code releases associated with the publication (29.5 GB). * [**PtyRAD Paper Repo**](https://github.com/chiahao3/ptyrad_paper): 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**](https://www.youtube.com/@ptyrad_official): Video tutorials, workshop recordings, and code walkthroughs. * [**PtyRAD Beta Test Materials (Cornell Box)**](https://cornell.box.com/s/n5balzf88jixescp9l15ojx7di4xn1uo): A curated collection containing raw demo data, tutorial recordings, and presentation slides. * [**Algorithms & Code Structure of PtychoShelves (Blog)**](https://chiahao3.notion.site/Theory-Algorithm-and-Code-structure-of-PtychoShelves-c7bf28a1068c4a4f90aa77272602ab19): A deep dive written by myself detailing the algorithms and code structure of `PtychoShelves` and `fold_slice`. * [**`fold_slice` Tutorial Slides (Argonne Box)**](https://anl.box.com/s/f7lk410lf62rnia70fztd5l7n567btyv): Educational slides compiled by Dr. Yi Jiang covering the mechanics of the `fold_slice` algorithm. ## Community & Ecosystem * [**py4D-browser-transform**](https://github.com/chiahao3/py4D-browser-transform): A plugin for [py4D-browser](https://github.com/sezelt/py4D-browser) that provides utility functions for transforming the datacube, currently including flipping, transposing, permuting axes. ```{image} https://github.com/chiahao3/py4D-browser-transform/raw/main/assets/demo.gif :width: 600px :alt: py4D-browser-transform demo * [**ptycho-packages**](https://github.com/chiahao3/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](https://github.com/chiahao3/ptyrad) (Lee 2025) | AD | Python | PyTorch-based AD package for electron and x-ray ptychography. | | 2025 | [phaser](https://github.com/hexane360/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](https://github.com/AdvancedPhotonSource/pty-chi) (Du 2025) | ePIE family, DM, LSQML, AD, BH | Python | PyTorch-based ptychography engine (use Ptychodus for preprocessing) | | 2025 | [ptyrodactyl](https://github.com/debangshu-mukherjee/ptyrodactyl) | AD | Python | Jax-based AD for electron and optical ptychography | | 2025 | [quantem](https://github.com/electronmicroscopy/quantem) | AD, direct ptycho | Python | Developing full suite of electron microscopy methods | | 2023 | [PtyLab](https://github.com/PtyLab) (Loetgering 2023) | ePIE family | MATLAB, Python, Julia | Fourier & conventional ptychography; mPIE, zPIE, aPIE, pcPIE, e3PIE. | | 2021 | [fold_slice](https://github.com/yijiang1/fold_slice) (Chen 2021) | ePIE, DM, LSQML | MATLAB | Modified PtychoShelves for electron ptychography. | | 2021 | [py4DSTEM](https://github.com/py4dstem/py4DSTEM) (Savitzky 2021, Varvanides 2023) | SSB, WDD, DM, RAAR, GD | Python | Full 4D-STEM toolbox beyond ptychography. | | 2021 | [Adorym](https://github.com/mdw771/adorym) (Du 2021) | AD | Python | HPC AD framework for 2D/3D ptychography, CDI, holography, tomography. | | 2020 | [PtychoShelves](https://www.psi.ch/en/sls/csaxs/software) (Wakonig 2020) | ePIE, DM, LSQML | MATLAB | MATLAB-based GPU-accelerated engines for mixed state multislice. X-ray focused. | | 2016 | [PtyPy](https://ptycho.github.io/ptypy/) (Enders 2016) | DM, RAAR, ePIE, ML | Python | Supports on-the-fly reconstructions; mixed probe and object. |