PtyRAD: Ptychographic Reconstruction with Automatic Differentiation

Docs | Install Guide | Quickstart | Paper | Youtube

PtyRAD performs ptychographic reconstruction using an automatic differention (AD) framework powered by PyTorch, enabling flexible and efficient implementation of gradient descent optimization. See our Microscopy and Microanalysis paper and the Zenodo record for more information and demo datasets.

Features

• Automatic Differentiation (AD) based optimization
• Gradient descent algorithms (Adam, SGD, LBFGS, etc.)
• Mixed-state probe and object
• Position correction
• Position-dependent object tilt correction
• Interoperability with PtychoShelves (fold_slice) and py4DSTEM
• Streamlined preprocessing of cropping, padding, resampling, adding noises, and many more
• Hyperparameter tuning
• Multi-GPU reconstructions
• JIT compilation with torch.compile

Recommended Tools

We recommend using Miniforge for Python environment management, and
Visual Studio Code for code editing and execution.

Major dependencies

• Recomend Python 3.12 or above
• PyTorch 2.4 or above
• While PtyRAD can run on CPU, GPU is strongly suggested for high-speed ptychographic reconstructions.
  • PtyRAD supports both NVIDIA GPUs with CUDA and Apple Silicon (MPS)
• PtyRAD was tested on Windows, MacOS, and Linux

Installation

We recommend installing PtyRAD using pip inside a fresh conda environment.

1. Create and Activate the Python Environment

First, create and activate a new conda environment (ptyrad) with Python > 3.10:

conda create -n ptyrad python=3.12
conda activate ptyrad

💡 Note: After activating the environment, your terminal prompt should show (ptyrad) at the beginning, indicating that the environment is active.

2. Install PtyRAD in the Python Environment

Then install PtyRAD in the activated (ptyrad) environment using:

pip install ptyrad

If you're using Windows with NVIDIA CUDA GPU, you will also need to install the GPU version of PyTorch with:

pip install torch torchvision --index-url https://download.pytorch.org/whl/cu118 --force-reinstall

PtyRAD can also be installed via conda. For detailed instructions on installing PtyRAD on different machines or pinning specific CUDA versions, see the installation guide.

How do I check if my installed PtyRAD has the GPU support?

CUDA version, GPU support, and PyTorch build across platforms can be extremely confusing, so PtyRAD provides handy CLI tools to help check these information for you!

Once you activated (ptyrad) environment and installed PtyRAD via pip install ptyrad, you'll have access to the following command:

# You can run this command anywhere, as long as (ptyrad) environment is activated
ptyrad check-gpu

This command will print your CUDA information and GPU availability if available.

How do I update my existing PtyRAD installation to a newer release?

Assuming you've activated the (ptyrad) environment, and you've installed PtyRAD via pip, you can simply update your PtyRAD installation with:

pip install -U ptyrad

Get Started with the Demo

💡 Note: PtyRAD now includes a starter kit that sets up the folder structure, tutorial notebooks, scripts, and example params files for you, with just one line of code!

1. Initialize a Workspace

Run the following command to create a new folder (e.g., ptyrad/) containing all necessary templates and scripts:

# Activate your (ptyrad) python environment
conda activate ptyrad

# This creates a workspace folder 'ptyrad/' in your current location
ptyrad init # or `ptyrad init <FOLDER_NAME> to use custom folder name

# Enter the directory
cd ptyrad/

The initialize workspace folder structure will look like this:

ptyrad/
├── data/             # Default directory for storing your 4D-STEM datasets
├── notebooks/        # Jupyter notebooks for common workflows and interactive analyses
├── output/           # Default directory where reconstruction results are saved
├── params/
│   ├── examples/     # Ready-to-run parameter files for included demo datasets (e.g., tBL_WSe2, PSO)
│   ├── templates/    # Templates ranging from minimal setups to full API reference
│   └── walkthrough/  # Tutorial-driven parameter files designed to guide you through specific features (e.g., multislice, advanced constraints, and hyperparameter tuning)
└── scripts/          # Utility scripts for fetching demo data and submitting batch jobs on computing clusters

2. Download the Demo Data

We provide a helper script to automatically fetch the example datasets, and place it in the correct ptyrad/data/ folder:

# Download and extract zip files (tBL-WSe2 and PSO, 1.3 GB), should be done in 1-2 mins.
python ./scripts/download_demo_data.py

After downloading and unzipping, the folder structure should look like this:

# Folder structure

ptyrad/
├── data/ 
│   ├── PSO/
│   └── tBL_WSe2/
├── notebooks/
├── output/   
├── params/
└── scripts/  

3. Run the Demo Reconstructions

Please check the following before running the demo:

1. Demo datasets are downloaded and placed to the correct location under ptyrad/data/
2. (ptyrad) environment is created and activated (in VS Code it's the "Select Kernel")

Now you're ready to run a quick demo using one of two interfaces:

• Interactive Jupyter interface (Recommended)

  Run the ptyrad/notebooks/run_ptyrad.ipynb in VS code, or run the following command in terminal:

  jupyter notebook ./tutorials/run_ptyrad.ipynb # Or direcly open it in VS code

• Command-line interface (like your Miniforge Prompt terminal)

  # Assume working directory is at `ptyrad/` and (ptyrad) environment is activated
  ptyrad run "params/examples/tBL_WSe2.yaml"

Documentation

PtyRAD documentation is available at https://ptyrad.readthedocs.io/en/latest/index.html.

Author

Chia-Hao Lee (cl2696@cornell.edu)

Developed at the Muller Group, Cornell University.

Citing PtyRAD

If you use PtyRAD in your research, we kindly ask that you cite our main paper:

Lee, C. H., Zeltmann, S. E., Yoon, D., Ma, D., & Muller, D. A. (2025). PtyRAD: A high-performance and flexible ptychographic reconstruction framework with automatic differentiation. Microscopy and Microanalysis, 31(4), ozaf070.

You can also use the following .bib for BibTex.

@article{lee2025ptyrad,
  title={PtyRAD: A high-performance and flexible ptychographic reconstruction framework with automatic differentiation},
  author={Lee, Chia-Hao and Zeltmann, Steven E and Yoon, Dasol and Ma, Desheng and Muller, David A},
  journal={Microscopy and Microanalysis},
  volume={31},
  number={4},
  pages={ozaf070},
  year={2025},
  publisher={Oxford University Press US}
}

Acknowledgments

Besides great support from the entire Muller group, this package gets inspiration from lots of community efforts, and specifically from the following packages. Some of the functions in PtyRAD are directly translated or modified from these packages as noted in their docstrings/comments to give explicit acknowledgment.

• PtychoShelves
• fold_slice
• py4dstem
• adorym
• SciComPty

Other resources

• ptycho-packages lists many available ptychography packages
• Cornell Box folder compiled by myself that keeps demo data, tutorial recordings, and slides for PtyRAD
• Argonne Box folder compiled by Dr. Yi Jiang that holds tutorial slides of fold_slice
• Blog post written by myself that details the algorithms and code structure of PtychoShelves / fold_slice
• py4D-browser-transform: A plugin for py4D-browser that provides utility functions for transforming the datacube, currently including flipping, transposing, permuting axes.