Awesome Ptychography 🔬✨

A curated list of ptychography reconstruction software from around the world.

🚧 Under construction: Please feel free to contribute.

📊 Software Comparison

The list includes only relatively recently updated open-source modules and packages.

Name	Author/Organization	Language	GPU Support	Algorithms	GUI
4D-STEM	NCEM/LBNL	Python	✅ CUDA	mPIE	✅
cdtools	MIT/PSI	Python	✅ CUDA through torch	ADAM, SGD, LBFGS	❌
PtychoShelves	PSI	MATLAB	✅	PIE, DM, ML	❌
PtyLab	-	Python, Julia, MATLAB	✅	ePIE, mPIE, pcPIE, e3PIE, lsqPIE, aPIE, sPIE, zPIE, pSD, mqNewton	❌
PtyPy	Diamond Light Source	Python	✅ CUDA	PIE, DM, RAAR, SDR	❌
PtyRAD	Cornell University	Python	✅ CUDA through torch	all torch optimizers	❌
Pty-chi	UChicago Argonne	Python	✅ CUDA through torch	ADADELTA, ADAGRAD, ADAM, ADAMAX, ADAMW, ASGD, LBFGS, RADAM, RMSPROP, SGD, SPARSE_ADAM, BH, DM, ePIE, LSQML, PIE, rPIE	❌
PyNX	ESRF	Python/OpenCL	✅ CUDA & OpenCL	PIE, DM, AP	❌
ssc-cdi	Sirius	C++, Python	✅ CUDA	rPIE, mPIE, AP, RAAR, ML	❌
quantem	Stanford	Python	✅ CUDA through torch	N/A	❔

🔤 Column Descriptions

• Name: Software package name
• Author/Organization: Primary developing organization or author
• Language: Main programming language(s)
• GPU Support: GPU acceleration framework (CUDA, OpenCL, etc.)
• Algorithms: Supported reconstruction algorithms
• GUI: Has graphical user interface
• Repository: Link to source code repository

🧮 Algorithm Abbreviations

Classical Ptychography Algorithms

• AP: Alternating Projections link
• DM: Difference Map link
• ML: Maximum Likelihood link
• LSQML: Least-squares Maximum Likelihood link
• RAAR: Relaxed Averaged Alternating Reflections link
• SDR: Semi-implicit relaxed Douglas-Rachford algorithm link

PIE (Ptychographic Iterative Engine) Variants

• PIE: Ptychographic Iterative Engine link
• aPIE: angle calibration PIE link
• e3PIE: Extended PIE with 3 (probe) modes
• ePIE: Extended PIE link
• lsqPIE: Least-squares PIE
• mPIE: Mixed PIE link
• pcPIE: Position-corrected PIE link
• rPIE: Regularized PIE link
• sPIE: Smoothed PIE
• zPIE: autofocusing PIE link

Specialized Ptychography Optimizers

• BH: Bilinear Hessian link
• mqNewton: Modified quasi-Newton
• pSD: projected Steepest Descent

General Optimization Algorithms

• ADADELTA: Adaptive Delta optimizer
• ADAGRAD: Adaptive Gradient optimizer
• ADAM: Adaptive Moment Estimation optimizer
• ADAMAX: ADAM with infinity norm
• ADAMW: ADAM with Weight decay
• ASGD: Averaged Stochastic Gradient Descent
• LBFGS: Limited-memory Broyden-Fletcher-Goldfarb-Shanno optimizer
• RADAM: Rectified ADAM
• RMSPROP: Root Mean Square Propagation
• SGD: Stochastic Gradient Descent
• SPARSE_ADAM: Sparse ADAM optimizer

📚 Datasets and Resources

🗃️ Public Datasets

• CXIDB - Coherent X-ray Imaging Data Bank

📖 Learning Resources

• Rodenburg, J.M. orcid.org/0000-0002-1059-8179 and Maiden, A.M. (2019) Ptychography. In: Hawkes, P.W. and Spence, J.C.H., (eds.) Springer Handbook of Microscopy. Springer Handbooks . Springer . ISBN 9783030000684 link to online version
• Guoan Zheng, A MATLAB tutorial, Fourier Ptychographic Imaging link to online version
• Chiao-Hao Lee, Introduction of PtyRAD, link to video/series

🤝 Contributing

To add or update software information please submit a PR.

🏷️ Tags

ptychography coherent-diffraction-imaging computational-imaging x-ray-imaging electron-microscopy phase-retrieval scientific-computing