About cryoSPARC

General description of cryoSPARC, origins and development.

What is cryoSPARC?

CryoSPARC (Cryo-EM Single Particle Ab-Initio Reconstruction and Classification) is a state of the art HPC software solution for complete processing of single-particle cryo-electron microscopy (cryo-EM) data. CryoSPARC is useful for solving cryo-EM structures of membrane proteins, viruses, complexes, flexible molecules, small particles, phase plate data and negative stain data.

CryoSPARC enables:

  • Extremely fast end-to-end processing of raw cryo-EM data through to reconstruction of electron density maps, ready for ingestion into model building software

  • Optimized, GPU-accelerated algorithms for anisotropic motion correction, CTF estimation, particle picking, 2D particle classification, 3D ab-initio structure determination, high resolution refinement, and heterogeneity analysis

  • Specialized and unique algorithms and tools for therapeutically relevant targets, membrane proteins, continuously flexible structures

  • Rapid reconstruction of biologically important targets with advanced tools for membrane proteins, heterogeneous samples and flexible molecules

  • Interactive, visual and iterative experimentation for complex workflows


Hundreds of studies have used cryoSPARC for cryo-EM data processing:


Punjani, A., Rubinstein, J.L., Fleet, D.J., and Brubaker, M.A. CryoSPARC: Algorithms for rapid unsupervised cryo-em structure determination. Nature Methods, 14:290–296, 2017. [ https://www.nature.com/articles/nmeth.4169 ]

Punjani, A., Zhang, H. & Fleet, D.J. Non-uniform refinement: Adaptive regularization improves single particle cryo-EM reconstruction. bioRxiv [ https://doi.org/10.1101/2019.12.15.877092 ]

Punjani, A. and Fleet, D.J. 3D Variability Analysis: Directly resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM images. bioRxiv [ https://doi.org/10.1101/2020.04.08.032466 ]


CryoSPARC was originally a research project with origins at the University of Toronto in 2014. As of 2016, all research and development for cryoSPARC is done by Structura Biotechnology Inc., a scientific software startup based in Toronto, Canada. By combining our expertise in image processing, algorithm development and professional software engineering, we aim to keep cryoSPARC at the forefront of software for cryo-EM. To that end, we are constantly working on new algorithms and software features which we release on an ongoing basis. CryoSPARC's GPU-accelerated code is written entirely from scratch in-house, with exception of certain wrappers to third party tools that are clearly indicated in the documentation. Many of the algorithms in cryoSPARC are novel developments for cryo-EM image processing and links to publications can be found throughout this documentation.