2026Obrien CryoJax

Citation

O’Brien, M.J., Silva-Sánchez, D., Woollard, G., Je, K., Hanson, S.M., Needleman, D.J., Cossio, P., Thiede, E.H. and Astore, M.A. 2026. CryoJAX: a cryo-electron microscopy image-simulation library in JAX. Acta Crystallographica Sec. D. 82, 3 (2026).

Abstract

While cryo-electron microscopy (cryo-EM) has come to prominence in the last decade due to its ability to resolve biomolecular complexes at atomic resolution, advancements in experimental and computational methods have made cryo-EM promising for investigating intracellular organization and heterogeneous molecular states. A primary challenge for these alternative applications is the development of techniques for cryo-EM data analysis, which are very computationally demanding. To this end, it is advantageous to leverage advanced scientific computing frameworks for statistical analysis. One such framework is JAX, an emerging array-oriented Python numerical computing package for automatic differentiation and vectorization with a growing ecosystem for statistical inference and machine learning. We have developed cryoJAX, a cryo-EM image-simulation library for building computational data-analysis applications in JAX. CryoJAX is a flexible modeling language for cryo-EM image formation and therefore can support a wide range of data analysis downstream. By integrating with the JAX ecosystem, cryoJAX enables the development and deployment of algorithms for the growing breadth of scientific applications for cryo-EM.

Links

https://journals.iucr.org/paper?zi5008