CryoJAX: a cryo-electron microscopy image-simulation library in JAX
Year: 2026
Type: article
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. Synopsis The authors have developed cryoJAX, a cryo-EM image simulation library for developing data analysis techniques across cryo-EM modalities. CryoJAX is built on JAX, an emerging scientific computing framework in Python well suited for cryo-EM data analysis.
Language: English
Subfield: Structural Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7127392808