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bioRxiv · 10.1101/2025.10.23.682564

CryoJAX - A Cryo-Electron Microscopy Image Simulation Library in JAX

O'Brien, M.·Silva-Sanchez, D.·Woollard, G.·Je, K.·Hanson, S. M.·Needleman, D. J.·Cossio, P.·Thiede, E.·Astore, M. A.
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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. SynopsisThe 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.

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O'Brien, M., Silva-Sanchez, D., Woollard, G., Je, K., Hanson, S. M., Needleman, D. J., Cossio, P., Thiede, E., Astore, M. A.. 2025-10-24. CryoJAX - A Cryo-Electron Microscopy Image Simulation Library in JAX. https://doi.org/10.1101/2025.10.23.682564

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