software | E.Z. Lab

Our group develops state-of-the-art machine learning algorithms for 3D reconstruction of dynamic protein structures from cryo-electron microscopy (cryo-EM) data. We have released and maintain these algorithms for cryo-EM reconstruction and associated workflows in the ml-struct-bio GitHub organization, including the cryodrgn software package.

Zhong et al. (2020). International Conference on Learning Representations (ICLR).

cryodrgn

Deep Reconstructing Generative Networks for cryo-EM and cryo-ET heterogeneous reconstruction

Commit activity

311 commits in the past year · Full history on GitHub

Last three commits to this repository
Time (UTC)	SHA	Message	Author	+/−
2026-05-30 22:32	6a47cae	cleaning up how volume animations are rendered and updating dashboard tests for refactored animatio…	Michal R. Grzadkowski	+227 −50
2026-05-30 21:30	e4ca280	updating dashboard code for refactored ChimeraX volume visualization and improving animation genera…	Michal R. Grzadkowski	+360 −600
2026-05-29 04:08	863a0a4	new module for optimized and refactored ChimeraX animation generation across interfaces	Michal R. Grzadkowski	+923 −0

Projects: open source methods, simulators, and benchmarks

cryobench

Jeon et al. (2024). NeurIPS.

Diverse and challenging datasets for the heterogeneity problem in cryo-EM (CryoBench).

drgnai

Levy et al. (2025). Nature Methods.

Ab initio heterogeneous cryo-EM and cryo-ET reconstruction with cryoDRGN-AI.

cahra

The Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms (CAHRA).

cryohype

Gu et al. (2026). Computer Vision and Pattern Recognition (CVPR).

Reconstructing a thousand cryo-EM structures with transformer-based hypernetworks (cryoHYPE).

chefnmr

Xiong et al. (2025). NeurIPS.

Atomic diffusion models for small molecule structure elucidation from NMR Spectra (ChefNMR).

cryoboltz

Raghu et al. (2025). NeurIPS.

Multiscale guidance of protein structure prediction with heterogeneous cryo-EM (CryoBoltz).

cryosim

Tools for generating synthetic cryo-EM images

hydra

Levy et al. (2024). NeurIPS.

Mixture of neural fields for conformational and compositional heterogeneity in cryo-EM (Hydra).

cryofire

Levy et al. (2022). NeurIPS.

Amortized inference for heterogeneous reconstruction in Cryo-EM (CryoFIRE).

Datasets: benchmarks, datasets, and other public resources

CAHRA (heterogeneity challenge)

Notion hub for the community-wide heterogeneity challenge—datasets, timelines, and submission information for CAHRA.

CryoBench (GitBook)

Jeon et al. (2024). NeurIPS.

GitBook site with benchmark tasks, evaluation metrics, and how to use the CryoBench suite (companion to the code repo in Projects).

sim2struct-1k (CryoHype)

Gu et al. (2026). CVPR.

Princeton landing page and download for the sim2struct-1k large-scale synthetic heterogeneous cryo-EM benchmark used with CryoHype (thousands of structures, particle images, and poses).

SpectraNP (ChefNMR)

Xiong et al. (2025). NeurIPS.

Zenodo record for the SpectraNP NMR training dataset and related files released with the ChefNMR structure-elucidation work.

EMPIAR-11658

Rangan et al. (2024). Nature Methods (related in situ work).

EMPIAR-11658 in situ cryo-ET of S. cerevisiae (cryo-plasmaFIB milling); tomogram tilt series and metadata for subtomogram / heterogeneity work.