A scalable platform for single-particle cryo-EM/ET image analysis

Features

nextPYP is an open-source, end-to-end platform for high-resolution single-particle cryo-EM/ET image analysis

Blog 1
On-the-fly data pre-processing

cryo-EM/ET

Analyze micrographs and tilt-series in real-time, including movie frame alignment, CTF estimation and particle picking. Learn more

Blog 3
Particle picking suite

2D/3D

Pick particles from micrographs or tomograms using size-based, geometry-based or neural network-based methods. Learn more

Blog 2
High-resolution refinement

Single-particle/Sub-tomogram averaging

Multi-mode constrained refinement and classification. Particle-based CTF refinement, movie frame alignment and exposure weighting. Learn more

Portable, easy-to-use, fully featured web-based GUI.

nextPYP features a storage-efficient architecture that avoids saving full-size tomograms, sub-volumes, and particle stacks, allowing routine processing of thousands of micrographs or tilt-series and tens of millions particle projections.

Try the live demo
Work 1 Work 2 Work 3

2024 nextPYP Virtual Workshop


Watch the recorded lectures and practical sessions from the workshop.



Funding


Development of nextPYP is supported by grants from NIH/NIGMS (R01-GM141223), NIH/NIAID (U54-AI170752), the Chan Zuckerberg Initiative (2021-234602), and Duke University.

References

MiLoPYP

Huang, Q., Zhou, Y., Bartesaghi, A., (2024) MiLoPYP: self-supervised molecular pattern mining and particle localization in situ, Nature Methods, in press.

nextPYP

Liu, HF., Zhou, Y., Huang, Q., Piland, J., Jin, W., Mandel, J., Du, X., Martin, J., Bartesaghi, A., (2023) nextPYP: a comprehensive and scalable platform for characterizing protein variability in-situ using single-particle cryo-electron tomography, Nature Methods, 20, 1909–1919.

BISECT/CSPT

Bouvette, J., Liu, HF., Du, X., Zhou, Y., Sikkema, AP., da Fonseca Rezende e Mello, J., …, Borgnia, MJ., Bartesaghi. A., (2021) Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography, Nature Communications 12, 1957.

High-throughput tomography

Liu, HF., Zhou, Y., Bartesaghi, A. (2022) High-resolution structure determination using high-throughput electron cryo-tomography, Acta Crystallographica Section D: Structural Biology 78 (7), pp. 817-824.

3D particle picking

Huang, Q., Zhou, Y., Liu, HF., Bartesaghi, A. (2022) Accurate Detection of Proteins in Cryo-Electron Tomograms from Sparse Labels, European Conference on Computer Vision (ECCV) 13681, pp. 644-660.

2D particle picking

Huang, Q., Zhou, Y., Liu, HF., Bartesaghi, A. (2022) Weakly Supervised Learning for Joint Image Denoising and Protein Localization in Cryo-Electron Microscopy, IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), pp. 3246-3255.

Automatic particle sorting

Zhou, Y., Moscovich, A., Bendory, T., Bartesaghi, A., (2019) Unsupervised particle sorting for high-resolution single-particle cryo-EM, Inverse Problems 36, 044002.

Movie-frame refinement

Bartesaghi, A., Aguerrebere, C., Falconieri, V., Banerjee, S., Earl, L. A., Zhu, X., …, Subramaniam, S. (2018). Atomic resolution cryo-EM structure of β-galactosidase, Structure 26(6), pp. 848-856.

Constrained single particle tomography

Bartesaghi, A., Lecumberry, F., Sapiro, G., Subramaniam, S., (2012) Protein secondary structure determination by constrained single-particle cryo-electron tomography, Structure 20(12), pp. 2003-2013.

3D size-based particle picking

Jin W., Zhou Y., Bartesaghi, A. (2024). Accurate size-based protein localization from cryo-ET tomograms, Journal of Structural Biology: X, in press.

Review of methods

Watson A., Bartesaghi, A. (2024) Advances in cryo-ET data processing: meeting the demands of visual proteomics, Current Opinion in Structural Biology, in press.