nextPYP: a scalable platform for cryo-EM/ET image analysis

Contents

nextPYP: a scalable platform for cryo-EM/ET image analysis¶

nextPYP is a comprehensive platform for single-particle cryo-EM/ET image analysis developed and maintained by the Bartesaghi Lab at Duke University.

Main features¶

Portable, easy-to-use, fully featured web-based GUI
On-the-fly data pre-processing (single-particle and tomography)
End-to-end pipeline for high-resolution structure determination (single-particle and tomography)
2D/3D particle picking using size-based, geometry-based and neural network-based approaches
Scalable, small storage footprint (no need to save full size tomograms, sub-volumes, or particle stacks)
Multi-mode constrained refinement and constrained classification for heterogeneity analysis
Particle-based CTF refinement, movie frame refinement and self-tuning exposure weighting
Import/export metadata in .star format to interface with external programs

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Citing nextPYP

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