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@nextpyp

nextPYP

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

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

See the full documentation for more details.

Pinned Loading

  1. pyp pyp Public

    Cryo-EM/ET image analysis

    Python 10

  2. csp csp Public

    Constrained single particle tomography

    C++ 1

  3. ettk ettk Public

    Electron tomography toolkit: geometric picking and sub-volume averaging

    C++ 1

  4. cet_pick cet_pick Public

    Cellular content mining and particle localization

    Python 8 1

  5. spr_pick spr_pick Public

    2D NN-based particle picking from sparse labels

    Python 2

  6. next next Public

    Web-interface for nextPYP

    Kotlin 9 1

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