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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 8

  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 7

  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 8 1

Repositories

Showing 10 of 10 repositories
  • cet_pick Public

    Cellular content mining and particle localization

    nextpyp/cet_pick’s past year of commit activity
    Python 7 BSD-3-Clause 0 8 0 Updated Nov 17, 2024
  • postprocessing Public

    Post-processing and generation of FSC curves

    nextpyp/postprocessing’s past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated Sep 20, 2024
  • pyp Public

    Cryo-EM/ET image analysis

    nextpyp/pyp’s past year of commit activity
    Python 8 BSD-3-Clause 0 0 0 Updated Apr 6, 2024
  • next Public

    Web-interface for nextPYP

    nextpyp/next’s past year of commit activity
    Kotlin 8 BSD-3-Clause 1 3 0 Updated Apr 6, 2024
  • cistem-2.0 Public

    cisTEM 2.0 fork

    nextpyp/cistem-2.0’s past year of commit activity
    C++ 0 BSD-3-Clause 0 0 0 Updated Jan 13, 2024
  • spr_pick Public

    2D NN-based particle picking from sparse labels

    nextpyp/spr_pick’s past year of commit activity
    Python 2 BSD-3-Clause 0 1 0 Updated Nov 12, 2023
  • cistem-1.0 Public

    cisTEM 1.0 fork (frealignx)

    nextpyp/cistem-1.0’s past year of commit activity
    C++ 0 BSD-3-Clause 0 0 0 Updated Oct 25, 2023
  • ettk Public

    Electron tomography toolkit: geometric picking and sub-volume averaging

    nextpyp/ettk’s past year of commit activity
    C++ 1 BSD-3-Clause 0 0 0 Updated Oct 24, 2023
  • csp Public

    Constrained single particle tomography

    nextpyp/csp’s past year of commit activity
    C++ 1 BSD-3-Clause 0 0 0 Updated Oct 24, 2023
  • .github Public
    nextpyp/.github’s past year of commit activity
    0 0 0 0 Updated Sep 26, 2023

People

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