Single particle tutorial¶

  • Introduction
  • Preprocessing
    • Getting organised
    • Beam-induced motion correction
    • CTF estimation
    • Manual particle picking
  • Particle picking
    • Select a subset of the micrographs
    • LoG-based auto-picking
    • Particle extraction
    • 2D class averaging to select good particles
    • Selecting good 2D classes for Topaz training
    • Re-training the TOPAZ neural network
    • Pick all micrographs with the re-trained TOPAZ neural network
    • Particle extraction
  • Reference-free 2D class averaging
    • Running the job
    • Selecting good particles for further processing
    • Analysing the Class2D results in more detail
    • Making groups
  • De novo 3D model generation
    • Running the job
    • Analysing the results
  • Unsupervised 3D classification
    • Running the job
    • Selecting good particles for further processing
    • Analysing the results in more detail
  • High-resolution 3D refinement
    • Running the auto-refine job
    • Analysing the results
  • Mask creation & Postprocessing
    • Making a mask
    • Post-processing
  • CTF and aberration refinement
    • Higher-order aberrations
    • Anisotropic magnification
    • Per-particle defocus values
  • Bayesian polishing
    • Running in training mode
    • Running in polishing mode
    • Re-running refinement and post-processing
    • When and how to run CTF refinement and Bayesian polishing
  • Local-resolution estimation
    • Running the job
    • Analysing the results
  • Checking the handedness
  • Wrapping up
    • Making a flowchart
    • Cleaning up your directories
    • Asking questions and citing us
    • Further reading

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Navigation

  • What’s new?
  • The team
  • Installation
  • Single particle tutorial
    • Introduction
    • Preprocessing
    • Particle picking
    • Reference-free 2D class averaging
    • De novo 3D model generation
    • Unsupervised 3D classification
    • High-resolution 3D refinement
    • Mask creation & Postprocessing
    • CTF and aberration refinement
    • Bayesian polishing
    • Local-resolution estimation
    • Checking the handedness
    • Wrapping up
  • Subtomogram tutorial
  • On-the-fly processing
  • Reference pages

  • Source repository of this documentation

Related Topics

  • Documentation overview
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