User Guide

Get Started

• Installation
• CPU/GPU/TPU Support
• GUI Setup
• Troubleshooting
  • pyFFTW
  • CuPy
  • Testing
• Support

Preprocessing

• Motivation
  • Background
  • References
• Filtering Techniques
  • Noise Removal
  • Component Emphasis
    • Frequency Filter
    • Spectral Whitening
    • CTF
    • Wedge Masks
  • References
• Masking
  • Mask Design
  • Mask Smoothing
  • References
• Practical Example
  • Using the API
  • Using the GUI
    • Filtering
    • Masking
  • References
• Summary

Template Matching

• Motivation
  • Background
• Practical Example
  • Picking Ribosomes
    • Template and Mask Generation
    • Template Matching
    • Parameter Comparison
    • Remarks on Tomogram Preprocessing
    • References
  • Fitting Atomic Structures
  • Alignment of Densities
  • Configuration
    • Input
    • Performance
    • Accuracy
    • Computation
• Cluster Execution
  • SLURM (EMBL)
  • CPU Execution
  • GPU Execution
  • References
• Summary

Postprocessing

• Motivation
  • Background
  • Template Matching Output
• Practical Example
  • Obtaining a Particle List
  • Refinement
    • Masking
    • Manual
    • Background Correction
  • Validation
  • Integrations
  • References
• Summary
  • References
• Integrations
  • RELION
    • Example
    • References
  • IMOD

Miscellaneous

• Contribute
  • Code Style and Guidelines
  • Feedback and Review
• Issues
• License
  • Software License Agreement (Academic Use Only)
  • PREAMBLE
  • 1. Licensed Software
  • 2. Rights of Use
  • 3. No Licensing Fee
  • 4. No Warranty
  • 5. Effective Date, Term and Termination
  • 6. Confidentiality
  • 7. Miscellaneous
  • Confirmation