User Guide

Get Started

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

Template Matching

• Practical Example
  • Picking Ribosomes
  • Constrained Template Matching
  • Fitting Atomic Structures
  • Alignment of Densities
• Cluster Execution
  • Dataset Organization
  • Basic Batch Processing
  • Processing Subsets
  • Advanced Options
  • Monitoring Progress
  • Environment Configuration
• Moving Forward
  • Summary
  • Scoring Functions
  • Compute Backend

Postprocessing

• Basics
  • Peak Calling Strategies
  • Number of Peaks
  • Background Correction
    • Single Background
    • Multiple Background
    • Multiple Entities
  • Local Optimization and Refinement
  • Coordinate System
  • Details for Developers
  • References
• Practical Example
  • Obtaining a Particle List
  • Refinement
    • Masking
    • Manual
    • Background Correction
  • Validation
  • References
• Summary

Further Reading

• Masking
  • Mask Design
  • Mask Smoothing
  • References
• Filtering Techniques
  • Noise Removal
  • Component Emphasis
    • Frequency Filter
    • Spectral Whitening
    • CTF
    • Wedge Masks
  • References
• Using the GUI
  • Filtering
  • Masking

Miscellaneous

• Contribute
  • Code Style and Guidelines
  • Feedback and Review
• Issues
• License