User Guide

Get Started

• Installation
• Troubleshooting
  • pyFFTW
  • CuPy
  • Testing (For Developers)
• Support
• Overview
  • Commands at a glance
  • pytme template
  • pytme match
    • Scoring functions
    • Compute backends
  • pytme postprocess
    • Peak calling strategies
    • Score cutoffs
    • Background correction
    • Output formats
  • pytme gui
  • pytme batch
  • pytme utils
  • References

Practical Examples

• Picking Ribosomes
  • Data Acquisition
  • Template and Mask Generation
  • Template Matching
  • Parameter Comparison
  • Obtaining a Particle List
  • Refinement
    • Target Masking
    • Manual Curation
  • Validation
• Constrained Template Matching
  • Prerequisites
  • Data Structure
  • Generating Seed Points
  • Creating Templates
  • Creating Template Masks
  • Template Matching
  • Analysis
  • References
• Fitting and Alignment
  • Atomic Structures
  • Density into Density
  • Refinement

Further Reading

• Cluster Execution
  • Dataset Organization
  • Basic Batch Processing
    • Matching
    • Analysis
    • Output
  • Processing Subsets
  • Advanced Options
    • Filtering
    • Mixed Formats
    • Background Correction
    • Multiple Entities and Backgrounds
• Masking
  • Mask Design
  • Mask Smoothing
  • References
• Filtering Techniques
  • Noise Removal
  • Component Emphasis
    • Frequency Filter
    • Spectral Whitening
    • CTF
    • Wedge Masks
  • References
• Using the GUI
  • Image actions
  • Masking

Miscellaneous

• Conventions
  • Coordinate System
  • Pickle File Layout
  • References
• Contribute
  • Code Style and Guidelines
  • Feedback and Review
• Issues
• License