Welcome to Topaz’s documentation!

Topaz

A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz also includes methods for micrograph and tomogram denoising using deep denoising models.

Check out our Discussion section for general help, suggestions, and tips on using Topaz.

Contents:

• Installation
  • Conda
  • Pip
  • Docker
  • Singularity
  • From Source
• Tutorials (coming soon)
• Topaz Commands
  • Particle Picking
    • Train
    • Segment
    • Extract
    • Precision Recall Curve
  • Image Processing
    • Downsample
    • Normalize
    • Preprocess
    • Denoise
    • Denoise 3D
  • File Utilities
    • Convert
    • Split
    • Particle Stack
    • Train Test Split
  • GUI
• Algorithms
• Denoising
• Methods
• Metrics and Statistics
• Models
  • Feature Extractors
    • Basic Conv Nets
    • DenseNets
    • MSNets
    • ResNets
  • Linear Classifier
  • Model Factory
  • Model Generator
  • Model Utilities
• Transformations
• Utilities
  • Conversions
  • File Utilities
  • Image Manipulations
  • Pick Masking
  • Printing
  • STAR File Manipulations
  • Data Utilities
    • Coordinate Manipulations
    • Image Loading
    • Dataset Partitioning
    • Dataset Sampling
• Scripts
• Use with RELION
• Use with CryoSPARC