Welcome to py2rely Documentation

py2rely - The Python Pipeline To Rely On for Relion Sub-tomogram Processing

py2rely simplifies and accelerates the execution of RELION-based sub-tomogram averaging (STA) workflows on SLURM-based high-performance computing (HPC) systems. Designed for rapid iteration and evaluation of particle picking strategies, py2rely integrates with existing tilt series alignment from AreTomo and particle coordinate storage from copick.

📚 Documentation

Getting Started

• Installation - Setup and dependencies
• Quick Start - Minimal commands to get started

User Guides

• Overview - Workflow selection and command groups
• Importing Data - Data import from various sources
• 3D Sub-tomogram Averaging - Complete STA pipeline guide
• 2D Slab Classification - 2D class averaging workflow
• Running on HPC with Submitit - Submit STA jobs to SLURM via Submitit

Reference

• API Reference - Detailed API documentation

💫 Key Features

• ⚙️ Automated job preparation: One-command setup of RELION STA workflows
• 🔄 Copick integration: Seamless import of particle coordinates
• 🧭 Tilt series-aware: Direct input from AreTomo processing pipelines
• 🚀 SLURM-native execution: Run the full STA pipeline with Submitit or generate sbatch scripts via py2rely-slurm
• 🧠 Validation-ready: Quickly test particle picking algorithms

🎯 Workflows

3D Sub-tomogram Averaging

Complete pipeline from particle extraction to high-resolution reconstruction:

• Multi-resolution refinement
• CTF refinement and Bayesian polishing
• Post-processing and resolution estimation

Learn more →

2D Slab Classification

High-throughput 2D class averaging for particle validation:

• Slab extraction from tomograms
• 2D classification with Relion Class2D
• Interactive visualization (Gradio or PyQt5)
• Bootstrap validation

Learn more →