Scipion

Scipion is an image processing framework for obtaining 3D models of macromolecular complexes using cryo-EM data. It integrates several software packages while presenting a unified interface.

Overview

Scipion provides a workflow-based environment that integrates multiple cryo-EM software packages into a single platform.

Key Features:

• Unified interface for multiple EM packages
• Workflow-based processing
• 2D/3D classification and refinement
• Integration with RELION, Xmipp, EMAN2, and more
• Web-based interface

Docker Compose Configuration

version: '3.8'

services:
  scipion:
    image: scipion/scipion:latest
    container_name: dxflow-scipion

    # Web interface port
    ports:
      - "8080:8080"

    # Volumes
    volumes:
      - ./projects:/home/scipion/ScipionUserData/projects
      - ./data:/home/scipion/ScipionUserData/data

    # GPU support
    deploy:
      resources:
        limits:
          cpus: '16'
          memory: 64G
        reservations:
          devices:
            - driver: nvidia
              count: 1
              capabilities: [gpu]

    # Environment
    environment:
      - DISPLAY=:0
      - SCIPION_DOMAIN=localhost

Usage

Deploy and Access

# Create directories
mkdir -p projects data

# Deploy Scipion
dxflow compose create --identity scipion scipion.yml
dxflow compose start scipion

# Access web interface
# Open browser: http://localhost:8080

Typical Workflow

1. Import movies - Import raw cryo-EM movies
2. Motion correction - Correct beam-induced motion
3. CTF estimation - Estimate contrast transfer function
4. Particle picking - Pick particles (manual/automatic)
5. 2D classification - Classify and average particles
6. 3D initial model - Generate initial 3D model
7. 3D refinement - Refine to high resolution
8. Post-processing - Sharpen and validate map

System Requirements

Workstation:

• CPU: 16+ cores
• RAM: 64GB minimum
• GPU: NVIDIA RTX 3090 or better
• Storage: 2TB+ NVMe SSD

Integrated Packages

• RELION - Refinement and classification
• Xmipp - Complete processing suite
• EMAN2 - 2D/3D reconstruction
• CTFfind4 - CTF estimation
• MotionCor2 - Motion correction
• Gautomatch - Particle picking

References

• Website: Scipion
• Documentation: Scipion Docs
• Tutorials: Scipion Tutorials

Start processing your cryo-EM data with Scipion's integrated workflow environment!