Technical Notes#
Cryo-EM Data Acquisition Scale#
Understanding the scale and volume of cryo-electron microscopy data acquisition is crucial for system design and performance considerations:
Micrograph Statistics#
Micrographs per foil hole: Typically 4-10 images per foil hole
Grid-level acquisition: 10,000-50,000 micrographs per complete grid session
Particle density: Approximately 300 particles identified per micrograph
Selection efficiency: Roughly 50% of identified particles are selected for further processing
These statistics inform the design requirements for data processing pipelines and storage allocation strategies.
System Architecture Considerations#
Decision-Making Framework#
The SmartEM system implements a modular decision-making architecture designed for flexibility and extensibility:
Modular design: Decision-making components are decoupled from data acquisition systems
Pluggable authorities: Different decision-making algorithms can be easily substituted
Future extensibility: Architecture supports integration of additional decision-making systems
API Integration#
Communication between SmartEM components and external cryo-EM control systems occurs through well-defined API interfaces, ensuring compatibility with various microscope control software packages.
Data Management and Storage#
ISPyB Integration#
The project integrates with the ISPyB database schema, which provides comprehensive metadata storage for:
Experimental run information
Session metadata and parameters
Image counts and acquisition statistics
Sample type and classification data
File System Organisation#
Data acquisition produces structured file system layouts that facilitate automated processing and quality assessment workflows.
Processing Pipeline Components#
Particle Processing Workflow#
The automated processing pipeline comprises several specialised services:
Particle Picking Service#
Input: JSON message via RabbitMQ containing image path and processing parameters
Processing: Automated particle identification and coordinate extraction
Output: List of particle coordinates for each processed micrograph
Implementation: CryOLO service
Particle Selection Service#
Function: Quality-based filtering and selection of identified particles
Integration: Seamless integration with particle picking results
Implementation: Selection service
Scientific Context and References#
The SmartEM system builds upon established methodologies and practices in automated cryo-electron microscopy:
Key Publications#
Structural Biology Methods - Comprehensive overview of automated cryo-EM data collection strategies
Advanced Automation Techniques - Recent developments in real-time decision making for cryo-EM workflows
These references provide scientific context for the automated decision-making algorithms implemented within the SmartEM framework.