EMBION

EMBION: Danish National Cryo-EM Facility Platform

The Project

EMBION is the Danish National Cryo-EM Facility at Aarhus University, established in 2018 with a grant of 30.8 million DKK (4.7 million USD) from the Ministry of Higher Education and Science. The facility represents a significant advancement in cryogenic electron microscopy (cryo-EM) research infrastructure in Denmark, enabling high-resolution data collection from various samples including protein molecules, macromolecular complexes, and cells.

Our Approach

We collaborated with the EMBION team to create a comprehensive digital platform that supports the facility's advanced research capabilities. Our solution included:

• A sophisticated booking system for managing access to multiple high-end electron microscopes
• Real-time data tracking and management system
• Custom forms for structured scientific data collection
• Integration with research workflows and existing university systems
• Multi-platform support (web, mobile, and desktop applications)
• Secure storage and management of sensitive research data

Technical Implementation

The platform was built using modern technologies to ensure reliability and scalability:

Technology Stack

The EMBION platform was developed using a robust, modern technology stack:

• Frontend: Flutter for cross-platform applications

  • Single codebase for web, iOS, and Android applications
  • Rich, responsive UI with native performance
  • Offline capabilities for uninterrupted data collection

• Backend: Golang (Go) for the server implementation

  • High-performance, concurrent request handling
  • Excellent memory management for resource-intensive operations
  • Type safety and reliability for critical research applications

• API Architecture: gRPC for efficient communication

  • Strongly typed contracts between client and server
  • Efficient binary serialization for large scientific datasets
  • Bidirectional streaming for real-time experiment monitoring

• Deployment: Kubernetes for orchestration

  • Scalable infrastructure to handle varying research loads
  • High availability for critical research operations
  • Automated rollouts and rollbacks for seamless updates
  • Resource isolation for security and performance

This technology stack was specifically chosen to meet the unique demands of a scientific research facility. Flutter enables researchers to access the platform from any device with a consistent experience. Golang provides the performance and reliability needed for processing large datasets. gRPC facilitates efficient communication between the microscopes, servers, and client applications. Finally, Kubernetes ensures the platform remains available and performant even during peak research periods.

Integration with Electron Microscopes

The system integrates with multiple electron microscopes including:

• Titan Krios G3i (300 keV)
• Titan Krios 300 kV TEM
• Aquilos 2 Cryo FIB
• Tecnai Spirit 120 kV TEM
• Versa 3D Focused Ion Beam SEM
• Nova NanoSEM

Results

The EMBION platform has significantly enhanced the research capabilities at Aarhus University:

• Streamlined access to state-of-the-art cryo-EM equipment
• Standardized data collection across research projects
• Improved collaboration between researchers
• Enhanced data security and backup capabilities
• Real-time monitoring of experiments
• Simplified application process for microscope time
• Integration with international research programs (iNEXT Discovery)

Client Testimonial

"The digital platform developed for EMBION has transformed how we manage our cryo-EM facility. It has become an essential tool for our researchers, enabling efficient scheduling, data collection, and analysis. The system's flexibility and reliability have made it a cornerstone of our research infrastructure."

— Thomas Boesen, Cryo-EM Facility Manager

The platform continues to evolve with new features and capabilities, supporting the facility's mission to advance structural biology research in Denmark and beyond. The project represents a successful collaboration between scientific research and digital innovation, demonstrating how technology can enhance cutting-edge scientific facilities.