How the documentation is structured

Documentation is split into four categories, also accessible from links in the top bar.

• Tutorials
  • Installation

Tutorials for installation and typical usage. New users start here.

• How-to Guides
  • Using the API Documentation
  • Configure Logging and Verbosity
  • Containerization
  • Contribute to the project
  • Database Migrations
  • Kubernetes Deployment
  • Development Tools
  • Generate Documentation
  • Managing Kubernetes Secrets
  • Run SmartEM Agent (EPU Agent)
  • Run SmartEM Backend
  • Run in a container
  • How to Use the SmartEM API Client
  • Using SmartEM MCP Interface

Practical step-by-step guides for the more experienced user.

• Explanations
  • Architectural Decision Records
  • EPU Output Directory Structure
  • Technical Notes

Explanations of how it works and why it works that way.

• Reference
  • API
  • Index
  • Release Notes

Technical reference material including APIs and release notes.

API Documentation

Interactive API documentation is available for all SmartEM Decisions services:

Athena Decision Service API

Complete interactive documentation for the Athena Decision Service API, including session management, decision recording, and algorithm results.

Features: Sessions • Decisions • Algorithm Results • Area Management • Configuration

api/athena/index.html

SmartEM Core API

Documentation for the SmartEM Core API for recording electron microscopy sessions and experimental data.

Features: Sessions • Grids • Atlases • Atlas Tiles • Grid Squares • Foil Holes • Micrographs

api/smartem/index.html