SmartScope Home

Note

This documentation website is still under construction.

SmartScope is a framework for automated cryo-electron microscopy (Cryo-EM). The main purpose is to automate specimen screening, document the process, and provide a portal for visualization and interaction with the microscope. The software bundles a database, the main imaging workflow and a web user-inteface for easy access. To run Smartscope, simply fill the form about which grids to be screened, press start and wait for live results to come in.

SmartScope webUI example

Site map

• Latest News
• Beta Program
  • Timeline
• Installation
  • Minimal requirements
  • Installation with Docker or Podman
    • Requirements
      • Docker
      • Podman
    • Nvidia GPU passthrough (optional)
    • Installation steps
      • How to prepare your docker-compose file
        • Services
          • smartscope
          • db
          • cache
          • nginx
        • Services settings
          • image
          • build
          • container-name
          • volumes
            • smartscope
            • db
            • nginx
          • environment
          • depends_on
          • networks
          • command
          • deploy
          • ports
      • Complete list of environment variables
        • General
        • Fake-scope mode
        • Database
        • AWS connection information
  • Installation with Anaconda/Miniconda
    • Requirements
    • Setting up the SmartScope environment
  • Additionnal information on installation
    • Complete list of environment variables
      • General
      • Fake-scope mode
      • Database
      • AWS connection information
• Updating SmartScope
  • Updating a podman installation
• Setup
  • Admin portal
    • Accessing the admin portal
      • Users
      • Groups
      • Microscope
      • Detector
  • SerialEM setup
    • Calibrations
    • 1- Setting up external python for SerialEM
      • Testing the connection to serialEM
    • 2- Register a microscope to the SmartScope database
      • General
      • Hardware constants
      • Smartscope Worker
      • SerialEM external python connection
      • Filesystem Paths
    • 3- Register a microscope to the SmartScope database
    • 4- Low-dose Presets
      • Search
      • View
      • Preview
      • Record
      • Focus/Trial
    • 5- Non Low-dose Presets
    • 6- Hole Reference Image
• Web Interface
  • Log in
  • Navigation
    • Session Browser
  • Report Panel
    • Report Panel Navigation
      • Collapsible Menus
      • Atlas Image
      • Square Image
      • Queueing Holes
      • Adding Targets
      • Hole Image
• Running SmartScope
  • How to prepare SerialEM
  • Set up SmartScope
    • Setup Smartscope
    • General
    • Collection Parameters
    • Autoloader
    • Submitting
  • Session page
    • Top section
    • Control buttons
      • Start/Stop
      • Pause between grid
    • Admin control buttons
      • Force start
      • Remove scope lock file
      • Force-kill all session processes
    • Logs
    • Pop-up notifications
      • Scope lock warnings
      • Stop signal received
      • Pause between grid prompt
• Testing and Troubleshooting
  • Testing SmartScope without the microscope
    • Setting up the image bank
• How to Cite
• Contact Us
  • Email
  • Slack
• License

Indices and tables

• Index

• Module Index

• Search