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

Site Map

• Latest News
• Latest Changes
  • Main changes
  • Minor changes
  • Bug fixes
• 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
  • Additionnal information on installation
    • Complete list of environment variables
      • General
      • Fake-scope mode
      • Database
      • AWS connection information
• Updating SmartScope
  • Updating a Docker 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 detector to the SmartScope database
    • 4- Low-dose Presets
      • Search
      • View
      • Preview
      • Record
      • Focus/Trial
    • 5- Non Low-dose Presets
• 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
  • Test commands for SmartScope
    • Testing GPU capabilities
  • Testing the connection to serialEM
  • List plugins and protocols
• Protocol API
  • Configure a protocol
    • Example
  • Protocol Commands
    • Available commands
  • Automatic protocol selection
    • Synthax
      • conditions
      • mode
      • protocol
• Plugins
  • Plugin Interface
    • Types of algorithms
  • Plugin configuration
    • Specific to class-based plugin
    • Specific to function-based plugin
    • Specific to Classifiers
    • Specific to Selectors
  • Examples
    • Finder and classifier combination
    • External plugin
  • Creating a new function-based plugin
    • Accepted output formats
    • additional_ouptut
  • Creating a new class-based plugin
    • Example
• External plugins
  • Available plugins
  • Capabilities
  • Conventions for automatic registration
    • Finder, Classifier, Selector algorithms plugins
    • Predefined protocols
    • Protocol commands
• REST API usage
  • Accessing the REST API through the browser
    • Examples
      • Manually changing the status of an area
      • Query holes from a squares that have not been selected for acquisition
  • Accessing the REST API programatically
    • Obtaining an API token
    • Using the request library to query the database
• How to Cite
• Contact Us
  • Email
  • Slack
• License