SmartScope Documentation

  • SmartScope Home
  • Latest News
  • Beta Program
  • Installation
    • Minimal requirements
    • Installation with Docker or Podman
      • How to prepare your docker-compose file
      • Complete list of environment variables
    • Installation with Anaconda/Miniconda
    • Additionnal information on installation
      • Complete list of environment variables
  • Updating SmartScope
    • Updating a podman installation
  • Setup
    • Admin portal
    • SerialEM setup
  • Web Interface
    • Log in
    • Navigation
  • Running SmartScope
    • How to prepare SerialEM
    • Set up SmartScope
    • Session page
  • Testing and Troubleshooting
    • Testing SmartScope without the microscope
  • How to Cite
  • Contact Us
  • License

Versions

  • 0.8
  • v0.7

Branches

  • dev
  • stable
Theme by the Executable Book Project
  • repository
  • open issue
  • .rst

Setup

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

previous

Updating a podman installation

next

Admin portal

By Jonathan Bouvette and Elizabeth Viverette
© Copyright 2022, NIEHS/NIH Molecular Microscopy Consortium and Bartesaghi Lab.