Welcome to SmartScope

For information about installation and usage, please visit the official documentation website

Citing SmartScope

Bouvette, Huang et al. eLife 2022;11:e80047

Docker basic installation

To avoid file permission issues, you should perform these steps as the user that will run the smartscope software.

1. Download the minimal configuration files.

wget docs.smartscope.org/downloads/SmartScopeInstallation.tar.gz --no-check-certificate
tar -xvf SmartScopeInstallation.tar.gz 
cd SmartScope

The directory contains 5 files that can be divided in 3 categories:

Docker files:

• docker-compose.yml: Main file for the docker environment. Should not need to be changed.
• smartscope.yml: Simpler version of the docker-compose.yml to add additional settings. This one needs to be changed.

Configuration:

• database.conf: Contains the configuration for the database connections to share between smartscope and the database.
• smartscope.conf: Contains the configuration that is unique to smartscope.

Script:

• smartscope.sh: Used to start and stop the smartsocpe software.

2. Create a directory on your SerialEM computer where SmartScope will save data and a storage area for smartscope.

mkdir /mnt/serialemComputer/smartscope
mkdir /mnt/nas/smartscope

3. Edit the smartscope.yml file to add your microscope path and the paths that you just created.

version: "3"
services:
smartscope:
    image: ghcr.io/niehs/smartscope:0.8-rc.2  
    user: ${UID}:${GID}
    volumes: 
    # - /home/ubuntu/SmartScope/:/opt/smartscope/
    ######## ADD YOUR MAIN DATA LOCATION ##########
    - /mnt/nas/smartscope/:/mnt/data/
    # Example:
    # - /nfs/data/:/mnt/data/
    ######## ADD YOUR MICROSCOPES #########
    # The synthax from the microscope volumes is as follows:
    # - /path/to/where/serialem/will/write/files/:/mnt/your_scope_name_here/
    - /mnt/serialemComputer/smartscope/:/mnt/myscope1/
    # Example:
    # - /mnt/gatan_Raid_X/smartscope/:/mnt/arctica/

Note You can add multiple microscopes to the same SmartScope installation. Simply add an additional entry to the volumes section.

4. (Optional) Edit the configuration files to your needs.

Detailed information about the environment variables can be found in the official documentation

5. Start SmartScope

The first start will download all the container images and is expected to last a few minutes.

./smartscope.sh start

#Outputs should look like this
Starting smartscope
[+] Running 5/5
⠿ Network installation_smartscopenet  Created      0.0s
⠿ Container installation-cache-1      Started      0.7s
⠿ Container smartscope-db             Started      0.6s
⠿ Container smartscope                Started      1.0s
⠿ Container installation-nginx-1      Started      1.4s

6. Log in to the web interface with the initial admin account.

You should now be able to access the smartscope interface at http://localhost:48000.

The initial account is admin with password smartscope.

7. The installation is done!

There is a few more set up steps to do in SerialEM and in the web portal to get up and running.