Windows/Docker installation¶

Step by step guide¶

Installation should take less than 1 h. Most time will be spent downloading the Docker container.
Install the latest Docker version.

Tip

For Windows, Docker uses WSL 2 (Windows Subsystem for Linux). By default all containers will be stored on C: drive. If you do not want to use this location, you must execute the following commands in Command prompt as outlined in this Stack Overflow post to change the location:

Make sure that Docker Desktop is shut down.
Check WSL state¶
wsl --list -v
Make sure the services are STOPPED¶
  NAME                   STATE           VERSION
* docker-desktop         Stopped         2
  docker-desktop-data    Stopped         2
Export docker-desktop-data to a file.
Export Docker Desktop data¶
wsl --export docker-desktop-data "D:\Docker\wsl\data\docker-desktop-data.tar"
Unregister docker-desktop-data.
Unregister Docker Desktop data¶
wsl --unregister docker-desktop-data
Import the data into a new location where your Docker containers will be stored. You must create the new location first before submitting this command.
Import Docker Desktop data into new location¶
wsl --import docker-desktop-data "D:\Docker\wsl\data" "D:\Docker\wsl\data\docker-desktop-data.tar" --version 2
After this you can start Docker Desktop and all containers should now be saved in the new location. You can now delete the .tar file.
Attention

For Windows, you need either at least Windows 11 or at least the 19044.1200 (21H2) Windows 10 Insider Preview Build for GPU support. You can sign up here for the Windows insider program.

Install the latest Miniconda version. Be sure to install Miniconda NOT Anaconda as the installation path will be different for the subsequent steps.
Retrieve the CeceliaDocker project. Either Download and unpack or clone the CeceliaDocker repository into a directory of your choice. In this tutorial we are using D:\Public\Cecelia\GIT\.

Clone repository with git¶

git clone https://github.com/schienstockd/ceceliaDocker.git

4. Create conda environment for napari to run. On Windows, you might want to use Anaconda Prompt to initialise the conda toolkit. Anaconda Prompt has to be used only to initialise the conda environment. It is not needed after this step is done.

Create conda environment¶
conda env create --file=conda-gui-env.yml
Attention

On Windows, if the conda environment fails to build due to missing compiler wou might need to install Microsoft Visual C++ >= 14.0 with Microsoft C++ Build Tools.

Adjust config files

You must adjust the filepaths in the config files docker-compose.yml and datashare/docker.yml located in D:\Public\Cecelia\GIT\ceceliaDocker\. This will tell Docker where your projects are stored and the data location that you can use to import data.
Windows example docker-compose.yml¶
services:
  app:
    volumes:
      - D:\Public\Cecelia\GIT\ceceliaDocker\datashare:/home/shiny/local
      - D:\Public\Cecelia\PROJECTS:/cecelia/projects
      - D:\Public\Cecelia\DATA:/cecelia/data
We must also tell Shiny to use the host directory to open images as they are opened outside of the container within the napari environment.
Windows example datashare/docker.yml¶
default:
  docker:
    useDocker: TRUE
    pathMapping:
      home:
        from: "/home/shiny/local/cecelia"
        to: "D:\\Public\\Cecelia\\GIT\\ceceliaDocker\\datashare\\cecelia"
      projects:
        from: "/cecelia/projects"
        to: "D:\\Public\\Cecelia\\PROJECTS"

Start Docker Desktop and retrieve Cecelia container.

Open the Docker Desktop application and run (or build) the Docker container with cecelia-MacOSX-docker.command (Mac) or cecelia-Windows-docker.bat (Windows) located in D:\Public\Cecelia\GIT\ceceliaDocker\. This will start the local napari environment, retrieve the Docker container during the first run and start the app.

Attention

If you installed Miniconda in a custom location, ie/ not your user account, you must specify that directory in the .command or .bat file by editing the file in a Text editor.