• Docker
  • https://github.com/Slicer/SlicerDocker/blob/main/README.rst#usage-of-slicer-notebook-image
  • SlicerDocker/slicer-notebook at main · Slicer/SlicerDocker the actual Dockerfile for slicer notebook
  • pieper/SlicerDockers: docker config files for slicer

    • 2y old but may be interesting

• https://github.com/Slicer/SlicerNotebooks has example notebooks
• Slicer in Cloud environments | NA-MIC Project Weeks someone researching this exact question

Basic case:

docker run -p 8888:8888 -p 49053:49053 -v "$PWD":/home/sliceruser/work --rm -ti lassoan/slicer-notebook:latest

Running the application:

• options

  • jupyter docker
  • extension inside slicer to run jupyter -http://127.0.0.1:8888/desktop/ seems to be the default place
  • just running the docker and starting jupyter means it’s empty
  • once you start the kernel the app appears

• How to start it without using/showing the jupyter interface?

  • old
    • as of 5 years ago VNC was one option: S_2019/remote.md at master · SlicerMorph/S_2019
    • How to run Slicer on the cloud and access in a web browser - Support - 3D Slicer Community (same as above)
  • SlicerMorph/SlicerMorphDocker: Docker for running SlicerMorph on Cloud 3 mo ago, turbovnc & docker.
    • scp or firefox to “bring the data in”
  • Actually relevant: Command line scripting with SlicerDockers - Support - 3D Slicer Community
    • Use the webserver to communicate with it
  • 2021 shows people basically doing that: New DICOMweb features: launch Slicer from web browser and download/upload data sets to the cloud using DICOMweb - Support - 3D Slicer Community
    • DICOMweb browser ?
      • dcmjs-org/dicomweb-server: Lightweight DICOMweb Server with CouchDB
      • I don’t see any slicer stuff immediately
  • pieper/SlicerDockers: docker config files for slicer
    • HA, the slicer one is literally a xfce w/ slicer running in it in a browser! :8080

      docker run -d -p 8080:8080 --name slicer stevepieper/slicer:5.0.3
      

      • only x11 works
      • it uses DIT4C for the menu
    • the x11 image has terminal + file management working, but no slicer+
  • jakubMitura14/SlicerNotebookCUDA: After building it we will get id for example 198a491286ae. Can be run sth like docker run –init –gpus all –ipc host –privileged –net host -p 8888:8888 -p49053:49053 -v “$PWD”:/home/sliceruser/work 198a491286ae
    • more modern notebook thing with CUDA and newer everything

• SlicerDockers/slicer-segmentation-server/Dockerfile at master · pieper/SlicerDockers shows how to load extensions in a slicer instance

  • SlicerDockers/slicer-plus/install-slicer-extension.py at master · pieper/SlicerDockers shows installing an extension

Other bits

• mviereck/x11docker: Run GUI applications and desktops in docker and podman containers. Focus on security.

Slicer-jupyter

• HA (part 2)
• using the main trueъ Slicer/SlicerDocker: Build, package, test, and run 3D Slicer and Slicer Extensions in Docker. thing and bash-ing inside it and running Slicer makes it run in the /desktop/ space as well.

docker run -p 8888:8888 -p 49053:49053 -v "$PWD":/home/sliceruser/work --rm -ti lassoan/slicer-notebook:latest

docker exec -it 0c1b5c249378 bash

(but it stops when I close the terminal)

OK OK OK THEN

then

• disable any kind of login/token on jupyter

CMD ["sh", "-c", "./Slicer/bin/PythonSlicer -m jupyter notebook --port=$JUPYTERPORT --ip=0.0.0.0 --no-browser --NotebookApp.default_url=/lab/ --NotebookApp.token=''"]

• start that thing
• go directly to /desktop
• PROBLEM: multiple users using the same instance?… damn

Fazit:

• Running Slicer inside x11 on :8080 is absolutely doable, and including a menu etc. for file upload can be done as well.
  • (SlicerDocker examples.)