Image Station

This container has interactive desktop access via web browser for image visualization.

How does it work?

• xfce4 provides desktop interface.
• VirtualGL redirects graphics to client.
• TurboVNC server provides VNC access.
• noVNC makes VNC access via web.

What's included?

• python (conda)
• napari
• Fiji - ImageJ
• Ilastik
• QuPath
• Jupyter notebook
• OMERO.insight

How to use it?

Run docker container

docker run --rm -it -e NOVNC_PORT=5901 -p 5901:5901 image-station:latest

Now point your browser to http://YOUR-IP:5901 and input the password you saw on the terminal.

Run singularity image

singularity run  /path/to/image-station.sif

Now follow Browse address shown.

📦 The already built image is avaiabale at /nfs/cellgeni/singularity/images/image-station-202303.sif

singularity run  /path/to/image-station.sif

Options

custom port

By default a random free port will be used for noVNC. If you want to use a custom port set the environment vairable NOVNC_PORT. For example:

docker run --rm -it -p 6080:6080 -e NOVNC_PORT=6080 image-station:latest

SINGULARITY_ENV_NOVN_PORT singularity run /path/to/image-station.sif

custom password

A random password is generated using the user name and 4 numbers. If you want to use a custom password set the environment variabel NOVNC_PASSWORD For example:

docker run --rm -it -p 5901:5901  -e NOVNC_PASSWORD=P4$$w0Rd image-station:latest

SINGULARITY_ENV_NOVNC_PASSWORD='P4$$w0Rd' singularity run /path/to/image-station.sif

Example on the farm

Launch container as a job with 4CPU and 32 GB RAM on the long queue. Replace team999 with your LSF group.

export PATH="/software/singularity-v3.9.0/bin:${PATH}"
bsub -q long \
  -G team999 \
  -n4 \
  -M32000 \
  -R"select[mem>32000] rusage[mem=32000] span[hosts=1]"  \
  -Is \
  singularity run -B /nfs,/lustre \
  /nfs/cellgeni/singularity/images/image-station-202303.sif

Example on the farm with GPU

Launch container as a job with 4CPU, 50 GB RAM with 1 GPU and 8 GB GPU RAM and 32 GB RAM on the long queue. Replace team999 with your LSF group.

export PATH="/software/singularity-v3.9.0/bin:${PATH}"
bsub -q gpu-basement \
  -G team999 \
  -n4 \
  -M50000 \
  -R"select[mem>50000] rusage[mem=50000] span[hosts=1]"  \
  -gpu "mode=shared:j_exclusive=no:gmem=8000:num=1"  \
  -Is \
  singularity run --nv -B /nfs,/lustre \
  /nfs/cellgeni/singularity/images/image-station-202303.sif

Build the image

Build docker image

docker build -t image-station:latest .

Build singularity image

After buliding the docker image. Convert it to a singularity image. The following command will produce an image-station.sif file as output.

singularity build image-station.sif docker-daemon://image-station:latest

Additional notes

• A $HOME/.vnc folder will be created to store necessary files for VNC to work.

• Clipbord works using the menu provided by noVNC. At the left side of the screen, click the clipboard icon and you can use that to copy and paste content to/from the running container.

• Desktop menu for Jupyter Notebook won't work for docker as root user because jupyter requires the option --allow-root in that case. Use it from terminal like so: jupyter notebook --allow-root --notebook-dir=/