Orthanc for Docker

Introduction

Docker images for the Orthanc core and its official plugins are freely available on the DockerHub platform. The source code of the corresponding Docker images is available on GitHub.

Note for CentOS users: The Docker environment might be difficult to configure on your platform. Hints are available on the Orthanc Users discussion group.

Running the Orthanc core

The following command will start the core of Orthanc, with all the plugins disabled:

$ sudo docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc

Once Orthanc is running, use Mozilla Firefox at URL http://localhost:8042/ to interact with Orthanc. The default username is orthanc and its password is orthanc.

The command above starts the mainline version of Orthanc, whose development is in continuous progress. Do not forget to regularly update the Docker image to benefit from the latest features:

$ sudo docker pull jodogne/orthanc

If more stability is required, you can select the official release of Orthanc to be run:

$ sudo docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.3.0

Passing additional command-line options (e.g. to make Orthanc verbose) can be done as follows (note the /etc/orthanc option that is required for Orthanc to find its configuration files):

$ sudo docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc /etc/orthanc --verbose

Usage, with plugins enabled

The following command will run the mainline version of the Orthanc core, together with its Web viewer, its PostgreSQL support, its DICOMweb implementation, and its whole-slide imaging viewer:

$ sudo docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins

Fine-tuning the configuration

For security reasons, you should at least protect your instance of Orthanc by changing this default user, in the RegisteredUsers configuration option. You will also probably need to fine-tune other parameters, notably the list of the DICOM modalities Orthanc knows about.

You can generate a custom configuration file for Orthanc as follows:

$ sudo docker run --rm --entrypoint=cat jodogne/orthanc /etc/orthanc/orthanc.json > /tmp/orthanc.json

Then, edit the just-generated file /tmp/orthanc.json and restart Orthanc with your updated configuration:

$ sudo docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc

Making the Orthanc database persistent

The filesystem of Docker containers is volatile (its content is deleted once the container stops). You can make the Orthanc database persistent by mapping the /var/lib/orthanc/db folder of the container to some path in the filesystem of your Linux host, e.g.:

$ mkdir /tmp/orthanc-db
$ sudo docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc:1.3.0

Whole-slide imaging support

The orthanc-plugins image includes support for microscopic whole-slide imaging (WSI). For instance, the following command will start the WSI viewer plugin transparently together with Orthanc:

$ sudo docker run -p 4242:4242 -p 8042:8042 --rm --name orthanc-wsi jodogne/orthanc-plugins

Note that we gave the name orthanc-wsi to this new Docker container. Then, the Dicomizer command-line tool can be invoked as follows:

$ sudo docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.tif:/tmp/Source.tif:ro jodogne/orthanc-plugins --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ /tmp/Source.tif

This command needs a few explanations:

  • --link=orthanc-wsi:orthanc links the container running the Dicomizer, to the Docker container running Orthanc that we started just before.
  • --entrypoint=OrthancWSIDicomizer specifies that the Dicomizer must be run instead of the Orthanc server.
  • -v /tmp/Source.tif:/tmp/Source.tif:ro maps the source image /tmp/Source.tif on the host computer into the Orthanc container as read-only file /tmp/Source.tif.
  • --orthanc=http://orthanc:8042/ instructs the Dicomizer to push images through the --link created above.
  • --username=orthanc --password=orthanc correspond to the default credentials of the orthanc-plugins image.

Obviously, you are free to add all the options you wish (check out the --help flag to list these options). In particular, the --dataset option allows to specify DICOM tags, in the JSON file format, so as to include them in the resulting DICOM series (the option --sample-dataset prints a sample JSON file that has the expected format).

If you have a source image that is not a hierarchical TIFF, you must instruct the Dicomizer to use OpenSlide to decode it by adding the --openslide option:

$ sudo docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.svs:/tmp/Source.svs:ro jodogne/orthanc-plugins --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ --openslide=libopenslide.so /tmp/Source.svs

PostgreSQL and Orthanc inside Docker

It is possible to run both Orthanc and PostgreSQL inside Docker. First, start the official PostgreSQL container:

$ sudo docker run --name some-postgres -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=pgpassword --rm postgres

Open another shell, and create a database to host the Orthanc database:

$ sudo docker run -it --link some-postgres:postgres --rm postgres sh -c 'echo "CREATE DATABASE orthanc;" | exec psql -h "$POSTGRES_PORT_5432_TCP_ADDR" -p "$POSTGRES_PORT_5432_TCP_PORT" -U postgres'

You will have to type the password (cf. the environment variable POSTGRES_PASSWORD above that it set to pgpassword). Then, retrieve the IP and the port of the PostgreSQL container, together with the default Orthanc configuration file:

$ sudo docker inspect --format '{{ .NetworkSettings.IPAddress }}' some-postgres
$ sudo docker inspect --format '{{ .NetworkSettings.Ports }}' some-postgres
$ sudo docker run --rm --entrypoint=cat jodogne/orthanc-plugins /etc/orthanc/orthanc.json > /tmp/orthanc.json

Add the following section to /tmp/orthanc.json (adapting the values Host and Port to what docker inspect said above):

"PostgreSQL" : {
  "EnableIndex" : true,
  "EnableStorage" : true,
  "Host" : "172.17.0.38",
  "Port" : 5432,
  "Database" : "orthanc",
  "Username" : "postgres",
  "Password" : "pgpassword"
}

Finally, you can start Orthanc:

$ sudo docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc-plugins

Debugging

For debugging purpose, you can start an interactive bash session as follows:

$ sudo docker run -i -t --rm --entrypoint=bash jodogne/orthanc
$ sudo docker run -i -t --rm --entrypoint=bash jodogne/orthanc-plugins