jodogne/orthanc Docker images

Contents

• jodogne/orthanc Docker images

  • Introduction

  • jodogne/orthanc vs. orthancteam/orthanc Docker images

  • Running the Orthanc core

  • Usage, with plugins enabled

  • Fine-tuning the configuration

  • Configuration management using Docker Compose

  • Making the Orthanc database persistent

  • Whole-slide imaging support

  • PostgreSQL and Orthanc inside Docker

  • Debugging

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.

jodogne/orthanc vs. orthancteam/orthanc Docker images

Two different flavors of Docker images for Orthanc are available:

• The jodogne/orthanc and jodogne/orthanc-plugins Docker images that are described on this page are regularly kept in sync with the latest releases of the Orthanc project, with a basic configuration system that is inherited from the Debian packages (i.e., manual edition of the configuration files).

  This is also where the new experimental features from Sébastien Jodogne’s research team at UCLouvain are initially released. The binaries used in these images correspond to the Linux Standard Base binaries.

  The default user interface is the built-in Orthanc Explorer.

  These images are most useful to software developers and researchers.

• Our commercial partner Orthanc Team also publishes separate Docker images.

  These orthancteam/orthanc images are released 2 or 3 times a month every time a new version of a plugin or Orthanc is available or every time the base Debian image needs to be updated for security reasons.

  Each image has a tag and the list of each component version is documented.

  These images support both AMD64 and ARM64 architectures.

  These images can be configured using congirutation files or environment variables (which is very handy if using Docker Compose or Kubernetes).

  The default user interface is the Orthanc Explorer 2 plugin.

  These images are targeted at ops teams and end-users.

  A specific page is available to describe how these images should be used.

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:

$ 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:

$ docker pull jodogne/orthanc

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

$ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.12.4

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):

$ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.12.4 /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:

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

Or you can also start a specific version of Orthanc for more stability:

$ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins:1.12.4

If you have an interest in the Python plugin, you can use the orthanc-python image. The latter image is a heavier version of the orthanc-plugins image, as it embeds the Python 3.7 interpreter. Here is how to start this image:

$ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python
$ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python:1.12.4

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:

$ docker run --rm --entrypoint=cat jodogne/orthanc:1.12.4 /etc/orthanc/orthanc.json > /tmp/orthanc.json

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

$ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc:1.12.4

Remark: These Docker images automatically set the environment variable MALLOC_ARENA_MAX to 5 in order to control memory usage. This default setting can be overriden by providing the option -e MALLOC_ARENA_MAX=1 when invoking docker run (the value 0 corresponds to the default value).

Configuration management using Docker Compose

Depending on the context, the Docker Compose tool might be easier to use than the plain Docker tool, as it allows replacing long command lines as above, by plain configuration files. The trick here is to provide the JSON configuration files to Orthanc as secrets (note that the related option configs could in theory be better, unfortunately it is only available to Docker Swarm).

First create the docker-compose.yml file as follows (this one uses the YAML file format):

version: '3.1'  # Secrets are only available since this version of Docker Compose
services:
  orthanc:
    image: jodogne/orthanc-plugins:1.12.4
    command: /run/secrets/  # Path to the configuration files (stored as secrets)
    ports:
      - 4242:4242
      - 8042:8042
    secrets:
      - orthanc.json
    environment:
      - ORTHANC_NAME=HelloWorld
secrets:
  orthanc.json:
    file: orthanc.json

Then, place the configuration file orthanc.json next to the docker-compose.yml file. Here is a minimalist orthanc.json:

{
  "Name" : "${ORTHANC_NAME} in Docker Compose",
  "RemoteAccessAllowed" : true
}

This single configuration file should contain all the required configuration options for Orthanc and all its plugins. The container can then be started as follows:

$ docker-compose up

Note how the environment variable ORTHANC_NAME has been used in order to easily adapt the configuration of Orthanc. This results from the fact that Orthanc injects environment variables once reading the content of its configuration files (since Orthanc 1.5.0).

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
$ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc:1.12.4

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:

$ docker run -p 4242:4242 -p 8042:8042 --rm --name orthanc-wsi jodogne/orthanc-plugins:1.12.4

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

$ docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.tif:/tmp/Source.tif:ro jodogne/orthanc-plugins:1.12.4 --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:

$ docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.svs:/tmp/Source.svs:ro jodogne/orthanc-plugins:1.12.4 --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:

$ 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:

$ 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:

$ docker inspect --format '{{ .NetworkSettings.IPAddress }}' some-postgres
$ docker inspect --format '{{ .NetworkSettings.Ports }}' some-postgres
$ docker run --rm --entrypoint=cat jodogne/orthanc-plugins:1.12.4 /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:

$ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc-plugins:1.12.4

Debugging

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

$ docker run -i -t --rm --entrypoint=bash jodogne/orthanc:1.12.4
$ docker run -i -t --rm --entrypoint=bash jodogne/orthanc-plugins:1.12.4