Page Contents


Feature List

Previous topic

Developing OMERO clients

Next topic

OMERO admin interface

This Page


This documentation is for OMERO 5.2. This version is now in maintenance mode and will only be updated in the event of critical bugs or security concerns. OMERO 5.3 is expected in the first quarter of 2017.

OMERO Application Programming Interface

All interaction with the OMERO server takes place via several API services available from a ServiceFactory. A service factory is obtained from the client connection e.g. Python:

client = omero.client("localhost")
session = client.createSession("username", "password")   # this is the service factory
adminService = session.getAdminService()                 # now we can get/create services
  • The Service factory API has methods for creating Stateless and Stateful services (see below).
    • Stateless services are obtained using “get…” methods e.g. getQueryService()
    • Stateful services are obtained using “create…” methods e.g. createRenderingEngine()
  • Services will provide access to omero.model.objects. You will then need the API for these objects, e.g. Dataset, Image, Pixels etc.

Services list

The ome.api package in the common component defines the central “verbs” of the OMERO system. All external interactions with the system should happen with these verbs, or services. Each OMERO service belongs to a particular service level with each level calling only on services from lower levels.

Service Level 1 (direct database and Hibernate connections)

  • AdminService: src, API for working with Experimenters, Groups and the current Context (switching groups etc).
  • ConfigService: src, API for getting and setting config parameters.
  • ContainerService: API for loading Project, Dataset and Image hierarchies.
  • LdapService: src, API for communicating with LDAP servers.
  • MetadataService: API for working with Annotations.
  • PixelsService: API for pixels stats and creating Images with existing or new Pixels.
  • ProjectionService API
  • QueryService: src, API for custom SQL-like queries.
  • RenderingSettingsService API for copying, pasting & resetting rendering settings.
  • RepositoryInfo API disk space stats.
  • RoiService API working with ROIs.
  • ScriptService API for uploading and launching Python scripts.
  • SessionService API for creating and working with OMERO sessions.
  • ShareService API
  • TimelineService API for queries based on time.
  • TypesService API for Enumerations.
  • UpdateService: src, API for saving and deleting omero.model objects.

Service Level 2

Stateful/Binary Services

A complete list of service APIs can be found here and some examples of API use in Python are provided. Java or C++ code can use the same API in a very similar manner.


Reads and writes

IQuery and IUpdate are the basic building blocks for the rest of the (non-binary) API. IQuery is based on QuerySources and QueryParemeters which are explained under Using server queries internally. The goal of this design is to make wildly separate definitions of queries (templates, db-stored, Java code, C# code, …) runnable on the server.

IUpdate takes any graph composed of IObject objects and checks them for dirtiness. All changes to the graph are stored in the database if the user calling IUpdate has the proper permissions, otherwise an exception is thrown.

Dirty checks follow the Three Commandments:

  1. Any IObject-valued field with unloaded set to true is treated as a place holder (proxy) and is re-loaded from the database.
  2. Any collection-valued field with a null value is re-loaded from the database.
  3. Any collection-valued field with the FILTERED flag is assumed to be dirty and is loaded from the database, with the future option of examining the filtered collection for any new and updated values and applying them to the real collection. (Deletions cannot happen this way since it would be unclear if the object was filtered or deleted.)


The IAdmin interface defines all the actions necessary to administer the Server security and firewalls . It is explained further on the OMERO admin interface page.

Model Object Java

Certain operations, like those dealing with data management and viewing, happen more frequently than others (like defining microscopes). Those have been collected in the IContainer interface. IContainer simplifies a few very common queries, and there is a related package (“omero.gateway.model.*”) for working with the returned graphs. OMERO.insight works almost exclusively with the IContainer interface for its non-binary needs.


// Saving a simple change
Dataset d = iQuery.get( Dataset.class,1L );
d.setName( "test" );
iUpdate.saveObject( d );

// Creating a new object
Dataset d = new Dataset();
d.setName( "test" ); // not-null fields must be filled in
iUpdate.saveObject( d );

// Retrieving a graph
Set<Dataset> ds = iQuery.findAllByQuery( "from Dataset d left outer join d.images where = 'test'",null );

Stateless versus stateful services

A stateless service has no client-noticeable lifecycle and all instances can be treated equally. A new stateful service, on the other hand, will be created for each client-side proxy (see the ServiceFactory.create\* methods). Once obtained, a stateful service proxy can only be used by a single user. After task completion, the service should be closed (proxy.close()) to free up server resources.

How to write a service

A tutorial is available at How To create a service. In general, if a properly annotated service is placed in any JAR of the OMERO EAR file (see Build System for more) then the service will be deployed to the server. In the case of OMERO.blitz, the service must be properly defined under components/blitz/resources.

OMERO annotations for validation

The server-side implementation of these interfaces makes use of ((JDK5)) Structured annotations and an AOP interceptor to validate all method parameters. Calls to pojos.findContainerHierarches are first caught by a method interceptor, which checks for annotations on the parameters and, if available, performs the necessary checks. The interceptor also makes proactive checks. For a range of parameter types (such as Java Collections) it requires that annotations exist and will refuse to proceed if not implemented.

An API call of the form:


is implemented as

pojos.findContainerHierarchies(@NotNull Class, @NotNull @Validate(Integer.class) Set, Map)