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OMERO API

This document is the main API specification for OMERO.

See: Description

A. Core System 
Package Description
ome.api
Contains the central verbs of the Omero System.
ome.conditions
Forms the basis of all Omero exception hierarchies.
ome.conditions.acl
Exceptions thrown due to access control violations.
ome.parameters
Contains necessary parameters for various API methods throughout OMERO.
ome.system
Provides the necessary container structure for the entire Omero system.
ome.system.metrics
General metrics registry for use by all server-side components.
B. Model 
Package Description
ome.model
Central interfaces in the Omero object model.
ome.model.acquisition  
ome.model.annotations  
ome.model.containers  
ome.model.core  
ome.model.display  
ome.model.enums  
ome.model.experiment  
ome.model.fs  
ome.model.internal
Contains non-code-generated model objects.
ome.model.jobs  
ome.model.meta  
ome.model.roi  
ome.model.screen  
ome.model.stats  
ome.model.units  
C. Client Packages 
Package Description
omero.gateway  
omero.gateway.cache  
omero.gateway.exception  
omero.gateway.facility  
omero.gateway.model  
omero.gateway.rnd  
omero.gateway.util  
D. Server Packages 
Package Description
ome.annotations
Runtime source annotation package for the OMERO server This includes classes that annotate source code and check metadata at runtime for server API calls.
ome.api.local
Non-client service API for OMERO This includes interfaces for the local administration of the OMERO server.
ome.io.bioformats  
ome.io.messages  
ome.io.nio
New Input/Output handling for the OMERO server This includes interfaces/classes for the input and output handling of data within the OMERO server.
ome.logic
The central repository of implementations which will be accessible through this server.
ome.security
JBoss and OMERO security handling This includes classes that provide security for the execution and usage of the OMERO server on a JBoss platform.
ome.security.auth  
ome.security.auth.providers  
ome.security.basic
Basic OMERO security contextual classes Basic classes that provide security context objects necessary to secure the implementation of the OMERO server on a JBoss platform.
ome.security.policy
Extensible service and security policies which can influence whether a user, group, or other agent can perform a certain action.
ome.security.sharing  
ome.services
Base services package for OMERO API services This includes classes that implement OMERO API services described as interfaces in the OMERO Common component.
ome.services.db  
ome.services.delete
Implementations of the ome.api.IDelete service.
ome.services.delete.files  
ome.services.eventlogs  
ome.services.formats  
ome.services.fulltext
All necessary classes for background indexing of metadata and attached binary files.
ome.services.fulltext.bridges
Custom FieldBridge implementations which can be configured to be run on each indexing activity.
ome.services.graphs
Server classes for handling complicated graphs of model objects.
ome.services.mail
General mail services.
ome.services.messages
Message implementations used throughout the server for internal communication.
ome.services.messages.stats  
ome.services.pixeldata  
ome.services.procs
Internal process and process management This includes interfaces and classes that provide thread process management for internal processes critical to the operation of the OMERO server.
ome.services.procs.scripts
Script processor infrastructure.
ome.services.projection  
ome.services.query
facilitates the creation of Hibernate Queries and Criteria.
ome.services.roi  
ome.services.scheduler  
ome.services.scripts  
ome.services.search
Internal search implementation classes.
ome.services.sessions  
ome.services.sessions.events  
ome.services.sessions.state  
ome.services.sessions.stats  
ome.services.sharing
ome.api.IShare support infrastructure.
ome.services.throttling  
ome.services.util
Helper classes to support OMERO service beans Instead of abstract classes, IOC methods and dependency injection is used to provide service interception for the Service (binary) bean classes.
ome.tools
OMERO Server Utility and Spring/Hibernate Tools Classes/Interfaces that implement File, Hibernate, Spring, Annotation, Hierarchy, etc. method mechanics for the OMERO server Related Documentation For more information, please see: TODO
ome.tools.hibernate
Hibernate specific tools for the OMERO Server Classes/Interfaces that implement Hibernate method mechanics for the OMERO server Related Documentation For more information, please see: TODO
ome.tools.lsid
Life Science Identifier (LSID) tools Classes/Interfaces that manage conversions and creation of LSID unique identifiers Related Documentation For more information, please see: TODO
ome.tools.spring
OMERO Server tools specific to Spring Classes/Interfaces that implement AOP, Post-processing injection, session flushing, and factory management.
E. Blitz Server 
Package Description
ome.services.blitz  
ome.services.blitz.fire  
ome.services.blitz.impl  
ome.services.blitz.impl.commands  
ome.services.blitz.measurements  
ome.services.blitz.redirect  
ome.services.blitz.repo  
ome.services.blitz.repo.path  
ome.services.blitz.util  
E. Blitz Client 
Package Description
omero  
omero.cmd  
omero.cmd.admin  
omero.cmd.basic  
omero.cmd.fs  
omero.cmd.graphs  
omero.cmd.mail  
omero.grid  
omero.log  
omero.model  
omero.sys  
omero.util  
G. Rendering Engine 
Package Description
omeis.providers.re
Red-Green-Blue (RGB) data structures and Image Rendering Service This package provides basic data structures to represent an RGB pixel set and provide a service for the rendering of this pixel set.
omeis.providers.re.codomain
Provides codomain pixel set data structures for Maps and Contexts.
omeis.providers.re.data
Provides classes needed to define XY planes within a dynamic 3D context.
omeis.providers.re.metadata  
omeis.providers.re.quantum  
H. Utilities 
Package Description
ome.util
Utilities for all of OMERO.
ome.util.actions  
ome.util.checksum  
ome.util.logback  
ome.util.math.geom2D
Plane geometry data structures for OMERO This includes a several implementations of various two dimensional simple geometry classes to represent these structures within the OMERO system.
ome.util.mem
Dynamic object instance and state management for OMERO This includes various implementations of copy and clonable operations.
ome.util.messages
Messages package for specialized exception handling for OMERO.
ome.util.search  
Other Packages 
Package Description
loci.ome.io
OME I/O: a library for OME database import, upload and download.
loci.ome.io.services  
ome.formats  
ome.formats.enums  
ome.formats.enums.handler  
ome.formats.importer  
ome.formats.importer.cli  
ome.formats.importer.exclusions
FileExclusion provides a mechanism for determining which potential filesets should be excluded from import.
ome.formats.importer.targets  
ome.formats.importer.transfers
FileTransfer provides a mechanism for shipping client-side files to the server-side.
ome.formats.importer.util  
ome.formats.model  
ome.formats.model.handler  
org.hibernate.stat  
This document is the main API specification for OMERO.

Main OMERO API [5.2.6-ice35-b35] Documentation

The Javadocs provided compose the bulk of the OMERO API documentation. However, the OMERO.py documentation is available under python and the slice2html generated documentation is available from slice2html. Where possible links between the various pieces of API references have been added. For an overview or getting started guide, see the links below.

Related Documentation

Further OMERO developer documentation is available. You may find the following particularly useful:

There is also documentation on the OME Data Model.

See Also:
OMERO.py Sphinx documentation, Slice2html documentation
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OmeroJava API

Version: 5.2.6-ice35-b35

Copyright © 2016 The University of Dundee & Open Microscopy Environment. All Rights Reserved.