OMERO API Reference Documentation.
See: Description
| 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.
|
| 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 |
| Package | Description |
|---|---|
| pojos | |
| pojos.util |
| 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.chgrp | |
| ome.services.chown | |
| ome.services.db | |
| ome.services.delete |
Implementations of the ome.api.IDelete service.
|
| ome.services.delete.files | |
| ome.services.eventlogs | |
| ome.services.export |
Helpers for implementing the necessary interfaces from Bio-Formats for
mapping OMERO objects (ome.model.*) to OME-XML and OME-TIFF
|
| 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.
|
| Package | Description |
|---|---|
| omero | |
| omero.cmd | |
| omero.cmd.admin | |
| omero.cmd.basic | |
| omero.cmd.fs | |
| omero.cmd.graphs | |
| omero.cmd.mail | |
| omero.grid | |
| omero.model | |
| omero.sys | |
| omero.util |
| 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 |
| 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 |
| 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 |
mechanism for determing
which potential filesets should be excluded from import.
|
| ome.formats.importer.transfers |
mechanism for shipping
client-side files to the server-side.
|
| ome.formats.importer.util | |
| ome.formats.model | |
| ome.formats.model.handler | |
| org.hibernate.stat |
OMERO API Reference Documentation.
OMERO API Reference Documentation. For complete documentation, see openmicroscopy.org
Main OMERO API [5.1.3-ice35-b52] 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.
OmeroJava Api
Version: 5.1.3-ice35-b52
Copyright © 2015 The University of Dundee & Open Microscopy Environment. All Rights Reserved.