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index.txt
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#######################
Developer Documentation
#######################
The following documentation is for developers wishing to write OMERO client
code or extend the OMERO server. Instructions on :downloads:`downloading <>`,
installation and administering OMERO can be found under the
:doc:`/sysadmins/index` of the main site.
.. figure:: /images/developer-api-figure.png
:align: center
:width: 80%
:alt:
**OMERO** is an open source client/server system written in Java for
visualizing, managing, and annotating microscope images and metadata.
The |OmeroApi| allows clients to be
written in :doc:`Java </developers/Java>`, :doc:`Python </developers/Python>`,
:doc:`C++ </developers/Cpp>` or :doc:`MATLAB </developers/Matlab>`. OMERO
releases include a Java client OMERO.insight, a Python-based web client
OMERO.web and the :doc:`/developers/cli/index`, which also uses
Python. There is also an ImageJ plugin. OMERO can be extended by modifying
these clients or by writing your own in any of the supported languages (see
figure). OMERO also supports a :doc:`Scripting Service <scripts/index>` which
allows Python scripts to be run on the server and called from any of the other
clients.
OMERO is designed, developed and released by the |OME|, with contributions
from |Glencoe| OMERO is released under the `GNU General Public License (GPL)`_
with commercial licenses and customization available from |Glencoe|. You can
read about how OMERO has developed since the project started in the
:doc:`/users/history`.
.. _GNU General Public License (GPL): http://www.gnu.org/copyleft/gpl.html
For help with any aspect of OMERO, see details of our
:community_plone:`forums and mailing lists <>`.
*********************
Introduction to OMERO
*********************
.. toctree::
:maxdepth: 1
:titlesonly:
whatsnew
installation
build-system
GettingStarted
testing
*******************
Using the OMERO API
*******************
.. toctree::
:maxdepth: 1
:titlesonly:
Python
PythonBlitzGateway
cli/index
Java
Matlab
Cpp
********
Analysis
********
.. toctree::
:maxdepth: 2
:titlesonly:
analysis
Tables
***************************
Scripts - plugins for OMERO
***************************
.. toctree::
:maxdepth: 1
:titlesonly:
scripts/index
scripts/user-guide
scripts/style-guide
scripts/matlab-scripts
scripts/advanced
.. _web_index:
***
Web
***
.. toctree::
:maxdepth: 1
:titlesonly:
Web
Web/Deployment
Web/CreateApp
Web/WebclientPlugin
Web/EditingOmeroWeb
Web/WebGateway
Web/ViewPort
Web/WritingViews
Web/WritingTemplates
Web/CSRF
.. toctree::
:maxdepth: 1
:hidden:
Web/PublicData
*******
Insight
*******
.. toctree::
:maxdepth: 1
:titlesonly:
Insight/Architecture
Insight/Configuration
Insight/Contributing
Insight/DirectoryContents
Insight/EventBus
Insight/HowTo/BuildAgent
Insight/HowTo/BuildAgentView
Insight/HowTo/RetrieveData
Insight/ImplementationView
Insight/TaskBar
*****************
More on API Usage
*****************
OMERO can be extended by modifying these clients or by writing your own in any
of the supported languages.
.. toctree::
:maxdepth: 1
:titlesonly:
GettingStarted/AdvancedClientDevelopment
Modules/Api
Modules/Api/AdminInterface
Modules/Delete
Clients/ImportLibrary
Modules/TempFileManager
Modules/ExceptionHandling
logging
Server/GraphsMigration
******************
The OME Data Model
******************
.. toctree::
:maxdepth: 1
:titlesonly:
Model
Model/StructuredAnnotations
Model/EveryObject
Model/Units
Model/KeyValuePairs
Model/XsltTransformations
*********
Searching
*********
.. toctree::
:maxdepth: 1
:titlesonly:
Modules/Search
Search/FileParsers
Modules/Search/Bridges
***************************
Authentication and Security
***************************
.. toctree::
:maxdepth: 1
:titlesonly:
Server/PasswordProvider
Server/LoginAttemptListener
Server/Ldap
Server/SecurityRoles
Server/SecuritySystem
Server/Permissions
*********************
OMERO.server in depth
*********************
.. toctree::
:maxdepth: 1
:titlesonly:
Server
Server/ExtendingOmero
server-blitz
Server/FS
ImportFS
server-processor
server-rendering
Server/Clustering
Server/CollectionCounts
Server/HowToCreateAService
Server/Sessions
Server/Aop
Server/Context
Server/Events
Server/Properties
Server/Queries
Server/Throttling
Server/RenderingEngine
Server/ScalingOmero
Server/SqlAction
Server/ObjectGraphs