OMERO clients overview
======================

Most laboratories use a number of different imaging platforms and thus
require tools to manage, visualize and analyze heterogeneous sets of
image data recorded in a range of file formats. Ideally a single set of
applications, running on a user's laptop or workstation, could access
all sets of data, and provide easy-to-use access to this data.

OMERO ships as a server application called :program:`OMERO.server` and a
series of client applications (known simply as clients): :program:`OMERO.web`,
:program:`OMERO.insight` and :program:`OMERO.importer`. All run on the major
operating systems and provide image visualization, management, and annotation
to users from remote locations. With a large number of OMERO.server
installations worldwide, OMERO has been shown to be relatively easy to install
and get running.

OMERO.insight and OMERO.importer are desktop applications written in Java
and require Java 1.7 (or higher) to be installed on the user's computer
(automatically installed on most up-to-date OS X and Windows XP systems).

Our user assistance :help:`help website<>` provides a series of 
workflow-based guides to performing common actions in the client applications, 
such as importing and viewing data, exporting images and using the measuring 
tool. 

Our partners within the OME consortium are also producing new clients and 
modules for OMERO, integrating additional functionality, particularly for more 
complex image analysis. See the :partner_plone:`Partner Projects <>` page for 
more details.

.. _omero-web:

OMERO.web
---------

OMERO.web is a web-based client for users who wish to access their data in the
browser. This offers a similar view to the OMERO.insight desktop client.
Figures :ref:`omeroweb_44` and :ref:`omero_web_4_4` present the user
interface [2]_ [4]_. Developers can use the |OmeroWeb| to build customized views.

.. _omeroweb_44:
.. figure:: /images/OmeroWeb_44.png
    :width: 60%
    :align: center
    :alt: OMERO.web user interface
    
    OMERO.web user interface

.. _omero_web_4_4:
.. figure:: /images/omero_web_4_4.png
    :width: 60%
    :align: center
    :alt: OMERO.web image viewer
    
    OMERO.web image viewer
    

For more information and guides to using OMERO.web, see our 
:help:`help website <>`.

.. _omero-insight:

OMERO.insight
-------------

OMERO.insight provides a number of tools for accessing and using data in an
OMERO server. The figure :ref:`omero_insight_4_4_viewer` presents the
OMERO.insight image viewer, whereas figure :ref:`omero_insight_screenshot_4_4`
presents the user interface [1]_ [3]_. To find out more, see the 
:help:`OMERO.insight user guides <>`.

.. _omero_insight_4_4_viewer:
.. figure:: /images/omero_insight_4_4_viewer.png
    :align: center
    :width: 60%
    :alt: OMERO.insight ImageViewer
    
    OMERO.insight ImageViewer
    
.. _omero_insight_screenshot_4_4:    
.. figure:: /images/omero_insight_screenshot_4_4.png
    :align: center
    :width: 60%
    :alt: OMERO.insight
    
    OMERO.insight

Among many features, the noteworthy OMERO.insight elements are:

- DataManager, a traditional tree-based view of the data hierarchies in an
  OMERO server. DataManager supports access to all image metadata,
  annotations, tags.
- ImageViewer, for visualization of 5D images (space, channel, time). The
  ImageViewer makes use of the OMERO server's Rendering Engine, and provides
  high-performance viewing of multi-dimensional images on standard
  workstations (e.g. scrolling through space and time), without requiring
  installation of high-powered graphics cards. Most importantly, image viewing
  at remote locations is enabled. Image rendering settings are saved and
  chosen by user ID.
- Measurement Tool, a sub-application of ImageViewer that enables size and
  intensity measurements of defined regions-of-interest (ROIs).
- Working Area, for viewing, annotating, and manipulating large sets of image
  data.
- User administration.
- Image import.

Our user assistance :help:`help website <>` features a number of
workflow-based guides to importing, viewing, managing and exporting your data
using OMERO.insight.

.. _omero-importer:

OMERO.importer
--------------

The OMERO.importer is part of the OMERO.insight client, but can also run as a
stand-alone application. The OMERO.importer allows the import of proprietary
image data files from a filesystem accessed from the user's computer to a
running OMERO server. This tool uses a standard file browser to select the
image files for import into an OMERO server.

The tool uses Bio-Formats for translation of proprietary file formats in
preparation for upload to an OMERO Server. Visit 
:bf_doc:`Supported Formats <supported-formats.html>`
for a detailed list of supported formats.

.. figure:: /images/omero_importer_4_4.png
    :align: center
    :width: 60%
    :alt: OMERO.importer
    
    OMERO.importer

.. rubric:: Citation

The screenshots make use of data from the `JCB DataViewer <http://jcb-dataviewer.rupress.org/>`_ under the Creative Commons
Attribution-Noncommercial-Share Alike 3.0 Unported License. For more
information see :about_plone:`Attribution <licensing-attribution/attribution>`.

.. [1] `Dantas, et al., JCB <http://jcb.rupress.org/content/193/2/307>`_
.. [2] `Krenn, et al., JCB <http://jcb.rupress.org/content/196/4/451>`_
.. [3] `Roscioli, et al., JCB <http://jcb.rupress.org/content/196/4/435>`_
.. [4] `Snider, et al., JCB <http://jcb.rupress.org/content/195/2/217>`_