|crick| Crick's OMERO guide
===========================

This OMERO guide is specific to the Crick's OMERO implementations. It offers step-by-step instructions on how to use components of the OMERO platform at the Crick.

Getting started
---------------

The OMERO guide is divided into several parts:

:doc:`core_features` covers OMERO terminology and concepts of project, dataset, image, metadata, users, groups,etc.
  * Basic operations - navigate to different groups, creating project & dataset, moving images, renaming images, copying links to images, etc.
  * Annote data and filter them.
  * Search for data

:doc:`web_addons` includes viewing using 
   * default viewer: imageviewer, 
   * OMERO.iviewer, 
   * PathViewer,
   * OMERO.figure - for making figures.

:doc:`import` covers how to put images into OMERO via in-place import and how to access (directly instead of download) that after import

:doc:`external_tools` introduces how to analyse data using third party tools 
   * QuPath |qupath|.
   * Fiji |fiji|.



More information
----------------
#. `OMERO-Guide`_ - To learn more about OMERO.  
#. `OME website <https://www.openmicroscopy.org/omero>`_ - We also recommend that you first visit the `Open Microscopy Environment Website <https://www.openmicroscopy.org/omero/>`_.
#. `OME Youtube <https://www.youtube.com/channel/UCyySB9ZzNi8aBGYqcxSrauQ/videos>`_- You can also watch videos of OMERO features or workshop recordings on the `Open Microscopy Environment YouTube channel <https://www.youtube.com/channel/UCyySB9ZzNi8aBGYqcxSrauQ/videos>`_. 

Please be aware that some of the operations are different from the Crick's OMERO.


.. _OMERO-Guide: https://omero-guides.readthedocs.io/en/latest/
.. |qupath| image:: images/logos/qupath.png
   :width: 0.46875in
   :height: 0.28125in
.. |fiji| image:: images/logos/fiji.png
   :width: 0.28125in
.. |crick| image:: images/logos/CRICK_Brandmark_01_transparent.png
   :width: 1in
   :height: 1in
.. toctree::
   :maxdepth: 1
   :hidden:

   core_features
   web_addons
   import
   external_tools