Fiji
====

Fiji is a popular free open-source image processing package based on ImageJ, \ https://imagej.net/Fiji\. We demonstrate how to use Fiji User Interface and OMERO and we also demonstrate how to analyze data in OMERO using Fiji scripting facility.

.. image:: https://mybinder.org/badge_logo.svg
   :target: https://mybinder.org/v2/gh/ome/omero-guide-fiji/master?filepath=notebooks


Install the plugins
*******************

.. toctree::
   :maxdepth: 1
   :titlesonly:

   installation

Manual Analysis
***************


.. toctree::
   :maxdepth: 1
   :titlesonly:

   crop
   manual_analysis
   threshold_manual


Automated Analysis
******************

.. toctree::
   :maxdepth: 1
   :titlesonly:

   threshold_scripting_macro_language
   threshold_scripting

Fiji and Zarr
*************


.. toctree::
   :maxdepth: 1
   :titlesonly:


   view_mobie_zarr

Contribute
----------

Changes to the documentation or the materials should be made directly in the `omero-guide-fiji repository <https://github.com/ome/omero-guide-fiji>`_.


.. toctree::
   :hidden:

   headless_notebook
   imagej_python