Segment using Groovy script
===========================

Description
-----------

The following workflows should work in
Fiji, after these have been correctly set up with the OMERO plugin for
Fiji/ImageJ.

Using the Scripting editor of Fiji, we will show:

-  How to connect to OMERO using the JAVA API.

-  How to load all the images within a given Dataset.

-  How to load the images in ImageJ using Bio-Formats.

-  How to analyze the images using *Auto Threshold* and *Analyze particles*
   plugins in ImageJ within a script.

-  How to save the segmented ROIs as polygons in OMERO.

-  How to collect the measurement associated to the ROIs and

   -  Save them as an OMERO.table and link the table to the Dataset.

   -  Save them as a CSV file and link it to the Dataset.

Setup
-----

-  Install Fiji on the local machine with the OMERO.insight-ij plugin.
   The installation instructions can be found at :doc:`installation`.

Resources
---------

-  Data: Samples images from the Image Data Resource (IDR) `idr0021 <https://idr.openmicroscopy.org/search/?query=Name:idr0021>`_.

-  `Java API documentation <https://docs.openmicroscopy.org/latest/omero/developers/Java.html>`__.

-  Script: Groovy script for automatic segmentation of images from OMERO using Fiji
   -  :download:`analyse_dataset_save_rois_and_summary_table.groovy <../scripts/groovy/analyse_dataset_save_rois_and_summary_table.groovy>`.

Step-by-Step
------------

We will now repeat the manual analysis :doc:`threshold_manual` on a
Dataset using the scripting facility available in Fiji.

Let’s go over the script to understand the logic and see how it matches
the UI steps.

This script explores the `JAVA API <https://docs.openmicroscopy.org/latest/omero/developers/Java.html>`__ using Groovy.

It will process all the Images in the specified Dataset,
applying threshold, analyzing particles and saving ROIs back in
OMERO i.e. we reproduce in a script the manual steps recorded.
Further, it will create a CSV and OMERO.table to be attached to
that Dataset in OMERO.

#. In your browser, go to the server address provided.

#. Log in using the credentials provided.

#. Make sure you are selecting your own data. Select the Dataset **A-Fiji-dataset**.

#. Launch Fiji.

#. Go to *File > New > Script...*.

#. A dialog pops up. In the *Language* menu, select *Groovy*.

#. Copy, into the text script editor of Fiji, :download:`analyse_dataset_save_rois_and_summary_table.groovy <../scripts/groovy/analyse_dataset_save_rois_and_summary_table.groovy>`.

#. You will be asked to enter your login credentials when you run the script.

#. Click *Run*.

#. Return to OMERO.web and open an Image from this Dataset in OMERO.iviewer.

#. Click the *ROIs* tab to see the added ROIs. Note that the ROIs have been assigned a Channel index to indicate which Channel they were derived from.

#. In the *Settings* tab, turning channels on/off will also show/hide
   ROIs assigned to those channels.

#. Open the image in OMERO.figure for a quick publication by going to
   Info tab in iviewer and clicking on OMERO.figure in the Open with
   line.\ |image1|


.. |image1| image:: images/threshold_script2.png
   :width: 1.89583in
   :height: 0.36458in