Crop and import
===============

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

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

Using the User Interface of the OMERO plugin, we will show:

-  How to connect to OMERO using the OMERO plugin for ImageJ/Fiji.

-  How to open an image from OMERO.server into Fiji/ImageJ.

-  How to import the cropped image from Fiji/ImageJ into OMERO.

Setup
-----

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

Resources
---------

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


Step-by-step
------------


In this example, we show how to open an OMERO image, crop the image and
import the cropped image back to OMERO as OME-TIFF.

#. Launch Fiji/ImageJ.

#. Go to *Plugins > OMERO > Connect* To OMERO. This will show a login
   screen where you can enter the name of the server to connect to,
   the username and password. The OMERO plugin will allow you to
   browse your data in a similar manner to OMERO.web.

#. In the OMERO login dialog, click the wrench icon\ |image1| and then
   add the server address in the dialog. By default, only "localhost"
   is listed. Click on the *plus* icon to add a new line to the list
   and type into the line the server address.

#. Click Apply.

   .. image:: images/manual2.png

#.  Enter your credentials and click *Login*.

#. Select a dataset, for example the *A-Fiji-dataset* Dataset.

#. Double-click on a thumbnail or on an Image in the left-hand tree to open an Image in Fiji/ImageJ.

#. Draw a Rectangle on the Image.

#. Select the option *Image > Crop*.

#. A new Image will be displayed in a Fiji/ImageJ window.

#. Go to *Plugins > OMERO > Save Image(s) To OMERO*.

#. An Import dialog will pop up.

   .. image:: images/manual5.png

#. Check that the option *Add Image from current window* is selected.

#. Select where to import the cropped Image, for example an existing Dataset, e.g. *A-Fiji-dataset*. You can also select *New From Folder* option which will create a new Dataset named with the name of the image you opened from OMERO to Fiji. In case you select *No Dataset* option, the new image will be displayed in the *Orphaned Images* folder in OMERO.

#. Click *Add to the Queue* button.

#. Then click *Import*. The import will start.

#. When the import is done, go back to the Tree view in the Fiji plugin or OMERO.web. Refresh. Check the new Image.

.. |image1| image:: images/manual1.png
   :width: 0.24105in
   :height: 0.24105in