In order to connect to an OMERO server and use the data stored there directly in Fiji/mageJ, plugins have to be installed.
The following instructions guide you through the download, installation and use of ImageJ, Fiji and the plugins.
1- Download the Omero-plugin for ImageJ/FIJI from https://downloads.openmicroscopy.org/omero/5.4.10/artifacts/OMERO.insight-ij-5.4.10-ice36-b105.zip
Warning: It is very important to get the correct version of the Omero-plugin, according to the OMERO server’s version at the time of the download. eg: 5.4.10-ice36-b105.
2- Copy and extract the downloaded .zip archive into the Plugins folder of your Fiji (or ImageJ) directory.
3- Launch the Fiji/ImageJ application and click on the Plugins menu. Select OMERO > Connect to OMERO.
4- Enter your icm login informations in the authentication screen to access your Omero group/user home.
5- You will then be taken to the OMERO.insight Data Manager screen.
6- Double click on the image in the data tree or select the image and View > View in ImageJ in the contextual menu.
7- You can work with imageJ as usual to transform the images or create segmentations ROIs … and finally, save the transformed images, ROIS or any excel/csv results back to Omero. Result files will be attached to the image in Omero.
See more in this OMERO-Fiji demo video.