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 Omero-plugin for ImageJ/FIJI from https://www.openmicroscopy.org/omero/downloads,
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.