4- OMERO & ImageJ plugin

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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://github.com/ome/omero-insight/releases/download/v5.5.12/omero_ij-5.5.12-all.jar

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.