How to install OMERO plugins for Fiji/ImageJ

Description

Fiji is a free open-source image processing package based on ImageJ. The following workflow shows how to install the OMERO plugin for Fiji and ImageJ.

The OMERO plugin does not have an update site yet.

Setup step-by-step

We assume that you have already Fiji/ImageJ installed locally. If not, download Fiji.

In this section, we will cover the steps required to install the OMERO plugin for Fiji. If you wish to install it for ImageJ, an additional step is needed.

We first describe the common installation steps for ImageJ and Fiji. We then describe how to install the Bio-Formats Package for ImageJ.

Installing the OMERO plugin in Fiji also adds the dependencies required to connect to OMERO using the Script Editor of Fiji.

Installation of the OMERO plugin for Fiji and ImageJ

Below are the common steps that need to be followed:

  • Find the Plugins folder of your Fiji application and check if it contains any old omero_ij-5.x.x-all.jar file(s) or OMERO.imagej-5.x.x folder(s). Remove any such jar files or folders from the Plugins folder.

  • Download from https://www.openmicroscopy.org/omero/downloads the latest 5.x.x version of ImageJ/Fiji plugin for OMERO

_images/setup1.png
  • For recent plugin versions (5.5.7 and higher): Note where you downloaded the omero_ij-5.x.x-all.jar file. Copy that file into the plugins folder of Fiji.

  • For plugin versions lower than 5.5.7: Extract the downloaded .zip archive. Remember where you extracted it to.

  • For plugin versions lower than 5.5.7: Copy the extracted folder and paste it to the plugins folder of Fiji.

  • Note: For plugin versions lower than 5.5.7: Some Windows unzip apps create a double folder enclosing the plugin. If that is the case, copy the inner OMERO.imagej-5.x.x folder into Fiji.app > plugins folder.

  • Now, restart Fiji. If you are using ImageJ, follow with the additional step below.

Installation of Bio-Formats Package, ImageJ only

_images/setup2.png
  • Move the downloaded file into the ImageJ > plugins folder.

  • Restart ImageJ.

Installation of the plugins to interact with OMERO using the ImageJ marco language

The plugins are developed and supported by Institute of genetics, reproduction & development (iGReD) in Clermont-Ferrand (France).

  • Download the latest version of simple-omero-client from https://github.com/GReD-Clermont/simple-omero-client:

    • Click on the Tags tab

    • Click on the most recent tag

    • Download the simple-omero-client-<tag>.jar file e.g. simple-omero-client-5.14.1.jar

  • Download the latest version of omero_macro-extensions from https://github.com/GReD-Clermont/omero_macro-extensions:

    • Click on the Tags tab

    • Click on the most recent tag

    • Download the omero_macro-extensions-<tag>.jar file e.g. omero_macro-extensions-1.3.2.jar

  • Move the downloaded jars into the Fiji > plugins folder.

  • Restart Fiji.