We will provide you with software that comes pre-packaged with all necessary plugins and libraries. You will find the downloads here:
Alternatively, you can download the software manually and install all plugins yourself.
If you are using MacOS, please install the software manually. We currently do not have a Mac available and it is impossible for us to prepare packages.
Important: Installing missing Icy component
We forgot to package the Icy version with an important file. If you are on Windows, you can re-download Icy now. Alternatively (or if you use Mac), you can download the file ( MorphoLibJ_-22.214.171.124.jar) and copy it into <Icy Directory>/ij/plugins
Setting up ImageJ/JIPipe
First, download ImageJ (Fiji) from the official website.
- Unpack/install ImageJ and start it for the first time. Fiji will ask you to install updates. Confirm installing updates and follow the steps until the software is up-to-date. If no update check is displayed, run the check manually by executing Help -> Update
- Close ImageJ
- Download the JIPipe plugin. Open/Extract the ZIP file and copy its contents into Fiji.app/plugins
- Open ImageJ. Because ImageJ is sometimes inconsistent with pre-packaged libraries, JIPipe sometimes supplies duplicate libraries that ImageJ will warn about. Just instruct ImageJ to delete the duplicates. If you are on Windows, delete the dependencies/Image5D.jar file.
- Use the search box to run "JIPipe GUI"
- If JIPipe has detected missing dependencies, follow the instructions to install them
- Close ImageJ after all dependencies have been installed
Setting up Icy
Icy comes with all plugins pre-installed. Download Icy from its official website and extract/install the ZIP file/the app.
You will need to install Java to be able to run Icy. Choose Java 8 or Java 11 (if possible) and run the installer. Enable setting JAVA_HOME and JavaSoft registry keys during the installation.
If Icy.exe does not run, try running icy.jar directly.
Setting up KNIME
You can download KNIME from its official website. Please follow these steps to install all necessary plugins for image analysis:
- Go to File -> Preferences -> then Install/Update -> Available Update sites
- Enable KNIME Community Extensions (Experimental)
- Click "Apply and Close"
- Go to File -> Install KNIME Extensions
- Open the category "Image Processing and Analysis" (click the triangle)
- Enable "KNIME Image Processing"
- Enable "ImageJ Integration (Beta)"