Download

Please choose how you want to install JIPipe
Recommended. An update site allows you to easily update JIPipe to newer versions with one click. It requires from you to have an existing installation of ImageJ.
  1. Download ImageJ or open your existing ImageJ installation
  2. Go to Help > Update ... and activate the JIPipe update site. Then let ImageJ download all necessary files.
  3. Click Manage update sites and select JIPipe. If JIPipe is not available, click Add update site and add a new site with the name JIPipe and the URL https://sites.imagej.net/JIPipe/
  4. Click Apply changes and wait until all downloads have been finished
  5. Restart ImageJ and go to Plugins/JIPipe/JIPipe GUI
  6. On the first start, JIPipe will most likely detect missing dependencies. You can find information about this feature here
Tip: If you want a desktop shortcut (Windows) or an entry in your application menu (Linux), open JIPipe and run Tools > Create launchers
Info: We have only limited capabilities to test software on Apple computers and are aware of issues regarding the integration of external software (Python, R, Cellpose, ...). We are open to contributions to resolve these problems.

Please note that this package might contain an older version of Fiji and JIPipe. We recommend to use the ImageJ update site to install JIPipe.

You can download a package that provides an existing Fiji installation plus all necessary files for JIPipe.
  1. Download the package
  2. Extract the *.zip file
  3. Run ImageJ-win64.exe
  4. Go to Plugins/JIPipe/JIPipe GUI
Tip: If you want a desktop shortcut, open JIPipe and run Tools > Create launchers

Please note that this package might contain an older version of Fiji and JIPipe. We recommend to use the ImageJ update site to install JIPipe.

You can download a package that provides an existing Fiji installation plus all necessary files for JIPipe.
  1. Download the package
  2. Extract the *.zip file
  3. Run ImageJ-win64
  4. Go to Plugins/JIPipe/JIPipe GUI
Tip: If you want an application menu entry, open JIPipe and run Tools > Create launchers

Please note that this package might contain an older version of Fiji and JIPipe. We recommend to use the ImageJ update site to install JIPipe.

You can download a package that provides an existing Fiji installation plus all necessary files for JIPipe.
  1. Download the package
  2. Drag the file to your desktop
Info: We only have limited capabilities to test software on Apple computers. If you experience any issues, try to install JIPipe via the ImageJ update site.
Info: We are aware of some issues regarding the integration of external software (Python, R, Cellpose, ...). We are open to contributions to resolve these problems.
Info: Please do not install the app globally (using administrator rights). This can prevent ImageJ updates.
JIPipe is available as standalone ImageJ plugin in *.jar format that you can install into an existing installation of ImageJ.
  1. Download the package
  2. Download ImageJ if you have no ImageJ installation, then open the ImageJ plugin folder
  3. Windows/Linux
    Open the Fiji.app directory and navigate into the plugins folder
    OSX
    Right-click the Fiji icon on the desktop and click Show package contents. Navigate into the plugins folder.
  4. Open the *.zip file you downloaded and extract its contents into the plugins folder.
  5. Start ImageJ. You can find the JIPipe GUI inside the plugin menu
  6. On the first start, JIPipe will most likely detect missing dependencies. You can find information about this feature here
Tip: If you want a desktop shortcut (Windows) or an entry in your application menu (Linux), open JIPipe and run Tools > Create launchers

Source code

The software is Open Source and licensed under BSD-2-Clause. You can find the source code on GitHub at https://github.com/applied-systems-biology/jipipe.

Logos

If you need the JIPipe logo for presentations, posters, or publications, feel free to download the logo package. It contains the JIPipe logos (text plus logo, square logo) in PNG and SVG formats.