Download
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.
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.
- Download ImageJ or open your existing ImageJ installation
- Go to Help > Update ... and activate the
JIPipe
update site. Then let ImageJ download all necessary files. - Click Manage update sites and select
JIPipe
. If JIPipe is not available, click Add update site and add a new site with the nameJIPipe
and the URLhttps://sites.imagej.net/JIPipe/
- Click Apply changes and wait until all downloads have been finished
- Restart ImageJ and go to Plugins/JIPipe/JIPipe GUI
- On the first start, JIPipe will most likely detect missing dependencies. Just click Resolve and follow the instructions.
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.
You can download a package that provides an existing Fiji installation plus all necessary files for JIPipe.
- Download the package
- Extract the *.zip file
- Run ImageJ-win64.exe
- Go to Plugins/JIPipe/JIPipe GUI
You can download a package that provides an existing Fiji installation plus all necessary files for JIPipe.
- Download the package
- Extract the *.zip file
- Run ImageJ-win64
- Go to Plugins/JIPipe/JIPipe GUI
You can download a package that provides an existing Fiji installation plus all necessary files for JIPipe.
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.
- Download the package
- Drag the file to your desktop
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.
- Download the package
- Download ImageJ if you have no ImageJ installation, then open the ImageJ plugin folder
- Windows/Linux
- Open the
Fiji.app
directory and navigate into theplugins
folder - OSX
- Right-click the Fiji icon on the desktop and click
Show package contents
. Navigate into theplugins
folder. - Open the *.zip file you downloaded and extract its contents into the plugins folder.
- Start ImageJ. You can find the JIPipe GUI inside the plugin menu
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.