Setup Omnipose integration
Table Of Contents
JIPipe features an integration of Omnipose. This software is not part of ImageJ and its update site ecosystem and thus requires additional installation steps. These steps are generally only necessary if JIPipe notifies you about the missing installation of the third-party software.
Notification: Omnipose not configuredIf JIPipe was not yet configured with a Omnipose Python environment, you will be notified on opening the application. Click the notifications button and select the "Install Omnipose" option and follow the instructions or choose "Configure Python".
Project > Application settings > Extensions > Omniposeif you clicked away the notification or if you want to make further changes.
Install Omnipose (prepackaged)On selecting the "Install Omnipose" option, JIPipe will provide you with a pre-made environment that is installed into the ImageJ directory. Choose any of the supported packages. If you already have existing Python environments with Omnipose installed, please follow the other tutorials on this page.
Selecting an existing Conda environment
1. Open the Python integration settingsUnless you clicked "Configure Python" in the notification panel, navigate to
Project > Application settings > Extensions > Omnipose. Click the "Select/Install" button in the "Python environment" setting and choose
Additional compatible installers > Select existing Conda environment.
2. Select the Conda executable and environmentProvide the path to the Conda executable and the environment name. Common locations for the executable are:
C:/Users/User/anaconda3/Scripts/conda.exe(adapt to your user name)
/home/user/anaconda3/bin/conda(adapt to your user name)
/Users/user/opt/anaconda3/bin/conda(adapt to your user name)
cellpose. Adapt the "Environment name" setting accordingly. Confirm the configuration by clicking "OK".