Installation
If you’re looking to use napari-imagej, there are a few ways to get it running.
Installing within napari
If you have napari installed already, you can install napari-imagej by following these steps:
Install OpenJDK 8 or OpenJDK 11
napari-imagej should work with whichever distribution of OpenJDK you prefer; we recommend zulu jdk+fx 8. You can also install OpenJDK from your platform’s package manager.
Install Maven
You can either download it manually or install it via your platform’s package manager. The
mvn --version
command can be used to verify installation.Install napari-imagej with napari
With napari running, navigate to the plugins menu
Plugins>Install/Uninstall Plugins
and type into the search barnapari-imagej
. ClickInstall
to install napari-imagej!
Once the installation is complete, napari-imagej is ready to use!
Installing from Mamba (Recommended)
Mamba is the easiest way to install napari-imagej. To install Mamba, follow the instructions here.
Create a Mamba environment:
mamba create -n napari-imagej napari-imagej openjdk=8
This command installs napari-imagej, napari, and OpenJDK8 into a new Mamba environment, named
napari-imagej
.Activate the Mamba environment:
This step must be done every time that you’d like to use napari-imagej:
mamba activate napari-imagej
Installing from pip
napari-imagej can also be installed using pip
; however, it requires more steps. You’ll need Python3 if you don’t have it already.
We recommend using virtualenv to isolate napari-imagej from your system-wide or user-wide Python environments. Alternatively, you can use Mamba purely for its virtual environment capabilities, and then pip install
everything into that environment:
mamba create -n napari-imagej python pip
mamba activate napari-imagej
Install OpenJDK 8 or OpenJDK 11
napari-imagej should work with whichever distribution of OpenJDK you prefer; we recommend zulu jdk+fx 8. You can also install OpenJDK from your platform’s package manager.
Install Maven
You can either download it manually or install it via your platform’s package manager. The
mvn --version
command can be used to verify installation.Install napari-imagej
Using pip, we can install napari-imagej:
pip install napari-imagej
Installing from Source
If you’re looking to develop napari-imagej, you’ll likely want to install from source.
Using Mamba
Mamba is the easiest way to install napari-imagej. To install Mamba, follow the instructions here.
Clone the napari-imagej repository
From a suitable location, use the following command to clone the napari-imagej repository:
git clone https://github.com/imagej/napari-imagej cd napari-imagej
Install napari-imagej
The following line will download all necessary components to run napari-imagej, installing them into a mamba environment named
napari-imagej
.mamba env create
Using pip
napari-imagej can also be installed using pip
; however, it requires more steps. You’ll need Python3 if you don’t have it already.
We recommend using virtualenv to isolate napari-imagej from your system-wide or user-wide Python environments. Alternatively, you can use Mamba purely for its virtual environment capabilities, and then pip install
everything into that environment:
mamba create -n napari-imagej python pip
mamba activate napari-imagej
Install OpenJDK 8 or OpenJDK 11
napari-imagej should work with whichever distribution of OpenJDK you prefer; we recommend zulu jdk+fx 8. You can also install OpenJDK from your platform’s package manager.
Install Maven
You can either download it manually or install it via your platform’s package manager. The
mvn --version
command can be used to verify installation.Install napari-imagej
The following code section will clone the napari-imagej source into a subfolder of the local directory and install all Python components necessary for napari-imagej.
git clone https://github.com/imagej/napari-imagej cd napari-imagej pip install .