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napari tutorials

tutorials for the napari image viewer

napari installation tutorial

Welcome to the napari installation tutorial!

This tutorial will teach you how to do a clean install of napari. It is aimed at people that just want to use napari. For people also interested in contributing to napari please check our contributing guidelines for more advanced installation procedures. At the end of the tutorial you should have napari successfully installed on your computer and be able to make the napari viewer appear.

installation

from pip, with “batteries included”

napari can be installed on most macOS, Linux, and Windows systems with Python 3.6 and later using pip:

pip install napari[all]

Note: while not strictly required, it is recommended to install napari into a clean virtual environment using an environment manager like conda or venv. For example, with conda:

conda create -y -n napari-env python=3.8
conda activate napari-env
pip install napari[all]

from conda-forge

If you prefer to manage packages with conda, napari is available on the conda-forge channel. You can install it with:

conda install -c conda-forge napari

install from the master branch on Github

To install the “next-release” version from github via pip, call

pip install git+https://github.com/napari/napari.git#egg=napari[all]

clone the repository locally and install in editable mode

To clone the github repository for local install

git clone https://github.com/napari/napari.git
cd napari
pip install -e .[all]

checking it worked

After installation you should be able to launch napari from the command line by simply running

napari

An empty napari viewer should appear as follows

image: An empty napari viewer

upgrading

If you installed napari with pip you can upgrade by calling

pip install napari[all] --upgrade

choosing a different Qt backend

ℹ️ NOTE

napari needs a library called Qt to run its user interface (UI). In Python, there are two alternative libraries to run this, called PyQt5 and PySide2. By default, we don’t choose for you, and simply running pip install napari will not install either. You might already have one of them installed in your environment, thanks to other scientific packages such as Spyder or matplotlib. If neither is available, running napari will result in an error message asking you to install one of them.

As mentioned above, pip install napari[all] will (currently) install PyQt.

If you wish to use PySide2, or specify the backend explicitly you may do using either

pip install napari[pyside2]

# or for PyQt5
pip install napari[pyqt5]

Note: if you switch backends, it’s a good idea to pip uninstall the one you’re not using.

installing as a bundled app

napari can also be installed as a bundled app on each of the major platforms, MacOS, Windows, and Linux with a simple one click download and installation process. You might want to install napari as a bundled app if you are unfamiliar with installing Python packages or if you were unable to get the installation process described above working. The bundled app version of napari is the same version that you can get through the above described processes, and can still be extended with napari plugins installed directly via the app.

To access the cross platform bundles you can visit our release page and scroll to the release you are interested in and expand the assets tab to get a view that looks like this:

image: release bundle assets

You can then download the appropriate zip file for your platform.

installing the MacOS bundle

Once you have downloaded the MacOS bundle zip you will have a zip file with a name like napari-0.3.7-macOS.zip. After unzipping you will have a file with a name like napari-0.3.7.dmg. Double clicking the dmg will open a new finder window giving you the option to install napari into your Applications folder by dragging the napari icon onto the Applications icon.

image: MacOS install to Applications

After you drag the napari icon onto the Applications icon napari will be installed in your Applications folder and available for opening by double clicking on it.

image: MacOS Applications folder with napari

The first time you try and open napari you will get the “unverified developer warning” that appears bellow:

image: MacOS developer warning

Don’t be alarmed, this is because the napari team has not yet obtained a developer certificate from Apple, but we will be doing this promptly. It is safe to click “Cancel”. To get napari to open you must enter “Systems Preferences” and click the “Security & Privacy” icon, circled in red below:

image: MacOS Security & Privacy settings

Once inside the “Security & Privacy” tab, you should see a message about napari being blocked and an “Open Anyway” button, circled in red below:

image: MacOS "Open Anyway" settings

After clicking this button you’ll get one final warning about napari not being verified, but now you’ll have an “Open” button, as seen below:

image: MacOS open bundle dialog box

After clicking “Open”, the viewer should appear. Don’t worry, you only have to go through this process once when you install a new bundle.

installing the Windows bundle

Once you have downloaded the Windows bundle zip you will have a zip file with a name like napari-0.3.7-Windows.zip. Unzip the bundle (you may like to use a tool like 7-zip for this) and double click on msi file, eg: napari-0.3.7.msi

The napari setup wizard will then open. Click “Next” to begin the installation.

image: Windows napari setup wizard

image: Windows napari setup wizard in progress

After the setup wizard has installed napari, click “Finish” to exit.

image: Windows napari setup wizard finished

Now you will be able to launch napari from the Windows start menu.

image: Windows launch napari from start menu

When you launch the bundled napari app on Windows, first you’ll see an empty command terminal appear (do not close this window), and then the main napari user interface window will appear a few seconds later.

The very first time you launch napari the startup time will be fairly slow, but after that you will find that napari launches more quickly.

installing the Linux bundle

(Guide coming soon… In the meantime, if you try it and encounter issues, see below for how to contact us.)

bug reports

If you are running into issues, please open a new issue on our issue tracker and include the output of the following command

napari --info

help

We’re a community partner on the imagesc forum and all usage support requests should be posted on the forum with the tag napari. We look forward to interacting with you there.

next steps

Now that you’ve got napari installed, checkout our getting started tutorial to start learning how to use it!

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