Python setup & Napari installation

Note

You can also find the official Napari installation instructions here.

Install Python using conda

Napari is a Python package. Therefore, to install it, you must first install Python. If you haven’t yet installed Python, Anaconda, or Miniconda on your machine, we recommend you install Miniconda which is based on the conda package manager. Click on the link below to download the installer:

Miniconda: https://docs.conda.io/en/latest/miniconda.html

Once you have downloaded the installer, run it to install Python.

Windows

1. Run the executable file you just downloaded (Miniforge3-Windows-x86_64.exe) and follow the instructions.

2. Launch the Anaconda Prompt terminal from the start menu.

Mac / Linux

1. Open your Terminal (you can search for it in spotlight - cmd + space)

2. Navigate to the folder you downloaded the installer to using cd. For example:

cd ~/Downloads

1. Execute the installer with the command below. You can use your arrow keys to scroll up and down to read it/agree to it.

bash Miniforge3-MacOSX-x86_64.sh -b

2. To verify that your installation worked, close your terminal window and open a new one. You should see (base) to the left of your prompt.

3. Finally, initialize miniforge with the command below. This makes sure that your terminal is set up correctly for your Python installation.

conda init

Verify your installation

Verify that you have conda installed by typing conda -V in your terminal. This should print out a version number.

Set up your Python environment

We will create a Python virtual environment that you can use for this workshop. Using a virtual environment is a good practice; it lets you isolate the packages and dependencies that you are using for a specific project, without them interfering with other Python projects you may be working on.

Type the following commands in your terminal to create a virtual environment (named napari-env) using conda:

conda create -n napari-env python=3.9

The -n parameter specifies the name of the virtual environment (here, napari-env). We also specify the Python version to be 3.9. Python is constantly evolving and new versions are regularly released. At the time of writing, modern versions include 3.8 to 3.11.

Tip

You can check which virtual environments are available on your machine by typing conda env list.

Next, let’s install a few Python packages into your napari-env virtual environment. To do that, you first have to activate the environment.

conda activate napari-env

If you successfully activated the environment, you should see (napari-env) to the left of your command prompt.

Install Napari using the pip package manager by typing the following commands:

pip install "napari[all]"

Install Jupyter lab:

pip install jupyterlab

Check your installation

With your virtual environment activated,

• type napari in your terminal. The Napari viewer should open in a separate window.

• type jupyter lab in your terminal. This should start the Jupyter lab application in your web browser. To stop Jupyter lab, close the web browser and press Ctrl+C in your terminal window.

You’re done with the Python setup. Congratulations! 🙌