Installing and opening napari#

This workshop walks you through the following topics and exercises:

This topic covers the following:

Although napari has a bundled app, the current recommended installation method requires some work with terminal or command prompt. Follow the steps below, copying and pasting the commands into terminal/command prompt when noted.

Install an environment manager#

miniconda versions

Mac users:#

  • Find the processor version: Apple > About this Mac.

  • Download the miniconda3 package file (Intel or M1 depending on your computer).
    Note: Please use the package file which is outlined in red in the above graphic and not the bash file.

  • Open the downloaded file and follow the instructions to install.

  • Search for terminal and open the terminal.

Windows users:#

  • Find the processor bit version:
    Start button > Settings > System > About shows the processor bit version.

  • Download the miniconda3 file (64-bit or 32-bit depending on your computer).

  • Open the downloaded file and follow the instructions to install.

  • Click the Start button and search for Anaconda.

  • Open the Anaconda Prompt.

Create an environment#

The environment can be named “napari-env” (or any other name you’d like). To create an environment, in terminal (Mac) or Anaconda Prompt (Windows), type:

conda create -y -n napari-env -c conda-forge python=3.9

Enter or activate the environment#

Enter these commands on the terminal (Mac) or at the Anaconda Prompt (Windows):

conda activate napari-env

Note: The environment is shown on the left end of the command line. In the example below, the environment is called cytodata:

cytodata-image

Install napari#

Type one of the following commands on the terminal (Mac) or at the Anaconda Prompt (Windows) and respond to the prompts:

  • Recommended command:

    conda install -c conda-forge napari=0.4.17

    Note: 0.4.17 can be replaced with any desired version of napari.

  • Alternative command if the above fails:

    pip install “napari[all]”

Open and close napari#

Open napari from the terminal (Mac) or the Anaconda prompt (Windows) by typing:

napari

Note: napari may take some time to open the first time.

OPTIONAL - Try closing and reopening napari.

  • To close napari:

    • In the napari top-bar or main menu:
      File > Close Window

    • Leave/deactivate the environment in the terminal or Anaconda Prompt by typing:
      conda deactivate

  • To enter the environment and open napari

    • At the terminal or Anaconda Prompt type:
      conda activate napari-env
      napari

The next topic in this workshop is Explore the viewer. It should take approximately 15 minutes to complete.