1. Welcome and First Images

Goal: Get napari installed and open your first images.

Welcome (10 min)¶

• Introduce instructors and helpers

• Share the Code of Conduct

• Ask about accessibility needs (private DMs ok)

• Share the Zulip #napari-workshop-[DATE] stream link in the Zoom chat; invite participants to post an introduction: “What field are you from, and what kind of images do you work with?”

• Zoom etiquette

  • Cameras tend to improve the experience, but it’s ok to keep off

  • 👍 reaction = ready to continue; ✋ = stuck/question

  • If asking questions in chat, please send them to everyone unless it needs to be private

Download napari¶

napari comes as a bundled application — a single installer, just like any other desktop app. No Python or command line required.

1. Download: Go to napari.org and download the installer for your OS (Windows, macOS, or Linux).

2. Install: Run the installer and follow the on-screen prompts.

3. Launch: Open napari from your Applications folder / Start Menu / desktop shortcut.

About napari (10 min)¶

napari is a free, open-source, multi-dimensional image viewer for Python and scientific image analysis. It is:

• Community-driven — built by scientists, for scientists

• Extensible — hundreds of plugins on napari-hub.org

• Interoperable — works with NumPy arrays, tiff files, zarr, and more

• Interactive — explore and annotate your data with a handy GUI

Install the downloaded bundle¶

napari Demo (10 min)¶

During this demo, just watch — you don’t need to follow along yet. Focus on seeing what napari can do, not on reproducing every step. You’ll have plenty of hands-on time shortly.

Installation Check-in (5 min)¶

Everyone should now have napari open. You should see:

• An empty canvas in the center

• A layer list panel on the left

• A layer controls panel on the top-left

• Viewer buttons at the bottom of the canvas

If napari is open, give a 👍 as a Zoom reaction.

import napari
from napari.utils import nbscreenshot

viewer = napari.Viewer()

nbscreenshot(viewer)

What Are Images? (10 min)¶

Before diving into napari, a quick conceptual grounding:

• Images are arrays of numbers — each pixel has a value (brightness, intensity)

• n-dimensional images — beyond rows and columns in an array, images can have more array indexes

• zero-based indexing — the first element/pixel is at position 0, not 1

• A common (but not universal) convention: TZYX ordering for time, depth, height, and width dimensions

• multi-channel images — can be just another dimension in the array (e.g. RGB(A) is shape height, width, 3 (or 4))

• labels — images where pixel values are integers representing categories (e.g. 0=background, 1=cell1, 2=cell2, etc.)

napari can display all of these — the dimension sliders let you navigate indexes beyond the 2D canvas.

Open Your First Image and take Screenshots (5 min)¶

1. In napari, select: File > Open Sample > napari builtins > Cells (3D + 2Ch)

2. Two layers appear in the layer list: membrane and nuclei

3. Use the dimension slider at the bottom to scroll through z-slices

4. Toggle each layer on/off with the eye icon next to its name

viewer.open_sample('napari', 'cells3d')

/home/runner/work/workshops/workshops/.pixi/envs/default/lib/python3.14/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
  from .autonotebook import tqdm as notebook_tqdm

nbscreenshot(viewer)

What you’re looking at: Confocal microscopy images of cells in 3D. The nuclei channel (channel 1) shows cell nuclei stained with a dye. The membrane channel (channel 0) shows cell membranes.

Screenshots¶

Save what you see in napari at any time:

• File > Save Screenshot... — saves the canvas as an image file

• File > Save Screenshot with Viewer — saves the canvas plus the entire GUI

• File > Copy Screenshot to Clipboard — paste it directly into a document or chat

Keyboard shortcut: Alt+S (saves to file) or Alt+C (copies to clipboard). Add Shift to include the viewer UI: Alt+Shift+S or Alt+Shift+C.

nbscreenshot(viewer=viewer,canvas_only=True)

viewer.close()