Summary and Schedule

This lesson provides a brief overview of Napari, a flexible, extendable software platform for visualising many different types of bioscience and medical imaging data. This session in particular is aimed at all researchers who are interested in working with light microscopy imaging data and how AI could help in such tasks like cell segmentation/tracking.

Prerequisite

Prerequisites

  • Some prior experience with acquiring/working with light microscopy data would be useful, but isn’t necessary. This course is aimed at anyone who is looking to work with light microscopy imaging data in their research projects.

  • No python experience is necessary or assumed, but you will get more out of the course if you know some basics e.g. from the online Software Carpentry python course.

  • Please bring a laptop (Windows, Mac or Linux) to the lesson. Before the start of the course, please follow the setup instructions so that your laptop is ready to run the material in the lessons.

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.

Data Sets

No datasets will be required to download for this taster session. All images will be pre-loaded examples that are already part of Napari. Provided Napari software is loaded correctly, you are all set!

Software Setup

Opening a Terminal

You will need a terminal to run some of the setup instructions and commands for this workshop:

  • Windows: Open PowerShell
  • macOS: Launchpad > Other Application > Terminal
  • Linux: Open a terminal window

Install uv

uv is a Python package manager and environment tool. Use the uv installation guide to install uv if it is not already installed.

Ensure no environment is active before you start

If any environment auto‑activates when you open PowerShell (Windows) or a terminal (MacOS / Linux), deactivate it. Otherwise uv may not behave correctly.

See the official documentation of your package manager (e.g. conda) for details.

For conda, the relevant section is Deactivating an environment

Create an environment with the required Python packages

Run the commands below in PowerShell. Lines starting with # are comments and will not be run.

BASH 

# Create a project folder (e.g. napari-ai-workshop) and move into it
mkdir napari-ai-workshop
cd napari-ai-workshop
# Update uv
uv self update
# Create a virtual environment 
uv venv
# Activate the environment
.venv\Scripts\activate
# Install required Python packages
uv pip install micro-sam napari-matplotlib napari-skimage-regionprops jupyterlab ipywidgets git+https://github.com/ChaoningZhang/MobileSAM.git

Run the commands below in the terminal. Lines starting with # are comments that will not be run.

You can run the commands by copy pasting them into the terminal and pressing the Enter key.

BASH 

# Create a project folder (e.g. napari-ai-workshop) and move into it
mkdir napari-ai-workshop
cd napari-ai-workshop
# Update uv
uv self update
# Create a virtual environment 
uv venv
# Activate the environment
source .venv/bin/activate
# Install required Python packages
uv pip install micro-sam napari-matplotlib napari-skimage-regionprops jupyterlab ipywidgets git+https://github.com/ChaoningZhang/MobileSAM.git

Run the commands below in the terminal. Lines starting with # are comments and will not be executed.

BASH 

# Create a project folder (e.g. napari-ai-workshop) and move into it
mkdir napari-ai-workshop
cd napari-ai-workshop
# Update uv
uv self update
# Create a virtual environment
uv venv 
# Activate the environment
source .venv/bin/activate
# Install required Python packages
uv pip install micro-sam napari-matplotlib napari-skimage-regionprops jupyterlab ipywidgets git+https://github.com/ChaoningZhang/MobileSAM.git

Testing the installation

After installing the packages and activating your napari-ai-workshop environment, you should be able to launch napari and JupyterLab.

To test whether napari opens, run:

BASH 

napari

An empty image viewer window titled napari should appear. This can take a few moments, especially the first time.

To check that JupyterLab launches correctly, run:

BASH 

jupyter lab

Your default web browser should open JupyterLab. It may open in a new tab or a new window, depending on your browser settings.

We are providing an optional environment for people who want to explore other napari plugins outside of this workshop. You do not need to create this environment for the workshop, and none of the course materials or website use this environment.

The reason: installing micro_sam plugin may disable the ability to search for plugins using the napari GUI. So if you want to explore other plugins, it is be best to do so in a separate environment without micro_sam.

To create a seperate environment, navigate outside of the napari-ai-workshop folder. You can do this by moving up one directory.

BASH 

cd ..

Next, follow the instructions below.