napari Cell Segmentation Course#

By the Bravo Cohort 🔬

Welcome to the napari Cell Segmentation course! This course will take a few hours to complete and will walk you from onboarding to napari to completing your first segmentation workflow using napari and plugins from the napari hub. You can find all of the plugins needed for the course in this Plugin Collection.

Although napari currently requires some coding in Python, we designed each lesson in this course for researchers with no prior coding experience. Whenever coding is needed, we’ve provided you detailed instructions to follow.

We want to emphasize that napari itself is in the alpha stage of development—meaning we are still actively updating and adding new napari features, including some core features you may have used on other analysis platforms.


If you encounter any issues, check the napari Github issues, the Github page for an individual plugin (linked on the napari hub plugin page),, or reach out at


This course is split into 3 sections consisting of both video and text. In the preface, you’ll learn about how this course came to be and find a list of resources for foundational image analysis concepts that will help you get the most out of these materials. In the onboarding section, you’ll learn more about what napari is, and be guided through installing napari and plugins on your computer. Finally in the workflows section, you’ll dig into three cell segmentation case studies (nuclei, foci in nuclei, and filaments) that illustrate how to perform a cell segmentation workflow from start to finish within napari, using sample data (or your own), and various napari plugins.

Supporting links
  • community and developer site

  • The napari hub for the latest plugins

  • Official Bravo Cohort plugin collection page

  • forum sticky thread on the napari segmentation course