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napari

Fast, interactive, multi-dimensional image viewer for Python.

Overview

napari displays n-dimensional images (2D/3D/4D+) with layered overlays for labels, points, shapes, and tracks. It's often used as the front-end for Python-based analysis workflows and as a host for plugins that wrap other tools (Cellpose, micro-sam, StarDist, and many more).

Key features

  • N-dimensional viewing with synchronized slicing
  • Layer system for images, labels, points, shapes, surfaces, tracks, vectors
  • Plugin ecosystem via napari-hub
  • Scriptable from Jupyter, IPython, or standalone scripts via the Python API

Installation

See Python environments for package manager setup (pixi or conda).

Recommended if you want napari alongside a specific tool. The AI_tools_pixi repository bundles napari into the environments where it's actually used:

  • AI_tools_pixi/omero — napari + napari-omero for browsing and annotating OMERO images.
  • AI_tools_pixi/micro_sam — napari + micro-sam + trackastra + napari-omero.
  • AI_tools_pixi/stardist — napari + StarDist.

Clone the repo, cd into the folder, then pixi install and pixi run napari.

Standalone napari (pixi).

mkdir napari && cd napari
pixi init
pixi add python=3.11 napari pyqt
pixi run napari

Standalone napari (conda).

conda create -n napari -c conda-forge python=3.11 napari pyqt
conda activate napari
napari

For pip or other install options, see the official install guide.

Official documentation

Learning resources

Written