BIOMAG Annotator


An annotator tool collection by the BIOMAG group.

Workflow step:
Image annotation
Image segmentation
Image segmentationCell segmentation
Image segmentationModel-based segmentation
Object classification
Image modality:
Fluorescence microscopy
Confocal microscopy
Electron microscopy
Medical imaging

This plugin allows object annotation on 2/3D images using 4 assisted annotation methods arising from two napari plugins:


Installation is possible with pip, napari or scripts.


You can install napari-biomag-annotator via [pip]:

pip install napari[all]
pip install napari-biomag-annotator

To install latest development version :

pip install git+

On Linux distributions, the following error may arise upon napari startup after the installation of the plugin: Could not load the Qt platform plugin “xcb” in “” even though it was found. In this case, the manual install of libxcb-xinerama0 for Qt is required:

sudo apt install libxcb-xinerama0


  • 0.0.3

Last updated:

  • 11 January 2024

First released:

  • 11 January 2024


Supported data:

Open extension:

Save extension:

Save layers:

GitHub activity:

  • Stars: 6
  • Forks: 0
  • Issues + PRs: 2

Python versions supported:

Operating system:


  • napari
  • napari-plugin-engine >=0.1.4
  • napari-annotatorj
  • napari-nD-annotator