napari labels overlap


create an overlap labels layer from two labels layers

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create an overlap labels layer from two labels layers


This plugin takes two labels layers (layerA, layerB) as inputs, and generate the overlapped regions as a binary labels layer. Three modes:
(1) A_OR_B: new layer = layerA OR layerB (union)
(2) A_AND_B: new layer = layerA AND layerB (intersection)
(3) A_OUTSIDE_B: new layer = layerA OUTSIDE layerB (complement)



  • Object colocalization
  • Merge separately identified objects

Future work

  • Support N labels layers
  • Basic coloc stats (% volume overlap)
  • Output Labels with distinct IDs and links to original label IDs

Release log

  • 0.0.2
    -- Run on npe2
    -- Add output types: binary/connected component
  • 0.0.1
    -- Run on npe1

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.


You can install napari-labels-overlap via pip:

pip install napari-labels-overlap

To install latest development version :

pip install git+


Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.


Distributed under the terms of the BSD-3 license, "napari-labels-overlap" is free and open source software


If you encounter any problems, please file an issue along with a detailed description.


  • 0.0.3

Last updated:

  • 22 June 2022

First released:

  • 30 November 2021


Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 1
  • Forks: 0
  • Issues + PRs: 0

Python versions supported:

Operating system:


  • scikit-image