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

    Release date:

    • 22 June 2022

    First released:

    • 30 November 2021


    • BSD-3-Clause

    Supported data:

    • Information not submitted

    Plugin type:

    GitHub activity:

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

    Python versions supported:

    Operating system:


    • scikit-image

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