Crop regions in napari manually

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Crop regions in napari manually

Crop in any dimension

Cut a volume using a plane

Note: this functionality currently only works with 3D data


Create a new shapes layer to annotate the region you would like to crop:

Use the rectangle tool to annotate a region. Start the crop tool from the Tools > Utilities > Crop region menu. Click the Run button to crop the region.

You can also use the Select shapes tool to move the rectangle to a new place and crop another region by clicking on Run.

Hint: You can also use the napari-tabu plugin to send all your cropped images to a new napari window.

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


You can install napari-crop via pip:

pip install napari-crop


Contributions are very welcome.


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


If you encounter any problems, please create a thread on along with a detailed description and tag @haesleinhuepf.


  • 0.1.9

Last updated:

  • 28 June 2023

First released:

  • 21 October 2021


Supported data:

  • Information not submitted

Plugin type:

  • Information not submitted

GitHub activity:

  • Stars: 7
  • Forks: 4
  • Issues + PRs: 16

Python versions supported:

Operating system:


  • napari-plugin-engine (>=0.1.4)
  • numpy
  • scikit-image
  • napari-tools-menu (>=0.1.17)
  • napari-workflows

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