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napari-plot-profile

napari-plot-profile

Plot intensity along a line and create topographical views in napari

License PyPI Python Version tests codecov Development Status napari hub

Plot a Line Profile

Plot intensities along a line in napari.

img.png

  • Open some images in napari.

  • Add a shapes layer.

img.png

  • Activate the line drawing tool or the path tool and draw a line.

img.png

  • After drawing a line, click on the menu Plugins > Measurements (Plot Profile)
  • If you modify the line, you may want to click the "Refresh" button to redraw the profile.

img.png

To see how these steps can be done programmatically from python, check out the demo notebook

Create a Topographical View

Create a 3D view of a 2D image by warping pixel intensities to heights. It can be displayed as a 3D image layer, a points cloud layer or a surface layer.

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


Installation

You can install napari-plot-profile via pip:

pip install napari-plot-profile

Contributing

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.

License

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

Issues

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

Version:

  • 0.2.2

Last updated:

  • 05 October 2022

First released:

  • 20 August 2021

License:

Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 17
  • Forks: 5
  • Issues + PRs: 11

Python versions supported:

Operating system:

Requirements:

  • napari-plugin-engine (>=0.1.4)
  • numpy
  • pyqtgraph
  • napari
  • napari-tools-menu
  • napari-skimage-regionprops (>=0.2.4)
  • imageio (!=2.22.1)

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