https://github.com/haesleinhuepf/napari-plot-profile

https://github.com/haesleinhuepf/napari-plot-profile

napari-plugin

Last synced: 10 months ago
JSON representation

• Host: GitHub
• URL: https://github.com/haesleinhuepf/napari-plot-profile
• Owner: haesleinhuepf
• License: bsd-3-clause
• Created: 2021-08-20T18:09:46.000Z (almost 5 years ago)
• Default Branch: main
• Last Pushed: 2022-10-12T16:34:13.000Z (almost 4 years ago)
• Last Synced: 2025-04-12T16:48:05.140Z (over 1 year ago)
• Topics: napari-plugin
• Language: Python
• Homepage:
• Size: 13.8 MB
• Stars: 17
• Watchers: 3
• Forks: 5
• Open Issues: 11
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-scientific-image-analysis - napari-plot-profile - Plot a line profile. (🏝️ Napari / Plugins)

README

          
# napari-plot-profile (npp)

[![License](https://img.shields.io/pypi/l/napari-plot-profile.svg?color=green)](https://github.com/haesleinhuepf/napari-plot-profile/raw/main/LICENSE)

[![PyPI](https://img.shields.io/pypi/v/napari-plot-profile.svg?color=green)](https://pypi.org/project/napari-plot-profile)

[![Python Version](https://img.shields.io/pypi/pyversions/napari-plot-profile.svg?color=green)](https://python.org)

[![tests](https://github.com/haesleinhuepf/napari-plot-profile/workflows/tests/badge.svg)](https://github.com/haesleinhuepf/napari-plot-profile/actions)

[![codecov](https://codecov.io/gh/haesleinhuepf/napari-plot-profile/branch/master/graph/badge.svg)](https://codecov.io/gh/haesleinhuepf/napari-plot-profile)

[![Development Status](https://img.shields.io/pypi/status/napari-plot-profile.svg)](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)

[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-plot-profile)](https://napari-hub.org/plugins/napari-plot-profile)

## Plot a Line Profile

Plot intensities along a line in [napari].

![img.png](https://github.com/haesleinhuepf/napari-plot-profile/raw/main/docs/napari-plot-profile-screencast.gif)

* Open some images in [napari].

  

* Add a shapes layer.

![img.png](https://github.com/haesleinhuepf/napari-plot-profile/raw/main/docs/add_shapes_layer_screenshot.png)

  

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

![img.png](https://github.com/haesleinhuepf/napari-plot-profile/raw/main/docs/draw_line_tool_screenshot.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](https://github.com/haesleinhuepf/napari-plot-profile/raw/main/docs/redraw_screenshot.png)

To see how these steps can be done programmatically from python, check out the [demo notebook](https://github.com/haesleinhuepf/napari-plot-profile/blob/main/docs/demo.ipynb)

## Working with RGB images

When working with RGB images, you need to split them into three different layers first in napari.

For this, right-click on the layer and select "Split RGB channels".

![img.png](docs/split-channels.png)

## Create a Topographical View

Create a 3D view of a 2D image by warping pixel intensities to heights using the menu `Tools > Visualization > Topographical view (npp)`. It can be displayed as a 3D image layer, a points cloud layer or a surface layer.

![](https://github.com/haesleinhuepf/napari-plot-profile/raw/main/docs/topographical_view_screencast.gif)

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

Note: This plugin is not compatible with napari 0.6.0 and later.

## 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].

[napari]: https://github.com/napari/napari

[Cookiecutter]: https://github.com/audreyr/cookiecutter

[@napari]: https://github.com/napari

[MIT]: http://opensource.org/licenses/MIT

[BSD-3]: http://opensource.org/licenses/BSD-3-Clause

[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt

[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt

[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0

[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt

[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin

[file an issue]: https://github.com/haesleinhuepf/napari-plot-profile/issues

[napari]: https://github.com/napari/napari

[tox]: https://tox.readthedocs.io/en/latest/

[pip]: https://pypi.org/project/pip/

[PyPI]: https://pypi.org/

[image.sc]: https://image.sc

[@haesleinhuepf]: https://twitter.com/haesleinhuepf