Multi Channel Surface

A napari plugin to enable easy interaction with multi-channel surfaces

Overview

The goal of this plugin is to provide a means for reading, writing, and interacting with surfaces containing multiple color channels in napari. When reading, color channel data is imported into the napari.layers.Surface metadata dictionary under the key 'point_data'. Different channels can be used to color the surface in napari using the Channel Select widget supplied with this plugin. Multi-channel surfaces are saved using the point_data metadata key to save each named channel.

Visualization of single channel vertex data is made possible in napari through the vertex_values Surface Layer property, while the vertex_colors property enables RGB and RGBA representations. Surface file formats such as '.vtu' provide the option of storing a variable number of features recorded at each vertex, and napari-multi-channel-surface provides functionality to utilise data in these formats.

Installation

In napari

This plugin was developed for use in the napari app. To install the plugin, go to

Plugins > Install/Uninstall Plugins...

Type napari-multi-channel-surface in the search box and click install next to the entry napari-multi-channel-surface in the search results.

With pip

You can install napari-multi-channel-surface via pip:

pip install napari-multi-channel-surface

If napari is not already installed, you can install napari-multi-channel-surface with napari and Qt via:

pip install "napari-multi-channel-surface[all]"

To install latest development version :

pip install git+https://github.com/judithlutton/napari-multi-channel-surface.git

Usage

Reading and writing

Reading and writing mesh files can be performed in napari using the read and save functions in the File menu.

File formats

napari-multi-channel-surface uses meshio to read and write mesh files, and supports files with the following extensions:

['.ply', '.vtk', '.vtu', '.xdmf', '.xmf', '.h5m', '.avs', '.e', '.exo', '.ex2', '.hmf', '.med', '.dat', '.tec']

This subset of file types supported by meshio can store color channel data.

Channel Select Widget

You can use the Channel Select widget with any data loaded with napari-multi-channel-surface. Simply load the surface(s) and open the widget with

Plugins > Channel Select (Multi Channel Surface)

The widget allows you to select the surface you wish to interact with, (Surface dropdown) and and which channel you wish to view (Channel dropdown).

Helpful hints for using the widget:

• If your channels have widely varying ranges, set auto-contrast to continuous
• Popular choices of colormaps include viridis, plasma, and turbo.

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 MIT license, "napari-multi-channel-surface" is free and open source software

Issues

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

This napari plugin was generated with copier using the napari-plugin-template.