User guide

Overview

napari-matplotlib contains a number of different napari Widgets. Each widget is designed to map one or more napari Layers on to a matplotlib plot. As an example, the HistogramWidget is used to map one or more Image layers on to a 1D histogram plot.

The widgets split into two categories:

Layer plotting

These widgets plot the data stored directly in napari layers. Currently available are widgets to plot:

• 1D histograms

• 2D scatter plots (switching to 2D histograms for a large number of points)

• 1D slice line plots

To use these:

1. Open the desired widget using the Plugins > napari-matplotlib menu in napari.

2. Select the required number of layers using the napari layers list in the bottom left-hand side of the window.

Features plotting

These widgets plot the data stored in the .features attribute of individual napari layers. Currently available are:

• 2D scatter plots of two features against each other.

• Histograms of individual features.

To use these:

1. Open the desired widget using the Plugins > napari-matplotlib menu in napari.

2. Select a single layer that has a features table using the napari layers list in the bottom left-hand side of the window.

3. Use the drop down menu(s) under the Matplotlib figure to select the feature(s) to plot.

Customising plots

napari-matplotlib uses colours from the current napari theme to customise the Matplotlib plots. See the example on creating a new napari theme for a helpful guide.