# Heatmap colors

Color range

In the Heatmap Settings pane, click the Colors tab. Under Select range, select one of the five color ranges:

▪From dark blue to dark red (default).

▪From dark blue to white.

▪From green to red.

▪A custom range where the end colors can be changed.

▪A custom range where the end and middle colors can be changed.

For the last two options, to change a color, click the corresponding button and choose the color you require.

The end colors represent the minimum and the maximum density of data points per pixel. Whether the colors represent the same value in different heatmaps depends on what you choose as Color level (see below).

Color level

In the Heatmap Settings pane, click the Colors tab. Under Color level, specify how the color range is mapped to the range of location frequencies between different heatmaps, and according to what variable:

▪Per heatmap. When you choose this option, the colors are mapped to the range of density of points in each heatmap separately. This means that a specific color may represent different densities of points in different heatmaps. Choose this option to compare the utilization of space within heatmaps.

▪Over heatmaps. When you choose this option, The colors are mapped to the global range of density of points, calculated over all the heatmaps plotted on your screen. This means that a specific color represents the same density of points in different heatmaps. Choose this option to compare the utilization of space between heatmaps.

When you choose this option:

▪The maximum color (e.g. dark red) is only displayed in the heatmap(s) with the highest absolute value of point density.

▪The way heatmaps will look like also depends on what Merging method for heatmaps you choose.

▪What (level) - heatmap color per variable

In addition to the track density heatmap, which shows how often the animal visited each location, EthoVision XT offers parameter heatmaps. A parameter heatmap displays the average value of a selected parameter (e.g., velocity or distance moved) at each location in the arena, color-coded from low to high. This lets you explore spatial patterns in behavior beyond mere presence, for example, where in the arena the animal moved fastest.

A Gaussian smoothing option is available to produce a visually gradual color gradient. However, when data is sparse, smoothing can distort the visualization: isolated high-value locations may be suppressed while dense low-value areas become amplified, giving a misleading impression of where extremes occurred. For accurate interpretation, consider using no smoothing or a low smoothing level. The unsmoothed view always reflects the true recorded values. Parameters with negative values (such as turn angle) are fully supported, a separate validity mask ensures that locations without data are excluded from the visualization and from the smoothing calculation.

Color smoothing

With Smoothing, you can specify the distance around a point at which the influence of the point will be felt when determining the color. Larger values result in greater smoothing, but smaller values may show finer details and variation.

1.In the Heatmap Settings pane, click the Colors tab.

2.Under Smoothing, choose the smoothing intensity (range 1 - 125).

Choose a small value when you work with small arenas, like in well plates, and when you want to view small-scale differences in location.

Notes

▪If your trials include two or more arenas, the options Per heatmap/over heatmaps do not have an effect on the difference in the color mapping between arenas. However, the duration of the tracks in two different arenas may influence the heatmaps. See an example in Plot heatmaps

▪The value of Smoothing is the standard deviation of the Gaussian kernel density function centered on a sample. The heatmap is created by summing up the density functions for the selected data points. Smoothing also influences how many points are represented by a multicolor blob. The following example, shows heatmaps created from two data points. A: with Smoothing = 1 pixel. B: with Smoothing = 3 pixel.