Brain contours

With cuisto, it is possible to plot 2D heatmaps on brain contours.

All the detections are projected in a single plane, thus it is up to you to select a relevant data range. It is primarily intended to give a quick, qualitative overview of the spreading of your data.

To do so, it requires the brain regions outlines, stored in a hdf5 file. This can be generated with brainglobe-atlasapi. The generate_atlas_outlines.py located in scripts/atlas will show you how to make such a file, that the cuisto.display module can use.

Alternatively it is possible to directly plot density maps without cuisto, using brainglobe-heatmap. An example is shown here.