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 cuisto.atlas module allows you to do so.

You can generate this file beforehand, using the following code snippet :

from cuisto import atlas
atlas.generate_outlines("allen_mouse_10um", "/path/to/output/file.h5")

Danger

Note that while the output file is relatively small (<100MB), it requires a lot of RAM. Make sure to use a powerful workstation (>32GB RAM) to avoid crashing your computer.

The cuisto.display module can use this file to draw structures outlines projected in three point of view (coronal, sagittal and top-view). The structures drawn are defined in the configuration file in the [atlas] section. If the outline_structures parameter is empty, no outlines will be shown -- this can be used to disable structure contours drawing.

The path to the hdf5 file should be specified in the [files] section of the configuration file.

Tip

If the parameter outlines in the [files] section is left empty, it will be looked up in the default directory, $HOME/.cuisto/{atlas_name}_outlines.h5. If the file does not exist, it will be attempted to download it from the brain-structures repository, though to date, only allen_mouse_10um and allen_cord_20um are available.

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