Brain Tissue and Color-Depth

The Amygdala

The neurons of the central nucleus of the Amygdala fire whenever we experience fear.



The Hippocampus

The neurons of the CA1 field of the hippocampus help us find our way (e.g. spatial navigation… but they do much more than this!)


Do neurons come in different colours?

Neurons are not colourful. they appear grey/white-ish under a regular microscope. However, if we selectively label a subset of these neurons with fluorescent proteins they will glow under the light (or laser) of a microscope.

Using colour to abstract the 3rd dimension

The microscope takes thin optical slices (i.e. pictures) of these neurons along the Z axis (depth) allowing the observer to appreciate the 3D structure of the neurons.

Here I have projected the images (optical slice) along the Z-axis and assigned a different colour to each optical slice using the beloved Fiji (ImageJ).

The result is a powerful image that reveals the complexity of the network (85-90% of the neurons in this picture are not visible!) and uses colour in a clever way: neurons and neuronal processes lying on the same plane are labeled with the same colour, while neurons and processes lying on different planes have different colours.

Another example that shows how we can use colour to both gain further insights into the data and to tell a “colourful” story 🙂


Leonardo Restivo

Behavioral Neuroscientist, M.Sc., Ph.D. - Passionate about Behavior, Data Visualization & Psychology. Read my CV+résumé. Follow me on twitter @scipleneuro