The Connectome: Video Journey Through Brain Microcircuitry

Dr. Stephen Smith’s team at the Stanford University School of Medicine developed a new technique to visualize the detailed anatomy, indeed the micro-circuitry, of brain tissue. The new technique is called array tomography and is based on

automated ultra-thin sectioning of brain tissue
putting arrays of these ultra-thin sections of brain tissue in order on optical coverslips
staining and imaging the two-dimensional arrays of ultra-thin sectioned brain tissue
computational reconstruction of the brain tissue into three dimensions

The following video is a considerable achievement. Smith’s team has reconstructed a section of the cerebral cortex in the mouse’s whisker (technically vibrissae) system. Whisker’s in rodents have functional similarities with our hands and are extremely important for active touch in rodents.

Mouse cortex associated with whiskers is known as barrel cortex. The following video takes you on a tour of a small sliver of this barrel cortex inside a single barrel associated with one whisker on the mouse’s snout.

The upper left area of the video shows the full slice of barrel cortex that you’re journeying through. At top is the surface of the brain and at bottom is the white matter (the communication lines of the brain). In between is the grey matter that contains six layers of brain cells (neurons) and their processes. The red box encompasses the area that you’re currently focused on.

Green – A subset of pyramidal cells express a green fluorescent protein marker (including axons and dendrites).

Blue – Some of the larger dendrites and axons are delineated by blue microtubule immunolabeling.

Red – Synapses are marked by red synapsin I immunofluorescence.