Barrel Cortex¶

Many of the tutorials will use the L5PT in the rat barrel cortex as an example.

The Barrel Cortex (BC) of the rat is a roughly \(4\) x \(4\) x \(2\) \(mm\) cortical area, containing about half a million of neurons, and half a billion of synapses. It is canonically thought of the primary processig unit of somatosensation of the whiskers. The rat whisker system is organized in arcs and columns, just like the barrel cortex; the barrel cortex is somatotopically alligned with the whisker system. Each whisker can be somatotopically linked to a barrel in the barrel cortex. A single barrel is a columnar structure that spans the depth of the neocortex. Since “column” would induce confusion with the somatotopical structure, “barrel” is used to denote these cortical units.

One can also identify layers across the barrel cortex, which are defined by soma sizes. Canonically, there are \(6\) layers in the BC, defined by the soma sizes of their containing neurons.

The L5PT¶

In the barrel cortex, we find (among others) the Layer 5 Pyramidal Tract (L5PT) neuron. An example morphology of L5PTs can be seen below.

“Apical dendrite” refers to the fact that the dendrite originates from the apex of the soma, or the “upper point” of the pyramidal shape.

Scaling the apical dendrite¶

The diameter of the L5PT’s apical dendrite has an important influence on the biophysical properties of the neuron. Biophysical parameters are expressed in units of conductance per area. This area scales with the square of the radius of the dendrite, making the diameter of the dendrites a very influential morphological property. At the same time, it is not always possible to accurately infer its diameter. For example, we reconstructed out morphologies from brain slices that were cut perpendicular to the apical dendrite. If you look at the apical dendrite from the top, figuring out if it is a thick dendrite, or simply corkscrewing, is not always clear. If you additionally consider e.g. diffraction artifacts, measurement uncertainty, dyes not fully diffusing through the cell body, inexperienced microscope operators… the certainty level on the dendritic diameters drastically shrinks. For this reason, we added a scaling parameter for the apical dendrite diameter under the name scale_apical. We only did this for the apical diameter, as this is the most influential one for dendritic coupling mechanisms in this cell type.