As the neural tube is growing, it develops bends or flexures along its length. The first is a 90 degree bend between the spinal cord and the brainstem called the cervical flexure. As we will see later, this flexure will straighten out so that the spinal cord is in line with the brainstem.

In addition, a mesencephalic or cranial flexure, has also developed at the junction between the mesencephalon and the diencephalon. This flexure will remain, and is responsible for the fact that the definitive diencephalon and telencephalon are situated at approximately at right angles to the brainstem and spinal cord in the newborn.

Allowing the three dimensional image to become see through once again reveals the neural canal and basal and alar columns. Three cross sections through the brainstem are shown in the right panel. Through the caudal medulla, the junction between the medulla and the pons, and the midbrain. Note that at this time, for the most part, these sections are identical, with the neural canal in the center, the basal plates ventral to the neural canal and the alar plates dorsal to the neural canal.

An arbitrary line on each side of the neural canal called the sulcus limitans separates the basal and alar plates. There are a thin roof and floor plates on the midline. Click the link to the right now to animate that animation. A final flexure develops in the region of the medulla and pons.

This pontine flexure is concave posteriorly, so that the brainstem bends back on itself. As part of this development, the roof plate near the ponto-medullary junction thins out, and the alar plates flare out laterally. This repositions the basal and alar plates in this region, so that the alar plates eventually lie lateral to the basal plates.

Note that, as indicated by the upper and lower cross sections to the right, this repositioning does not occur at the cranial or caudal regions of the brainstem. The flaring out of the neural tube is gradual, so that serial sections starting in the caudal medulla and moving cranially will gradually expand, will show the greatest flaring at the ponto-medullary junction, and then would close up again as one proceeded cranially, toward the rostral pons and into the midbrain.

Also note that this expansion that occurs in conjunction with the pontine flexure creates an enlarged region of the neural canal called the fourth ventricle. The neural canal in the midbrain remains narrow and is called the cerebral or mesencephalic aqueduct.