Doubts in the Annotation Workflow in Allen Brain CCFv3

  1. In the Allen Brain CCFv3 paper it says that

“Neuroanatomists delineated each structure across coronal, sagittal and horizontal planes at regular intervals, depending on the size and shape of the structure (Figure 2B). This “weaved’ structure was filled in, refined and smoothed by illustration specialists (Figure 2C), and then validated by the neuroanatomists.”

Does that mean that all the voxels in the reference atlas were manually labelled.

  1. “Once a critical number of 3D reconstructions was reached, individual and local structure groups were merged.”

What does this line mean. The words “structure groups” is used only twice in the paper. I don’t understand what is meant by individual and local structure groups.

Also how do you ensure that the borders you are drawing in itk snap are consistent and smooth across slices.

The “structure group” means that each major subcortical brain region is composed of several structures. For example, the thalamus contains more than 40 nuclei. We delineated several nuclei in 3D and call it “structure group”. The great thing in 3D annotation is that the boundaries of some structures are not clear in coronal plate but easily seen in horizontal or sagittal plates. 3D annotation can make each structure smoothly and accurately.