Registering a Whole Brain Morphology in an Atlas

Use case


This specification describes the process of register a whole brain morphology into an atlas. The process starts with reconstruction the whole brain morphologies from image stack. The image stack is used to register to the reference atlas, resulting in a transformation. This transformation is then used to transform the reconstructed whole brain cell into the reference atlas space.

Supported Data Queries

  • Get the whole brain morphology from a given atlas spatial reference system.
  • Get the whole brain morphologies derived from a image stack

Data Provenance pattern

Registering a brain atlas



The different entity types involved are described below.

Type Description
Subject Subject that was used in the experiment
TemplateVolume Template volume generated from the template image data
AtlasSpatialReferenceSystem The spatial coordinate system of the atlas space
ImageStack Image stack obtained from the brain tissue of the subject
ReconstructedCell Reconstructed cell
Transform A linear or non-linear transform
Protocol Protocol that describes the method used in the design and execution of the experiment


Type Description
BrainImaging Technique used to obtain an image stack of the brain tissue containing the cells for reconstruction
ReconstructionFromImage Technique used to reconstruct the stained cell
Transformation Transform a geometric object


Type Description
Person Person associated with an activity
SoftwareAgent Software associated with an activity
Organization Organization associated with an activity