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Here we explain our workflow to set up a registration job.
In a multimodality dataset, some images are acquired in the same space, meaning they are sampled on the same voxel grid. Some examples include an atlas image and its annotations, or a T1 and T2 MRI. We also consider serial section histology to be a single space.
Now we describe which space our images belong to.
Now we define what registrations to perform to connect each space. Typically with histology, we align all other stains to Nissl stain. In this example, we will register the atlas Serial Two Photon (STP) image to the T2 MRI, then we will align the T1 MRI to the Nissl serial section dataset. We will also rigidly align each Nissl slice to its neighboring Myelin and H&E slices.
We apply transformations to reconstruct images from one space in another space. These images need not be registered, our algorithm will compose registrations or their inverses along an appropraite path to provide the reconstructions requested. In this example, we will transform the Atlas labels and the myelin stained sections into the MRI space.
Spaces, images, registrations, and transformations sould be described in a multimodality configuration file .
Each registration requires a registration config file .