Atlas-based indexing of brain sections via 2-D to 3-D image registration

Smadar Gefen*, Nahum Kiryati, Jonathan Nissanov

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


A 2-D to 3-D nonlinear intensity-based registration method is proposed in which the alignment of histological brain sections with a volumetric brain atlas is performed. First, sparsely cut brain sections were linearly matched with an oblique slice automatically extracted from the atlas. Second, a planar-to-curved surface alignment was employed in order to match each section with its corresponding image overlaid on a curved-surface within the atlas. For the latter, a PDE-based registration technique was developed that is driven by a local normalized-mutual-information similarity measure. We demonstrate the method and evaluate its performance with simulated and real data experiments. An atlas-guided segmentation of mouse brains' hippocampal complex, retrieved from the Mouse Brain Library (MBL) database, is demonstrated with the proposed algorithm.

Original languageEnglish
Pages (from-to)147-156
Number of pages10
JournalIEEE Transactions on Biomedical Engineering
Issue number1
StatePublished - Jan 2008


  • 2-D to 3-D nonlinear registration
  • Normalized mutual information
  • PDE-based methods


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