Automated Segmentation of 3D Histological Mouse Brains Using a MRI-Based 3D Digital Atlas

Jessica Lebenberg¹, Anne-Sophie Hrard¹, Albertine Dubois², Marc Dhenain¹, Philippe Hantraye¹, Vincent Frouin³, Thierry Delzescaux¹

We propose a method to register MRI-based 3D digital atlas on histological and autoradiographic mouse brain images to automatically segment those post mortem data. To co-register the atlas with these data, we first deformed the MRI volume to match with 3D-reconstructed post mortem volumes. We then applied the deformation parameters to warp the MRI-based 3D digital atlas. The reliability of this method was evaluated by qualitatively and quantitatively comparing the atlas-based with manual segmentations, considered as gold standard. Our results show that this approach is promising to investigate post mortem datasets in the mouse, and make group or strain comparisons.