3-D Reconstruction of Macroscopic Optical Brain Slice Images

Colchester, Alan C. F. and Ourselin, Sébastien and Zhu, Yonggen and Bardinet, Eric and He, Yang and Roche, Alexis and Al-Sarraj, Safa and Nailon, Bill and Ironside, James and Ayache, Nicholas (2000) 3-D Reconstruction of Macroscopic Optical Brain Slice Images. In: Delp, Scott L. and DiGioia, Anthony M. and Jaramaz, Branislav, eds. Medical Image Computing and Computer-Assisted Intervention - MICCAI 2000. Lecture Notes in Computer Science, 1935. Springer, Berlin pp. 95-105. ISBN 3-540-41189-5 . (The full text of this publication is not currently available from this repository. You may be able to access a copy if URLs are provided)

The full text of this publication is not available from this repository. (Contact us about this Publication)
Official URL


We present a method for reconstruction of macroscopic optical images of post-mortem brain slices to form a 3-D volume. This forms a key part of a series of procedures to allow post mortem findings to be accurately registered with MR images, and more generally provides a method for 3-D mapping of the distribution of pathological changes throughout the brain. In this preliminary work, four brains from a study of Creutzfeldt-Jakob disease were examined. After brain fixation, the pathologist cut coronal slices several mm thick through the brain. The anterior and posterior faces of each slice were photographed. We show that the 2-D co-registration of each such pair of images was most effectively obtained if the slice was placed in a jig before photographing. Fiducials on the jig were detected automatically and point-based rigid registration computed. For co-registration between slices, i.e., across a single cut, an intensity-based method for 2-D non-rigid registration is used which provided satisfactory results. By propagating the 2-D registrations through the volume and using the known slice thickness, the 3-D volume was reconstructed.

Item Type: Conference or workshop item (Paper)
Uncontrolled keywords: registration magnetic resonance image-to-pathology correlation Creutzfeldt-Jakob disease
Subjects: R Medicine
T Technology > TA Engineering (General). Civil engineering (General) > TA1637 Image Analysis, Image Processing
Divisions: Faculties > Science Technology and Medical Studies > Kent Institute of Medicine and Health Sciences (KIMHS)
Depositing User: M.P. Stone
Date Deposited: 08 Aug 2009 19:14
Last Modified: 30 Apr 2014 09:03
Resource URI: https://kar.kent.ac.uk/id/eprint/12075 (The current URI for this page, for reference purposes)
  • Depositors only (login required):


Downloads per month over past year