Accuracy of image registration between MRI and light microscopy in the ex vivo brain

Ann S. Choe, Yurui Gao, Xia Li, Keegan B. Compton, Iwona Stepniewska, Adam W. Anderson

Research output: Contribution to journalArticlepeer-review


A multistep procedure was developed to register magnetic resonance imaging (MRI) and histological data from the same sample in the light microscopy image space, with the ultimate goal of allowing quantitative comparisons of the two datasets. The fixed brain of an owl monkey was used to develop and test the procedure. In addition to the MRI and histological data, photographic images of the brain tissue block acquired during sectioning were assembled into a blockface volume to provide an intermediate step for the overall registration process. The MR volume was first registered to the blockface volume using a combination of linear and nonlinear registration, and two dimensional (2D) blockface sections were registered to corresponding myelin-stained sections using a combination of linear and nonlinear registration. Before this 2D registration, two major types of tissue distortions were corrected: tissue tearing and independent movement of different parts of the brain, both introduced during histological processing of the sections. The correction procedure utilized a 2D method to close tissue tears and a multiple iterative closest point (ICP) algorithm to reposition separate pieces of tissue in the image. The accuracy of the overall MR to micrograph registration procedure was assessed by measuring the distance between registered landmarks chosen in the MR image space and the corresponding landmarks chosen in the micrograph space. The average error distance of the MR data registered to micrograph data was 0.324±0.277 mm, only 8% larger than the width of the MRI voxel (0.3 mm).

Original languageEnglish (US)
Pages (from-to)683-692
Number of pages10
JournalMagnetic Resonance Imaging
Issue number5
StatePublished - Jun 2011
Externally publishedYes


  • Brain
  • Image registration
  • Light microscopy

ASJC Scopus subject areas

  • Biophysics
  • Biomedical Engineering
  • Radiology Nuclear Medicine and imaging


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