An image warping technique for rodent brain MRI-histology registration based on thin-plate splines with landmark optimization

Yutong Liu, Mariano Uberti, Huanyu Dou, R. Lee Mosley, Howard E. Gendelman, Michael D. Boska

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations


Coregistration of in vivo magnetic resonance imaging (MRI) with histology provides validation of disease biomarker and pathobiology studies. Although thin-plate splines are widely used in such image registration, point landmark selection is error prone and often time-consuming. We present a technique to optimize landmark selection for thin-plate splines and demonstrate its usefulness in warping rodent brain MRI to histological sections. In this technique, contours are drawn on the corresponding MRI slices and images of histological sections. The landmarks are extracted from the contours by equal spacing then optimized by minimizing a cost function consisting of the landmark displacement and contour curvature. The technique was validated using simulation data and brain MRI-histology coregistration in a murine model of HIV-1 encephalitis. Registration error was quantified by calculating target registration error (TRE). The TRE of approximately 8 pixels for 20-80 landmarks without optimization was stable at different landmark numbers. The optimized results were more accurate at low landmark numbers (TRE of approximately 2 pixels for 50 landmarks), while the accuracy decreased (TRE approximately 8 pixels for larger numbers of landmarks (70- 80). The results demonstrated that registration accuracy decreases with the increasing landmark numbers offering more confidence in MRI-histology registration using thin-plate splines.

Original languageEnglish (US)
Title of host publicationMedical Imaging 2009 - Image Processing
StatePublished - 2009
EventMedical Imaging 2009 - Image Processing - Lake Buena Vista, FL, United States
Duration: Feb 8 2009Feb 10 2009

Publication series

NameProgress in Biomedical Optics and Imaging - Proceedings of SPIE
ISSN (Print)1605-7422


ConferenceMedical Imaging 2009 - Image Processing
Country/TerritoryUnited States
CityLake Buena Vista, FL


  • Brain
  • Histology
  • Image registration
  • Image warping
  • Landmark optimization
  • MRI
  • Magnetic resonance imaging
  • Nonlinear registration
  • Rodent
  • Thin-plate splines

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Atomic and Molecular Physics, and Optics
  • Biomaterials
  • Radiology Nuclear Medicine and imaging


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