Registration of in vivo MR to histology of rodent brains using blockface imaging

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

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

7 Scopus citations

Abstract

Registration of MRI to histopathological sections can enhance bioimaging validation for use in pathobiologic, diagnostic, and therapeutic evaluations. However, commonly used registration methods fall short of this goal due to tissue shrinkage and tearing after brain extraction and preparation. In attempts to overcome these limitations we developed a software toolbox using 3D blockface imaging as the common space of reference. This toolbox includes a semi-automatic brain extraction technique using constraint level sets (CLS), 3D reconstruction methods for the blockface and MR volume, and a 2D warping technique using thin-plate splines with landmark optimization. Using this toolbox, the rodent brain volume is first extracted from the whole head MRI using CLS. The blockface volume is reconstructed followed by 3D brain MRI registration to the blockface volume to correct the global deformations due to brain extraction and fixation. Finally, registered MRI and histological slices are warped to corresponding blockface images to correct slice specific deformations. The CLS brain extraction technique was validated by comparing manual results showing 94% overlap. The image warping technique was validated by calculating target registration error (TRE). Results showed a registration accuracy of a TRE < 1 pixel. Lastly, the registration method and the software tools developed were used to validate cell migration in murine human immunodeficiency virus type one encephalitis.

Original languageEnglish (US)
Title of host publicationMedical Imaging 2009
Subtitle of host publicationBiomedical Applications in Molecular, Structural, and Functional Imaging
DOIs
StatePublished - Jun 22 2009
EventMedical Imaging 2009: Biomedical Applications in Molecular, Structural, and Functional Imaging - Lake Buena Vista, FL, United States
Duration: Feb 8 2009Feb 10 2009

Publication series

NameProgress in Biomedical Optics and Imaging - Proceedings of SPIE
Volume7262
ISSN (Print)1605-7422

Conference

ConferenceMedical Imaging 2009: Biomedical Applications in Molecular, Structural, and Functional Imaging
CountryUnited States
CityLake Buena Vista, FL
Period2/8/092/10/09

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Keywords

  • Blockface
  • Bone marrow macrophages.
  • Brain extraction
  • Cell tracking
  • Level set
  • Mouse brain MRI
  • Registration
  • Thin-plate splines
  • Warping

ASJC Scopus subject areas

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

Cite this

Uberti, M., Liu, Y., Dou, H., Mosley, R. L., Gendelman, H. E., & Boska, M. (2009). Registration of in vivo MR to histology of rodent brains using blockface imaging. In Medical Imaging 2009: Biomedical Applications in Molecular, Structural, and Functional Imaging [726213] (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; Vol. 7262). https://doi.org/10.1117/12.812711