Three-dimensional reconstruction of stained histological slices and 3D non-linear registration with in-vivo MRI for whole baboon brain

doi:10.1016/j.jneumeth.2007.04.017

Journal of Neuroscience Methods

Volume 164, Issue 1, 15 August 2007, Pages 191-204

https://doi.org/10.1016/j.jneumeth.2007.04.017 Get rights and content

Abstract

The correlation between post-mortem data and in-vivo brain images is of high interest for studying neurodegenerative diseases. This paper describes a protocol that matches a series of stained histological slices of a baboon brain with an anatomical MRI scan of the same subject using an intermediate 3D-consistent volume of “blockface” photographs taken during the sectioning process.

Each stained histological section of the baboon brain was first registered to its corresponding blockface photograph using a novel “hemi-rigid” transformation. This piecewise rigid 2D transformation was specifically adapted to the registration of slices which contained both hemispheres. Subsenquently, to correct the global 3D deformations of the brain caused by histological preparation and fixation, a 3D elastic transformation was estimated between the blockface volume and the MRI data. This 3D elastic transformation was then applied to the histological volume previously aligned using the hemi-rigid method to complete the registration of the series of stained histological slices with the MRI data.

We assessed the efficacy of our method by evaluating the quality of matching of anatomical features as well as the difference of volume measurements between the MRI and the histological images. Two complete baboon brains (with the exception of cerebellum) were successfully processed using our protocol.

Section snippets

Material and methods

Two adult baboons (Papio papio) involved in a study concerning the implantation of a cortical electrode for Parkinson's disease (see Drouot et al., 2004, for more details) were processed. An in-vivo T1 MRI scan was acquired for each baboon using a 1.5 T magnet (General Electric Medical Systems, Waukesha, WI) with a resolution of 0.78 mm × 0.78 mm × 1 mm.

The brain of each baboon was fixed by transcardial perfusion of 4% paraformaldehyde (PFA). The brains were divided into three blocks in the coronal

Results

Intermediary results were illustrated on one baboon. Final in-vivo/post-mortem matching were presented for the two baboons’ brains.

For each baboon, three spatially consistent volumes were obtained after direct stacking of the series of photographs within the anterior, central and posterior blocks. The manual segmentation performed allowed the method to clearly process the brain in the images without background. No global deformation between the three different blocks was noted. A small part of

Interest of the blockface volume as an intermediary modality

As described in the results section, the blockface volume presented fewer artifacts (displacement of gyri, torn or missing parts, foldings) than the histological one. The blockface volume was obtained by direct stacking since the method of acquisition of the photographs guaranteed a direct alignment of all the images inside each individual block. Moreover, despite some missing slices, the blocks assembly could be resolved leading to a 3D consistent blockface volume. Since each histological

Conclusion

The protocol described in this paper offers a framework to match a series of stained histological slices with the MRI scan of primate brains. Two complete baboon brains were first reconstructed from stained histological slices and then brought back to their original in-vivo geometry. The final reconstructed stained histological volumes were presented for the whole brain (including both hemispheres) of two baboons, in high resolution with no smoothing, in coronal, axial and sagittal orientation,

Acknowledgments

We would like to thank Xavier Drouot, Stéphane Palfi and Haruhiko Kishima for involving us in the cortical stimulation study and for the in-vivo imaging of the baboons. We are also grateful to Kerwin Tang for his attentive revision of the manuscript. This work was supported by Commissariat à l’Énergie Atomique (CEA), France.

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View full text

Three-dimensional reconstruction of stained histological slices and 3D non-linear registration with in-vivo MRI for whole baboon brain

Abstract

Section snippets

Material and methods

Results

Interest of the blockface volume as an intermediary modality

Conclusion

Acknowledgments

J Neurosci Methods

Neuro Image

Med Image Anal

Neuro Image

Neuroimage

Comp Vis Image Understanding: CVIU

Neuron

Neuroimage

J Neurosci Methods

Neuro Image

Med Image Anal

Neuro Image

Neurolmage

Image Vis Comp

Med Image Anal

Med Image Anal

Med Image Anal

Neuro Image

Spatial transformation of images

Co-registration of histological, optical and MR data of the human brain

A limited memory algorithm for bound constrained optimization

SIAM J Sci Comp

Volumetric transformation of brain anatomy

IEEE Trans Med Imaging

Consistent linear-elastic transformations for image matching

Robust non-rigid registration to capture brain shift from intra-operative MRI

IEEE Trans Med Imaging

Automatic matching of homologous histological sections

IEEE Trans Biomed Eng

BrainVISA: software platform for visualization and analysis of multi-modality brain data