3D reconstruction of 2D fluorescence histology images and registration with in vivo MR images: Application in a rodent model of stroke

TY - JOUR

T1 - 3D reconstruction of 2D fluorescence histology images and registration with in vivo MR images

T2 - Application in a rodent model of stroke

AU - Stille, Maik

AU - Smith, Edward

AU - Crum, William R

AU - Modo, Michel

N1 - Copyright © 2013. Published by Elsevier B.V.

PY - 2013/9/30

Y1 - 2013/9/30

N2 - To validate and add value to non-invasive imaging techniques, corresponding histology is required to establish biological correlates. We present an efficient semi-automated image-processing pipeline that uses immunohistochemically-stained sections to reconstruct a 3D brain volume from 2D histological images before registering these with the corresponding 3D in vivo magnetic resonance images (MRI). A multistep registration procedure that first aligns the "global" volume by using the center of mass and then applies a rigid and affine alignment based on signal intensities is described. This is applied to a training set of three rat brain volumes before being validated on three more normal brains. Application of the approach to register "abnormal" images from a rat model of stroke allows the neurobiological correlates of the variations in the hyper-intense MRI signal intensity caused by infarction to be investigated. For evaluation, corresponding anatomical landmarks in MR and histology were defined to measure the accuracy of registration. A registration error of 0.249mm (approximately one in-plane voxel dimension) was evident in healthy rat brains and 0.323mm in a rodent model of stroke. The proposed reconstruction and registration pipeline allows precise analysis of non-invasive MRI and corresponding microstructural histological features in 3D. We were thus able to interrogate histology to deduce the cause of MRI signal variations in the lesion cavity and the peri-infarct area.

AB - To validate and add value to non-invasive imaging techniques, corresponding histology is required to establish biological correlates. We present an efficient semi-automated image-processing pipeline that uses immunohistochemically-stained sections to reconstruct a 3D brain volume from 2D histological images before registering these with the corresponding 3D in vivo magnetic resonance images (MRI). A multistep registration procedure that first aligns the "global" volume by using the center of mass and then applies a rigid and affine alignment based on signal intensities is described. This is applied to a training set of three rat brain volumes before being validated on three more normal brains. Application of the approach to register "abnormal" images from a rat model of stroke allows the neurobiological correlates of the variations in the hyper-intense MRI signal intensity caused by infarction to be investigated. For evaluation, corresponding anatomical landmarks in MR and histology were defined to measure the accuracy of registration. A registration error of 0.249mm (approximately one in-plane voxel dimension) was evident in healthy rat brains and 0.323mm in a rodent model of stroke. The proposed reconstruction and registration pipeline allows precise analysis of non-invasive MRI and corresponding microstructural histological features in 3D. We were thus able to interrogate histology to deduce the cause of MRI signal variations in the lesion cavity and the peri-infarct area.

U2 - 10.1016/j.jneumeth.2013.06.003

DO - 10.1016/j.jneumeth.2013.06.003

M3 - Article

C2 - 23816399

VL - 219

SP - 27

EP - 40

JO - Journal of Neuroscience Methods

JF - Journal of Neuroscience Methods

IS - 1

ER -