Registration of in-vivo to ex-vivo MRI of surgically resected specimens: A pipeline for histology to in-vivo registration

Abstract

h i g h l i g h t s• We present a protocol for registration of in-vivo to ex-vivo brain specimens.• This protocol completes a registration pipeline for histology to in-vivo MRI.• A TRE of 1.35 ± 0.11 mm (neocortex) and 1.41 ± 0.33 mm (hippocampus) was found.• Deformable registration significantly improved the registration accuracy.• This pipeline allows for the assessment of pathological correlates in MRI. a r t i c l e i n f o t r a c tBackground: Advances in MRI have the potential to improve surgical treatment of epilepsy through improved identification and delineation of lesions. However, validation is currently needed to investigate histopathological correlates of these new imaging techniques. The purpose of this work is to develop and evaluate a protocol for deformable image registration of in-vivo to ex-vivo resected brain specimen MRI. This protocol, in conjunction with our previous work on ex-vivo to histology registration, completes a registration pipeline for histology to in-vivo MRI, enabling voxel-based validation of novel and existing MRI techniques with histopathology. New method: A combination of image-based and landmark-based 3D registration was used to register in-vivo MRI and the ex-vivo MRI from patients (N = 10) undergoing epilepsy surgery. Target registration error (TRE) was used to assess accuracy and the added benefit of deformable registration. Results: A mean TRE of 1.35 ± 0.11 and 1.41 ± 0.33 mm was found for neocortical and hippocampal specimens respectively. Statistical analysis confirmed that the deformable registration significantly improved the registration accuracy for both specimens.Comparison with existing methods: Image registration of surgically resected brain specimens is a unique application which presents numerous technical challenges and that have not been fully addressed in previous literature. Our computed TRE are comparable to previous attempts tackling similar applications, as registering in-vivo MRI to whole brain or serial histology. Conclusion: The presented registration pipeline finds dense and accurate spatial correspondence between in-vivo MRI and histology and allows for the spatially local and quantitative assessment of pathological correlates in MRI.

The Role of Micro-CT in 3D Histology Imaging

“…While some of our initial results were surprising, the data that we collected begin to elucidate elements of the 3D histology workflow that are seldom examined and facilitate the understanding of a pipeline to correspond in vivo and ex vivo imaging modalities [2,3,4,5,6]. Our results also indicate that micro-CT imaging technology is a very useful addition to the current workflow through its capacity to provide information on tissue morphology, volume of interest, tissue block quality and reference data for 3D histology models.…”

“…High- resolution 3D histology imaging is particularly advantageous to the discovery of diagnostic patterns in its capacity to improve correlation between imaging modalities, such as MRI, conventional CT and glass histology [2,3,4,5,6]. We are interested in using multimodality 3D imaging and 3D histology image data to accurately model, analyze, understand and test disease at high resolution in tissue samples imaged at ×20 to ×40 (0.46-0.23 μm/pixel).…”

Deformable image registration between pathological images and MR image via an optical macro image

“…Choe’s group [5] and Goubran’s group [11] reported registration methods with accuracies of 0.32 ± 0.28 mm and 0.40 ± 1.8 mm, respectively. Both of their accuracies were superior to those in the present study.…”

“…Among these studies, several developed methods can be used for images of the brains of small animals, such as rats, mice, and rabbits [15,16,25,29], while others employed methods may be applied to a small part of the human brain [11,22]. Ideally, a whole human organ should be analyzed with the PT and MR images.…”

Quantitative validation of a nonlinear histology-MRI coregistration method using generalized Q-sampling imaging in complex human cortical white matter

“…Another option is the use of exogeneous fiducial markers that can be injected into the tissue prior to imaging, and used as reference points following sectioning and staining however, this approach is highly vulnerable to inaccurate injections and subsequent migration of the markers resulting in displacement errors as high as 600 μm (Lazebnik et al, 2003; White et al, 2011; Zemmoura et al, 2014). Strategies to perform automated feature extraction have been successful in cases where the gradient of the histological image has a high degree of correspondence with the structural MRI image (Goubran et al, 2013; Goubran et al, 2015). However, an edge detection based approach often fails when coregistering tissue stained for pathological markers which are only localized to specific regions, such as AT8 for tau tangles in sulcal depths, because of high reliance on similar contrast properties of MRI and histology data (Goubran et al, 2013; Goubran et al, 2015).…”