Image registration of ex-vivo MRI to sparsely sectioned histology of hippocampal and neocortical temporal lobe specimens

Goubran, Maged; Crukley, Cathie; Ribaupierre, Sandrine de; Peters, T. M.; Khan, Ali R.

doi:10.1016/j.neuroimage.2013.07.053

Cited by 40 publications

(56 citation statements)

References 37 publications

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“…Temporal lobe epilepsy patients who had been discussed at multidisciplinary surgical rounds and found to be candidates for anterior temporal lobectomy were recruited as part of an ongoing study (N=14) correlating MRI with histology of resected surgery specimens (Goubran et al, 2013). This project has been approved by the office of research and ethics of Western University, and informed consent was obtained from all patients and control subjects prior to their recruitment in the study.…”

Section: Methodsmentioning

confidence: 99%

Quantitative relaxometry and diffusion MRI for lateralization in MTS and non-MTS temporal lobe epilepsy

et al. 2014

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We developed novel methodology for investigating the use of quantitative relaxometry (T1, T2) and diffusion tensor imaging (DTI) for lateralization in temporal lobe epilepsy. Patients with mesial temporal sclerosis confirmed by pathology (N=8) and non-MTS unilateral temporal lobe epilepsy (N=6) were compared against healthy controls (N=19) using voxel-based analysis restricted to the anterior temporal lobes, and laterality indices for each MRI metric (T1, T2, fractional anisotropy (FA), mean diffusivity, axial and radial diffusivity) were computed based on the proportion of significant voxels on each side. The diffusivity metrics were the most lateralizing MRI metrics in MTS and non-MTS subsets, with significant differences also seen with FA, T1 and T2. Patient-specific multi-modal laterality indices were also computed and were shown to clearly separate the left-onset and right-onset patients. Marked differences between leftonset and right-onset patients were also observed, with left-onset patients exhibiting stronger laterality indices. Finally, neocortical abnormalities were found to be more common in the non-MTS patients. These preliminary results on a small sample size support the further investigation of quantitative MRI and multi-modal image analysis in clinical determination of seizure onset.The presence of more neocortical abnormalities in the non-MTS group suggests a role in seizure onset or propagation and motivates the investigation of more sensitive histopathological analysis to detect and delineate potentially subtle neocortical pathology.

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Section: Methodsmentioning

confidence: 99%

Quantitative relaxometry and diffusion MRI for lateralization in MTS and non-MTS temporal lobe epilepsy

et al. 2014

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“…We have previously demonstrated (Goubran et al, 2013) that the errors for the intermediate ex-vivo to histology registration were 0.98 ± 0.60 mm and 0.76 ± 0.66 mm for neocortical and hippocampal specimens respectively, resulting in a cumulative total error close to 2.33 mm and 2.17 mm for the in-vivo to histology registration. Table 3 presents a summary of the studies reporting algorithms for in-vivo MRI to histology of the brain in the last 15 years.…”

Section: Discussionmentioning

confidence: 92%

“…We divide this process into two distinct steps through the use of an intermediate 3D ex-vivo MRI of the specimen, I ex . Our previous work (Goubran et al, 2013) described and validated methodology for generating a 3D reconstruction of the histology slides, I h3D , with an iterative approach that alternates between aligning I ex to I h3D , and correcting for within-slices deformations using the aligned I ex as a reference. The registration detailed in this work relates to finding the transformations between I in and I ex , thus connecting images obtained in-vivo with histological slides, as depicted in Fig.…”

Section: Image Registrationmentioning

confidence: 99%

“…Transformations obtained via methodology outlined in our previous study (Goubran et al, 2013) were used to reconstruct a 3D histology stack and register the ex-vivo MRI to this stack. This work also described a supplementary co-registration to bring additional immunohistochemistry (IHC) stains, such as neuronal nuclei (NeuN) and glial fibrillary acidic protein (GFAP), into alignment with the H&E stains used for registration with the MRI.…”

Section: In-vivo Mri To Histology Registrationmentioning

confidence: 99%

“…The deformations induced during histological processing can be isolated from those from surgery and handling by employing an intermediary MRI image of the specimen or using blockface images for histological reconstruction, splitting the in-vivo MRI to histology registration procedure into two distinct problems (in-vivo to reference and reference to histology). As described in our previous work registering ex-vivo MRI to sparsely sectioned hippocampal and neocortical temporal lobe specimens, the intermediate ex-vivo MRI or blockface stack can function as an anatomical reference with which the 2D histological slices can be corrected against (Goubran et al, 2013). In this work, however, we focus on the first problem of registering the in-vivo MRI to the intermediate ex-vivo MRI, and completing a pipeline for histology to in-vivo MRI registration in temporal lobe epilepsy.…”

Section: Introductionmentioning

confidence: 99%

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

Goubran

Ribaupierre

Hammond

et al. 2015

Journal of Neuroscience Methods

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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.

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Three‐dimensional histology reveals dissociable human hippocampal long‐axis gradients of Alzheimer's pathology

Ortega‐Cruz,

Bress,

Gazula

et al. 2024

Alzheimer's & Dementia

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INTRODUCTIONThree‐dimensional (3D) histology analyses are essential to overcome sampling variability and understand pathological differences beyond the dissection axis. We present Path2MR, the first pipeline allowing 3D reconstruction of sparse human histology without a magnetic resonance imaging (MRI) reference. We implemented Path2MR with post‐mortem hippocampal sections to explore pathology gradients in Alzheimer's disease.METHODSBlockface photographs of brain hemisphere slices are used for 3D reconstruction, from which an MRI‐like image is generated using machine learning. Histology sections are aligned to the reconstructed hemisphere and subsequently to an atlas in standard space.RESULTSPath2MR successfully registered histological sections to their anatomic position along the hippocampal longitudinal axis. Combined with histopathology quantification, we found an expected peak of tau pathology at the anterior end of the hippocampus, whereas amyloid‐beta (Aβ) displayed a quadratic anterior‐posterior distribution.CONCLUSIONPath2MR, which enables 3D histology using any brain bank data set, revealed significant differences along the hippocampus between tau and Aβ.Highlights Path2MR enables three‐dimensional (3D) brain reconstruction from blockface dissection photographs. This pipeline does not require dense specimen sampling or a subject‐specific magnetic resonance (MR) image. Anatomically consistent mapping of hippocampal sections was obtained with Path2MR. Our analyses revealed an anterior‐posterior gradient of hippocampal tau pathology. In contrast, the peak of amyloid‐beta (Aβ) deposition was closer to the hippocampal body.

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Image registration of ex-vivo MRI to sparsely sectioned histology of hippocampal and neocortical temporal lobe specimens

Cited by 40 publications

References 37 publications

Quantitative relaxometry and diffusion MRI for lateralization in MTS and non-MTS temporal lobe epilepsy

Quantitative relaxometry and diffusion MRI for lateralization in MTS and non-MTS temporal lobe epilepsy

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

Three‐dimensional histology reveals dissociable human hippocampal long‐axis gradients of Alzheimer's pathology

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