Accuracy of image registration between MRI and light microscopy in the ex vivo brain

Choe, Ann S.; Gao, Yurui; Li, Xia; Compton, Keegan B.; Stepniewska, Iwona; Anderson, Adam W.

doi:10.1016/j.mri.2011.02.022

Cited by 76 publications

(70 citation statements)

References 21 publications

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“…Moreover, the histology sections may not be cut exactly perpendicular to the axis of spinal cord tracts, which in turn may also cause biased estimations. 3D OGSE measurements and histology analyses may overcome these effects, but an accurate and sophisticated imaging co-registration procedure covering in vivo applications should be used (Choe et al, 2011). …”

Section: Discussionmentioning

confidence: 99%

Mapping mean axon diameter and axonal volume fraction by MRI using temporal diffusion spectroscopy

et al. 2014

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Mapping mean axon diameter and intra-axonal volume fraction may have significant clinical potential because nerve conduction velocity is directly dependent on axon diameter, and several neurodegenerative diseases affect axons of specific sizes and alter axon counts. Diffusion-weighted MRI methods based on the pulsed gradient spin echo (PGSE) sequence have been reported to be able to assess axon diameter and volume fraction non-invasively. However, due to the relatively long diffusion times used, e.g. > 20 ms, the sensitivity to small axons (diameter < 2 µm) is low, and the derived mean axon diameter has been reported to be overestimated. In the current study, oscillating gradient spin echo (OGSE) diffusion sequences with variable frequency gradients were used to assess rat spinal white matter tracts with relatively short effective diffusion times (1 – 5 ms). In contrast to previous PGSE-based methods, the extra-axonal diffusion cannot be modeled as hindered (Gaussian) diffusion when short diffusion times are used. Appropriate frequency-dependent rates are therefore incorporated into our analysis and validated by histology-based computer simulation of water diffusion. OGSE data were analyzed to derive mean axon diameters and intra-axonal volume fractions of rat spinal white matter tracts (mean axon diameter ~ 1.27 – 5.54 µm). The estimated values were in good agreement with histology, including the small axon diameters (< 2.5 µm). This study establishes a framework for quantification of nerve morphology using the OGSE method with high sensitivity to small axons.

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Section: Discussionmentioning

confidence: 99%

Mapping mean axon diameter and axonal volume fraction by MRI using temporal diffusion spectroscopy

et al. 2014

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“…Eighteen cortical regions of interest (ROIs) in the frontal and parietal lobes were manually labeled by an experienced neuroanatomist on the digitized Nissl-stained slides (labelling was performed using ITK-SNAP, Version 2.4.0). The labels in micrograph space were transformed to the frozen blockface space, and subsequently to the native ex vivo high resolution diffusion weighted space by a multi-step registration procedure described in (Choe et al 2011), a process shown to result in registration errors of approximately one MRI voxel (300um in that study). Thus, for each of 3 monkeys, 18 cortical labels exist in ex vivo diffusion space.…”

Section: Methodsmentioning

confidence: 99%

The VALiDATe29 MRI Based Multi-Channel Atlas of the Squirrel Monkey Brain

et al. 2017

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We describe the development of the first digital atlas of the normal squirrel monkey brain and present the resulting product, VALiDATe29. The VALiDATe29 atlas is based on multiple types of magnetic resonance imaging (MRI) contrast acquired on 29 squirrel monkeys, and is created using unbiased, nonlinear registration techniques, resulting in a population-averaged stereotaxic coordinate system. The atlas consists of multiple anatomical templates (proton density, T1, and T2* weighted), diffusion MRI templates (fractional anisotropy and mean diffusivity), and ex vivo templates (fractional anisotropy and a structural MRI). In addition, the templates are combined with histologically defined cortical labels, and diffusion tractography defined white matter labels. The combination of intensity templates and image segmentations make this atlas suitable for the fundamental atlas applications of spatial normalization and label propagation. Together, this atlas facilitates 3D anatomical localization and region of interest delineation, and enables comparisons of experimental data across different subjects or across different experimental conditions. This article describes the atlas creation and its contents, and demonstrates the use of the VALiDATe29 atlas in typical applications. The atlas is freely available to the scientific community.

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“…Performing voxel-based registration allows for spatially local comparison of MRI and histology, and the scale of this analysis is dependent on the achievable registration accuracy. Many previous studies in MRI and histology registration (see Table 3 2004; Meyer et al, 2006;Lebenberg et al, 2010;Schormann et al, 1995;Yelnik et al, 2007;Osechinskiy and Kruggel, 2011;Bardinet et al, 2002), and furthermore many previous studies included evaluation on only one dataset (Malandain et al, 2004;Choe et al, 2011;Meyer et al, 2006;Schormann et al, 1995;Kim et al, 2000;Yelnik et al, 2007;Osechinskiy and Kruggel, 2011;Bardinet et al, 2002;Lazebnik et al, 2003). Of the studies that did report accuracy on more than one dataset, TRE ranged from sub-millimeter (Ceritoglu et al, 2010;Jacobs et al, 1999;Yang et al, 2012) to 3-5 mm (Liu et al, 2012;Singh et al, 2008).…”

Section: Discussionmentioning

confidence: 99%

“…In the past two decades, there have also been many studies specifically dealing with in-vivo brain MRI to post-mortem histology. The majority of these studies focused on primates (Dauguet et al, 2007;Malandain et al, 2004;Breen et al, 2005;Ceritoglu et al, 2010;Choe et al, 2011) or rodents (Jacobs et al, 1999;Humm et al, 2003;Meyer et al, 2006;Lebenberg et al, 2010;Yang et al, 2012;Liu et al, 2012). The few studies that registered human brain MRIto histology were performed on wholebrain (Schormann et al, 1995;Kim et al, 2000;Singh et al, 2008), or single hemisphere (Yelnik et al, 2007;Osechinskiy and Kruggel, 2011) post-mortem serially sectioned data (Amunts et al, 2013) created a 3D model of single subject's brain using post-mortem histological sections reconstructed at 20 m isotropic resolution and registered it to a T1 average atlas created from 24 subjects.…”

Section: Introductionmentioning

confidence: 99%

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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Accuracy of image registration between MRI and light microscopy in the ex vivo brain

Cited by 76 publications

References 21 publications

Mapping mean axon diameter and axonal volume fraction by MRI using temporal diffusion spectroscopy

Mapping mean axon diameter and axonal volume fraction by MRI using temporal diffusion spectroscopy

The VALiDATe29 MRI Based Multi-Channel Atlas of the Squirrel Monkey Brain

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

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