Mapping Histology to Metabolism: Coregistration of Stained Whole-Brain Sections to Premortem PET in Alzheimer's Disease

Mega, Michael S.; Chen, Sylvia S; Thompson, Paul M.; Woods, Roger P.; Karaca, Timur; Tiwari, Abhishek; Vinters, Harry V.; Small, Gary W.; Toga, Arthur W.

doi:10.1006/nimg.1996.0255

Cited by 129 publications

(79 citation statements)

References 23 publications

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“…Intra-or inter-patient, mono or multimodal registration has been studied extensively (Maintz and Viergever, 1998;Zitova and Flusser, 2003), but coregistration of 2D histological and 3D MRI data of the same specimen requires a specific methodology which can mimic the data acquisition protocol (Malandain et al, 2004;Mega et al, 1997;Schormann and Zilles, 1998).…”

Section: Atlas Data Coregistrationmentioning

confidence: 99%

“…Second, this 3D block needed to be registered with the corresponding MRI data. As the data acquisition protocol included photographs taken during frozen brain cutting with fiducial markers (the rivets) included in the field of view, marker-based alignment of these photographs produced intermediate 3D blocks that possess the 3D shape properties of the specimen (Malandain et al, 2004;Mega et al, 1997;Schormann and Zilles, 1998;Streicher et al, 1997). Alignment was performed using rigid transforms in order to correct for small variations of the cryomicrotome stage position during photography.…”

Section: Atlas Data Coregistrationmentioning

confidence: 99%

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A three-dimensional, histological and deformable atlas of the human basal ganglia. I. Atlas construction based on immunohistochemical and MRI data

et al. 2007

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Section: Atlas Data Coregistrationmentioning

confidence: 99%

Section: Atlas Data Coregistrationmentioning

confidence: 99%

A three-dimensional, histological and deformable atlas of the human basal ganglia. I. Atlas construction based on immunohistochemical and MRI data

et al. 2007

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“…Data from single subjects, pre-mortem and post-mortem, provide a unique view of the relationship between in vivo imaging and histological assessment. For example, Mega et al 121 scanned patients in the terminal stages of Alzheimer's disease using both MRI and PET. These data were combined with a stain of neurofibrillary tangles and post-mortem three-dimensional histological images that show the gross anatomy122.…”

Section: Multimodal Mappingmentioning

confidence: 99%

Towards multimodal atlases of the human brain

et al. 2006

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Atlases of the human brain have an important impact on neuroscience. The emergence of ever more sophisticated imaging techniques, brain mapping methods and analytical strategies has the potential to revolutionize the concept of the brain atlas. Atlases can now combine data describing multiple aspects of brain structure or function at different scales from different subjects, yielding a truly integrative and comprehensive description of this organ. These integrative approaches have provided significant impetus for the human brain mapping initiatives, and have important applications in health and disease.The concept of the brain atlas is not new1. Cartographic approaches have been used for centuries to identify and target specific regions in the brain and to establish spatial relationships between a coordinate and a structure. Comprehensive maps of brain structure have been created, at a variety of spatial scales, from anatomical specimens2 -5 and various histological preparations that reveal regional cytoarchitecture6 , 7, myelination patterns8 -10, and protein and mRNA distributions. Most early and some more recent atlases of the human brain were derived from one, or at best a few, individual post-mortem specimens3 -5 , 11 -14. Such atlases provide anatomical references or represent a particular feature of the brain15 , 16, such as a specific neurochemical distribution17 or the cellular architecture of the cerebral cortex6. For example, Brodmann's map (1909) exclusively describes the cytoarchitectonic segregation of the cortex6, Dejerine's map (1901) describes fibre tract anatomy18, and the map by Schaltenbrand and Wahren (1977) describes the thalamus14. NIH Public Access Author ManuscriptNat Rev Neurosci. Author manuscript; available in PMC 2011 June 13. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author ManuscriptBeyond these traditional, anatomical atlases based on post-mortem tissue, modern brain atlases are being developed that incorporate flexible, computable systems, which accommodate the sometimes considerable variation in a population. The application of magnetic resonance imaging (MRI) to acquire detailed descriptions of anatomy in vivo is a driving force in brain mapping research. Tomographic imaging has the advantage of largely retaining the spatial integrity of the data by maintaining the intrinsic three-axis registration and simple volumetric coordinates19 , 20. The atlases derived from these images are digital, allowing a wealth of computational algorithms to be applied to automatically align new twoand three-dimensional imaging data into the coordinate systems of these atlases21. Furthermore, there is an increasing ability to image various structural (as well as functional and chemical) features in the brain such as nuclei, cytoarchitectural details and white matter tracts. Technological advances continue to improve spatial and contrast resolution and have led to multispectral characterization (using MRI) of brain anatomy, reflecting features such as lipid content or water ...

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“…Previous work to co-register in-vivo MRIs to microscopically examined samples has been reported mostly for small animal studies [Jacobs et al 1999;Jiang et al 2004;Meyer et al 2006;Anderson et al 2006], a limited number of primates [Malandain et al 2004;Kaufman et al 2005;Dauguet et al 2007] and relatively few human studies [Schormann et al 1995;Mega et al 1997;Toga et al 1999;Kenwright et al 2003]. Most studies involve brain imaging.…”

Section: Introductionmentioning

confidence: 99%

“…Not only is it difficult to define landmarks in the histological sections, but warping the high-resolution histological images to match relatively low-resolution specific MRI regions introduces significant interpolation errors. In another set of studies, the postmortem brain was cryogenically frozen, micro-sectioned, stained and then elastically warped either to in-vivo PET images [Mega et al 1997] or to MRIs [Toga et al 1999]. The cryosectioning approach, however, is not readily available and introduces non-linear distortions during the freezing process itself, which requires additional warping procedures and significantly increases the computational expenses.…”

Section: Introductionmentioning

confidence: 99%

Co‐registration of in vivo human MRI brain images to postmortem histological microscopic images

Singh

Rajagopalan

Kim

et al. 2008

Int J Imaging Syst Tech

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Certain features such as small vascular lesions seen in human MRI are detected reliably only in postmortem histological samples by microscopic imaging. Co-registration of these microscopically detected features to their corresponding locations in the in-vivo images would be of great benefit to understanding the MRI signatures of specific diseases. Using non-linear Polynomial transformation, we report a method to co-register in-vivo MRIs to microscopic images of histological samples drawn off the postmortem brain. The approach utilizes digital photographs of postmortem slices as an intermediate reference to co-register the MRIs to microscopy. The overall procedure is challenging due to gross structural deformations in the postmortem brain during extraction and subsequent distortions in the histological preparations. Hemispheres of the brain were co-registered separately to mitigate these effects. Approaches relying on matching single-slices, multiple-slices and entire volumes in conjunction with different similarity measures suggested that using four slices at a time in combination with two sequential measures, Pearson correlation coefficient followed by mutual information, produced the best MRI-postmortem co-registration according to a voxel mismatch count. The accuracy of the overall registration was evaluated by measuring the 3D Euclidean distance between the locations of microscopically identified lesions on postmortem slices and their MRIpostmortem co-registered locations. The results show a mean 3D displacement of 5.1 ± 2.0 mm between the in-vivo MRI and microscopically determined locations for 21 vascular lesions in 11 subjects.

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Mapping Histology to Metabolism: Coregistration of Stained Whole-Brain Sections to Premortem PET in Alzheimer's Disease

Cited by 129 publications

References 23 publications

A three-dimensional, histological and deformable atlas of the human basal ganglia. I. Atlas construction based on immunohistochemical and MRI data

A three-dimensional, histological and deformable atlas of the human basal ganglia. I. Atlas construction based on immunohistochemical and MRI data

Towards multimodal atlases of the human brain

Co‐registration of in vivo human MRI brain images to postmortem histological microscopic images

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