Examining brain microstructure using structure tensor analysis of histological sections

Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI,
NeuroImage (Impact Factor: 6.36). 06/2012; 63(1):1-10. DOI: 10.1016/j.neuroimage.2012.06.042
Source: PubMed


The mammalian central nervous system has a tremendous structural complexity, and diffusion tensor imaging (DTI) is unique in its ability to extract microstructural tissue properties at a macroscopic scale. However, despite its widespread use and applications in clinical and research settings, accurate validation of DTI has notoriously lagged the advances in image acquisition and analysis. In this report, we demonstrate an approach to visualize and quantify the microscopic features of histological sections on multiple length scales using techniques derived from image texture analysis. Structure tensor (ST) analysis was applied to fluorescence microscopy images of rat brain sections to visualize and quantify tissue microstructure. Images were digitally color-coded based on the local orientation in the pixelwise ST implementation, which allowed direct visualization of white matter complexity at the microscopic level. A piecewise ST algorithm was also employed to quantify anisotropy and orientation at a resolution comparable to that typically acquired with DTI. Anisotropy measured with ST analysis of stained histological sections was highly correlated with anisotropy measured by ex vivo DTI of the same brains (R(2)=0.92). Furthermore, angular histograms, or Fiber Orientation Distributions (FODs), were computed to mimic similar measures derived from high angular resolution diffusion imaging methods. The FODs for each pixel were fit to a mixture of von Mises distributions to identify putative regions of multiple fiber populations (i.e. crossing fibers). Despite its current application to two-dimensional microscopy, the ST analysis is a novel approach to visualize and quantify microstructure in the central nervous system in both health and disease, and advances the available set of tools for validating DTI and other diffusion MRI techniques.

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    • "In layer IV and Vb , these radial dendritic bundles cross the horizontally oriented bands of Baillarger which could explain the orthogonal orientation mismatch between DT and ST . This issue should be further elaborated in future studies using alternative histological labels , such as lipophilic dyes ( Budde and Frank , 2012 ) or immunohistochemical staining of different neuronal or glial compounds . Such approaches could also enable the study of orientation distributions in layers I and II , which are weakly myelinated ( Vogt and Vogt , 1919 ; Sanides , 1962 ; Nieuwenhuys , 2013 ) . "
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    ABSTRACT: Diffusion tensor imaging (DTI) is amongst the simplest mathematical models available for diffusion magnetic resonance imaging, yet still by far the most used one. Despite the success of DTI as an imaging tool for white matter fibers, its anatomical underpinnings on a microstructural basis remain unclear. In this study, we used 65 myelin-stained sections of human premotor cortex to validate modeled fiber orientations and oft used microstructure-sensitive scalar measures of DTI on the level of individual voxels. We performed this validation on high spatial resolution diffusion MRI acquisitions investigating both white and gray matter. We found a very good agreement between DTI and myelin orientations with the majority of voxels showing angular differences less than 10°. The agreement was strongest in white matter, particularly in unidirectional fiber pathways. In gray matter, the agreement was good in the deeper layers highlighting radial fiber directions even at lower fractional anisotropy (FA) compared to white matter. This result has potentially important implications for tractography algorithms applied to high resolution diffusion MRI data if the aim is to move across the gray/white matter boundary. We found strong relationships between myelin microstructure and DTI-based microstructure-sensitive measures. High FA values were linked to high myelin density and a sharply tuned histological orientation profile. Conversely, high values of mean diffusivity (MD) were linked to bimodal or diffuse orientation distributions and low myelin density. At high spatial resolution, DTI-based measures can be highly sensitive to white and gray matter microstructure despite being relatively unspecific to concrete microarchitectural aspects.
    Full-text · Article · Aug 2015 · Frontiers in Neuroanatomy
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    • "Probabilistic tractography in contrast to deterministic tractography yields multiple pathways from a single seed point to account for the uncertainty of the fiber orientations (Yamada et al., 2009). Highspatial resolution imaging of ex vivo tissue along with tractography may be a useful approach to assay structural integrity of small axonal pathways (Budde and Frank, 2012; Ford et al., 2013; Powell et al., 2012). For example, anterograde tracing studies in primate have shown that axons project from the entorhinal cortex into the dentate gyrus (Amaral et al., 2014). "
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    ABSTRACT: Background Emerging high-field diffusion weighted MR imaging protocols, along with tractography, can elucidate microstructural changes associated with brain disease at the sub-millimeter image resolution. Epilepsy and other neurological disorders are accompanied by structural changes in the hippocampal formation and associated regions; however, these changes can be subtle and on a much smaller scale than the spatial resolution commonly obtained by current clinical magnetic resonance (MR) protocols in vivo. Methods We explored the possibility of studying the organization of fresh tissue with a 17.6 Tesla magnet using diffusion MR imaging and tractography. The mesoscale organization of the temporal lobe was estimated using a fresh unfixed specimen obtained from a subject who underwent anterior temporal lobectomy for medically refractory temporal lobe epilepsy (TLE). Following ex vivo imaging, the tissue was fixed, serial-sectioned, and stained for correlation with imaging. Findings We resolved tissue microstructural organizational features in the temporal lobe from diffusion MR imaging and tractography in fresh tissue. Conclusions Fresh ex vivo MR imaging, along with tractography, revealed complex intra-temporal structural variation corresponding to neuronal cell body layers, dendritic fields, and axonal projection systems evident histologically. This is the first study to describe in detail the human temporal lobe structural organization using high-field MR imaging and tractography. By preserving the 3-dimensional structures of the hippocampus and surrounding structures, specific changes in anatomy may inform us about the changes that occur in TLE in relation to the disease process and structural underpinnings in epilepsy-related memory dysfunction.
    Full-text · Article · Aug 2015 · Clinical neuroimaging
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    • ") to show directionality of the underlying fibers using the OrientationJ analysis tool ( in Fiji ( using a cubic spline gradient of 30 pixels (Budde and Frank, 2012; Rezakhaniha et al., 2012 "
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    ABSTRACT: The hippocampus is a very important structure in memory formation and retrieval, as well as in various neurological disorders such as Alzheimer's disease, epilepsy and depression. It is composed of many intricate subregions making it difficult to study the anatomical changes that take place during disease. The hippocampal hilus may have unique neuroanatomy in humans compared to monkeys and rodents, with field CA3h greatly enlarged in humans compared to rodents, and a white-matter pathway, called the endfolial pathway, possibly only present in humans. In this study we have used newly developed 7.0T whole brain imaging, balanced steady-state free precession (bSSFP) that can achieve 0.4mm isotropic images to study, in vivo, the anatomy of the hippocampal hilus. A detailed hippocampal subregional segmentation was performed according to anatomic atlases segmenting the following regions: CA4, CA3, CA2, CA1, SRLM (stratum radiatum lacunosum moleculare), alveus, fornix, and subiculum along with its molecular layer. We also segmented a hypointense structure centrally within the hilus that resembled the endfolial pathway. To validate that this hypointense signal represented the endfolial pathway, we acquired 0.1mm isotropic 8-phase cycle bSSFP on an excised specimen, and then sectioned and stained the specimen for myelin using an anti-myelin basic protein antibody (SMI 94). A structure tensor analysis was calculated on the myelin-stained section to show directionality of the underlying fibers. The endfolial pathway was consistently visualized within the hippocampal body in vivo in all subjects. It is a central pathway in the hippocampus, with unknown relevance in neurodegenerative disorders, but now that it can be visualized noninvasively, we can study its function and alterations in neurodegeneration. Copyright © 2015. Published by Elsevier Inc.
    Full-text · Article · Feb 2015 · NeuroImage
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