Dataset Information

Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI.

ABSTRACT: 3D histology, slice-based connectivity atlases, and diffusion MRI are common techniques to map brain wiring. While there are many modality-specific tools to process these data, there is a lack of integration across modalities. We develop an automated resource that combines histologically cleared volumes with connectivity atlases and MRI, enabling the analysis of histological features across multiple fiber tracts and networks, and their correlation with in-vivo biomarkers. We apply our pipeline in a murine stroke model, demonstrating not only strong correspondence between MRI abnormalities and CLARITY-tissue staining, but also uncovering acute cellular effects in areas connected to the ischemic core. We provide improved maps of connectivity by quantifying projection terminals from CLARITY viral injections, and integrate diffusion MRI with CLARITY viral tracing to compare connectivity maps across scales. Finally, we demonstrate tract-level histological changes of stroke through this multimodal integration. This resource can propel investigations of network alterations underlying neurological disorders.

SUBMITTER: Goubran M

PROVIDER: S-EPMC6890789 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI.

Goubran Maged M Leuze Christoph C Hsueh Brian B Aswendt Markus M Ye Li L Tian Qiyuan Q Cheng Michelle Y MY Crow Ailey A Steinberg Gary K GK McNab Jennifer A JA Deisseroth Karl K Zeineh Michael M

Nature communications 20191203 1

3D histology, slice-based connectivity atlases, and diffusion MRI are common techniques to map brain wiring. While there are many modality-specific tools to process these data, there is a lack of integration across modalities. We develop an automated resource that combines histologically cleared volumes with connectivity atlases and MRI, enabling the analysis of histological features across multiple fiber tracts and networks, and their correlation with in-vivo biomarkers. We apply our pipeline i ...[more]

PMID: 31796741

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Project description:Objective/methodsNeuroimaging research has predominantly focused on exploring how cortical or subcortical brain abnormalities are related to language dysfunction in patients with neurological disease through the use of single modality imaging. Still, limited knowledge exists on how various MRI measures relate to each other and to patients' language performance. In this study, we explored the relationship between measures of regional cortical thickness, gray-white matter contrast (GWMC), white matter diffusivity [mean diffusivity (MD) and fractional anisotropy (FA)] and the relative contributions of these MRI measures to predicting language function across patients with temporal lobe epilepsy (TLE) and healthy controls. T1- and diffusion-weighted MRI data were collected from 56 healthy controls and 52 patients with TLE. By focusing on frontotemporal regions implicated in language function, we reduced each domain of MRI data to its principal component (PC) and quantified the correlations among these PCs and the ability of these PCs to explain the variation in vocabulary, naming and fluency. We followed up our significant findings by assessing the predictive power of the implicated PCs with respect to language impairment in our sample.ResultsWe found significant positive associations between PCs representing cortical thickness, GWMC and FA that appeared to be partially mediated by changes in total brain volume. We also found a significant association between reduced FA and increased MD after controlling for confounding factors (e.g., age, field strength, total brain volume). Reduced FA was significantly associated with reductions in visual naming while increased MD was associated with reductions in auditory naming scores, even after controlling for the variability explained by reductions in hippocampal volumes. Inclusion of FA and MD PCs in predictive models of language impairment resulted in significant improvements in sensitivity and specificity of the predictions.ConclusionsQuantitative MRI measures from T1 and diffusion-weighted scans are unlikely to represent perfectly orthogonal vectors of disease in individuals with epilepsy. On the contrary, they exhibit highly intercorrelated PCs in their factor structures, which is consistent with an underlying pathological process that affects both the cortical and the subcortical structures simultaneously. In addition to hippocampal volume, the PCs of diffusion weighted measures (FA and MD) increase the sensitivity and specificity for determining naming impairment in patients with TLE. These findings underline the importance of combining multimodal imaging measures to better predict language performance in TLE that could extend to other patients with prominent language impairments.

Project description:With the introduction of multi-camera systems in modern plant phenotyping new opportunities for combined multimodal image analysis emerge. Visible light (VIS), fluorescence (FLU) and near-infrared images enable scientists to study different plant traits based on optical appearance, biochemical composition and nutrition status. A straightforward analysis of high-throughput image data is hampered by a number of natural and technical factors including large variability of plant appearance, inhomogeneous illumination, shadows and reflections in the background regions. Consequently, automated segmentation of plant images represents a big challenge and often requires an extensive human-machine interaction. Combined analysis of different image modalities may enable automatisation of plant segmentation in "difficult" image modalities such as VIS images by utilising the results of segmentation of image modalities that exhibit higher contrast between plant and background, i.e. FLU images. For efficient segmentation and detection of diverse plant structures (i.e. leaf tips, flowers), image registration techniques based on feature point (FP) matching are of particular interest. However, finding reliable feature points and point pairs for differently structured plant species in multimodal images can be challenging. To address this task in a general manner, different feature point detectors should be considered. Here, a comparison of seven different feature point detectors for automated registration of VIS and FLU plant images is performed. Our experimental results show that straightforward image registration using FP detectors is prone to errors due to too large structural difference between FLU and VIS modalities. We show that structural image enhancement such as background filtering and edge image transformation significantly improves performance of FP algorithms. To overcome the limitations of single FP detectors, combination of different FP methods is suggested. We demonstrate application of our enhanced FP approach for automated registration of a large amount of FLU/VIS images of developing plant species acquired from high-throughput phenotyping experiments.

Dataset Information

Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI.

Publications

Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI.

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