2,823 research outputs found
Voxel-wise comparisons of cellular microstructure and diffusion-MRI in mouse hippocampus using 3D Bridging of Optically-clear histology with Neuroimaging Data (3D-BOND)
A key challenge in medical imaging is determining a precise correspondence between image properties and tissue microstructure. This comparison is hindered by disparate scales and resolutions between medical imaging and histology. We present a new technique, 3D Bridging of Optically-clear histology with Neuroimaging Data (3D-BOND), for registering medical images with 3D histology to overcome these limitations. Ex vivo 120 × 120 × 200 μm resolution diffusion-MRI (dMRI) data was acquired at 7 T from adult C57Bl/6 mouse hippocampus. Tissue was then optically cleared using CLARITY and stained with cellular markers and confocal microscopy used to produce high-resolution images of the 3D-tissue microstructure. For each sample, a dense array of hippocampal landmarks was used to drive registration between upsampled dMRI data and the corresponding confocal images. The cell population in each MRI voxel was determined within hippocampal subregions and compared to MRI-derived metrics. 3D-BOND provided robust voxel-wise, cellular correlates of dMRI data. CA1 pyramidal and dentate gyrus granular layers had significantly different mean diffusivity (p > 0.001), which was related to microstructural features. Overall, mean and radial diffusivity correlated with cell and axon density and fractional anisotropy with astrocyte density, while apparent fibre density correlated negatively with axon density. Astrocytes, axons and blood vessels correlated to tensor orientation
Geometry-Aware Neighborhood Search for Learning Local Models for Image Reconstruction
Local learning of sparse image models has proven to be very effective to
solve inverse problems in many computer vision applications. To learn such
models, the data samples are often clustered using the K-means algorithm with
the Euclidean distance as a dissimilarity metric. However, the Euclidean
distance may not always be a good dissimilarity measure for comparing data
samples lying on a manifold. In this paper, we propose two algorithms for
determining a local subset of training samples from which a good local model
can be computed for reconstructing a given input test sample, where we take
into account the underlying geometry of the data. The first algorithm, called
Adaptive Geometry-driven Nearest Neighbor search (AGNN), is an adaptive scheme
which can be seen as an out-of-sample extension of the replicator graph
clustering method for local model learning. The second method, called
Geometry-driven Overlapping Clusters (GOC), is a less complex nonadaptive
alternative for training subset selection. The proposed AGNN and GOC methods
are evaluated in image super-resolution, deblurring and denoising applications
and shown to outperform spectral clustering, soft clustering, and geodesic
distance based subset selection in most settings.Comment: 15 pages, 10 figures and 5 table
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