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Estimating Fiber Orientation Distribution Functions in 3D-Polarized Light Imaging.

Axer M, Strohmer S, Gräßel D, Bücker O, Dohmen M, Reckfort J, Zilles K, Amunts K - Front Neuroanat (2016)

Bottom Line: We have successfully established a concept to bridge the spatial scales from microscopic fiber orientation measurements based on 3D-Polarized Light Imaging (3D-PLI) to meso- or macroscopic dimensions.By creating orientation distribution functions (pliODFs) from high-resolution vector data via series expansion with spherical harmonics utilizing high performance computing and supercomputing technologies, data fusion with Diffusion Magnetic Resonance Imaging has become feasible, even for a large-scale dataset such as the human brain.Validation of our approach was done effectively by means of two types of datasets that were transferred from fiber orientation maps into pliODFs: simulated 3D-PLI data showing artificial, but clearly defined fiber patterns and real 3D-PLI data derived from sections through the human brain and the brain of a hooded seal.

View Article: PubMed Central - PubMed

Affiliation: Research Centre Jülich, Institute of Neuroscience and Medicine Jülich, Germany.

ABSTRACT
Research of the human brain connectome requires multiscale approaches derived from independent imaging methods ideally applied to the same object. Hence, comprehensible strategies for data integration across modalities and across scales are essential. We have successfully established a concept to bridge the spatial scales from microscopic fiber orientation measurements based on 3D-Polarized Light Imaging (3D-PLI) to meso- or macroscopic dimensions. By creating orientation distribution functions (pliODFs) from high-resolution vector data via series expansion with spherical harmonics utilizing high performance computing and supercomputing technologies, data fusion with Diffusion Magnetic Resonance Imaging has become feasible, even for a large-scale dataset such as the human brain. Validation of our approach was done effectively by means of two types of datasets that were transferred from fiber orientation maps into pliODFs: simulated 3D-PLI data showing artificial, but clearly defined fiber patterns and real 3D-PLI data derived from sections through the human brain and the brain of a hooded seal.

No MeSH data available.


Related in: MedlinePlus

Brain section from the human occipital lobe. (A) Segmented blockface image acquired from the surface of the frozen human occipital lobe during the sectioning process. The small white rectangles (1) to (3) indicate the selected regions of interest for which pliODFs were determined (cf. B–D). The enlarged extract shows the delineation of anatomical structures, such as the tapetum, the calcar avis, and the stratum sagittale. (B) pliODF representations in region (1) with super-voxel dimensions of 20 × 20 × 1, 40 × 40 × 1 and 200 × 200 × 1 native voxels; the magnified images show the same cortical region, which is characterized by crossing fibers (indicated by the white arrows). The largest super-voxel size is equivalent to 260 × 260 × 70 μm3 and corresponds approximately to the level of high-resolution post mortem dMRI measurements. (C) Region (2) demonstrates for a super-voxel dimension of 50 × 50 × 1 native voxels the preservation of the overall fiber structure in comparison with the original high-resolution FOM obtained with the polarizing microscope. Zooming into the data reveals pliODFs with multiple fiber orientations in inhomogeneous white matter regions. (D) For region (3), pliODFs (super-voxel dimension of 50 × 50 × 1 native voxels) are opposed to the vector-based representation of the FOM of the same brain region measured with the large-area polarimeter at 64 × 64 × 70 μm3 voxel size. The white arrows indicate a crossing zone of fibers.
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Figure 6: Brain section from the human occipital lobe. (A) Segmented blockface image acquired from the surface of the frozen human occipital lobe during the sectioning process. The small white rectangles (1) to (3) indicate the selected regions of interest for which pliODFs were determined (cf. B–D). The enlarged extract shows the delineation of anatomical structures, such as the tapetum, the calcar avis, and the stratum sagittale. (B) pliODF representations in region (1) with super-voxel dimensions of 20 × 20 × 1, 40 × 40 × 1 and 200 × 200 × 1 native voxels; the magnified images show the same cortical region, which is characterized by crossing fibers (indicated by the white arrows). The largest super-voxel size is equivalent to 260 × 260 × 70 μm3 and corresponds approximately to the level of high-resolution post mortem dMRI measurements. (C) Region (2) demonstrates for a super-voxel dimension of 50 × 50 × 1 native voxels the preservation of the overall fiber structure in comparison with the original high-resolution FOM obtained with the polarizing microscope. Zooming into the data reveals pliODFs with multiple fiber orientations in inhomogeneous white matter regions. (D) For region (3), pliODFs (super-voxel dimension of 50 × 50 × 1 native voxels) are opposed to the vector-based representation of the FOM of the same brain region measured with the large-area polarimeter at 64 × 64 × 70 μm3 voxel size. The white arrows indicate a crossing zone of fibers.

Mentions: Three high-resolution FOMs of selected regions of interest from a coronal section through the human occipital lobe (Figure 6A) were resampled at different super-voxel dimensions (Figure 6B), but with fixed histogram binning (50 latitudes × 100 longitudes + 2 polar caps = 5002 bins). The targeted super-voxel sizes of 26 × 26 × 70 μm3, 52 × 52 × 70 μm3, and 260 × 260 × 70 μm3 correspond to 20 × 20 × 1, 40 × 40 × 1, and 200 × 200 × 1 native voxels, respectively. The series expansion was confined to the 6th band. The pliODFs were compared both with the underlying high-resolution FOMs acquired with the polarizing microscope (Figure 6C) and FOMs obtained with the large-area polarimeter (Figure 6D).


Estimating Fiber Orientation Distribution Functions in 3D-Polarized Light Imaging.

Axer M, Strohmer S, Gräßel D, Bücker O, Dohmen M, Reckfort J, Zilles K, Amunts K - Front Neuroanat (2016)

Brain section from the human occipital lobe. (A) Segmented blockface image acquired from the surface of the frozen human occipital lobe during the sectioning process. The small white rectangles (1) to (3) indicate the selected regions of interest for which pliODFs were determined (cf. B–D). The enlarged extract shows the delineation of anatomical structures, such as the tapetum, the calcar avis, and the stratum sagittale. (B) pliODF representations in region (1) with super-voxel dimensions of 20 × 20 × 1, 40 × 40 × 1 and 200 × 200 × 1 native voxels; the magnified images show the same cortical region, which is characterized by crossing fibers (indicated by the white arrows). The largest super-voxel size is equivalent to 260 × 260 × 70 μm3 and corresponds approximately to the level of high-resolution post mortem dMRI measurements. (C) Region (2) demonstrates for a super-voxel dimension of 50 × 50 × 1 native voxels the preservation of the overall fiber structure in comparison with the original high-resolution FOM obtained with the polarizing microscope. Zooming into the data reveals pliODFs with multiple fiber orientations in inhomogeneous white matter regions. (D) For region (3), pliODFs (super-voxel dimension of 50 × 50 × 1 native voxels) are opposed to the vector-based representation of the FOM of the same brain region measured with the large-area polarimeter at 64 × 64 × 70 μm3 voxel size. The white arrows indicate a crossing zone of fibers.
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Related In: Results  -  Collection

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Figure 6: Brain section from the human occipital lobe. (A) Segmented blockface image acquired from the surface of the frozen human occipital lobe during the sectioning process. The small white rectangles (1) to (3) indicate the selected regions of interest for which pliODFs were determined (cf. B–D). The enlarged extract shows the delineation of anatomical structures, such as the tapetum, the calcar avis, and the stratum sagittale. (B) pliODF representations in region (1) with super-voxel dimensions of 20 × 20 × 1, 40 × 40 × 1 and 200 × 200 × 1 native voxels; the magnified images show the same cortical region, which is characterized by crossing fibers (indicated by the white arrows). The largest super-voxel size is equivalent to 260 × 260 × 70 μm3 and corresponds approximately to the level of high-resolution post mortem dMRI measurements. (C) Region (2) demonstrates for a super-voxel dimension of 50 × 50 × 1 native voxels the preservation of the overall fiber structure in comparison with the original high-resolution FOM obtained with the polarizing microscope. Zooming into the data reveals pliODFs with multiple fiber orientations in inhomogeneous white matter regions. (D) For region (3), pliODFs (super-voxel dimension of 50 × 50 × 1 native voxels) are opposed to the vector-based representation of the FOM of the same brain region measured with the large-area polarimeter at 64 × 64 × 70 μm3 voxel size. The white arrows indicate a crossing zone of fibers.
Mentions: Three high-resolution FOMs of selected regions of interest from a coronal section through the human occipital lobe (Figure 6A) were resampled at different super-voxel dimensions (Figure 6B), but with fixed histogram binning (50 latitudes × 100 longitudes + 2 polar caps = 5002 bins). The targeted super-voxel sizes of 26 × 26 × 70 μm3, 52 × 52 × 70 μm3, and 260 × 260 × 70 μm3 correspond to 20 × 20 × 1, 40 × 40 × 1, and 200 × 200 × 1 native voxels, respectively. The series expansion was confined to the 6th band. The pliODFs were compared both with the underlying high-resolution FOMs acquired with the polarizing microscope (Figure 6C) and FOMs obtained with the large-area polarimeter (Figure 6D).

Bottom Line: We have successfully established a concept to bridge the spatial scales from microscopic fiber orientation measurements based on 3D-Polarized Light Imaging (3D-PLI) to meso- or macroscopic dimensions.By creating orientation distribution functions (pliODFs) from high-resolution vector data via series expansion with spherical harmonics utilizing high performance computing and supercomputing technologies, data fusion with Diffusion Magnetic Resonance Imaging has become feasible, even for a large-scale dataset such as the human brain.Validation of our approach was done effectively by means of two types of datasets that were transferred from fiber orientation maps into pliODFs: simulated 3D-PLI data showing artificial, but clearly defined fiber patterns and real 3D-PLI data derived from sections through the human brain and the brain of a hooded seal.

View Article: PubMed Central - PubMed

Affiliation: Research Centre Jülich, Institute of Neuroscience and Medicine Jülich, Germany.

ABSTRACT
Research of the human brain connectome requires multiscale approaches derived from independent imaging methods ideally applied to the same object. Hence, comprehensible strategies for data integration across modalities and across scales are essential. We have successfully established a concept to bridge the spatial scales from microscopic fiber orientation measurements based on 3D-Polarized Light Imaging (3D-PLI) to meso- or macroscopic dimensions. By creating orientation distribution functions (pliODFs) from high-resolution vector data via series expansion with spherical harmonics utilizing high performance computing and supercomputing technologies, data fusion with Diffusion Magnetic Resonance Imaging has become feasible, even for a large-scale dataset such as the human brain. Validation of our approach was done effectively by means of two types of datasets that were transferred from fiber orientation maps into pliODFs: simulated 3D-PLI data showing artificial, but clearly defined fiber patterns and real 3D-PLI data derived from sections through the human brain and the brain of a hooded seal.

No MeSH data available.


Related in: MedlinePlus