Journal: Frontiers in Neuroanatomy

Article Title: Estimating Fiber Orientation Distribution Functions in 3D-Polarized Light Imaging

doi: 10.3389/fnana.2016.00040

Figure Lengend Snippet: pliODFs based on different super-voxel sizes. (A) The FOM of the simulated dataset (cf. Figure ) was divided into super-voxels composed of (B) 10 × 10 × 1, (C) 20 × 20 × 1, and (D) 40 × 40 × 1 native voxels. pliODFs were generated by means of series expansions to the 6th band for the different super-voxels. The color sphere defines the relation between orientation and color-coding.

Article Snippet: The established software package to generate pliODFs from 3D-PLI datasets described in this work will be made available through an ICT portal currently being developed by the human brain project consortium.

Techniques: Generated

Journal: Frontiers in Neuroanatomy

Article Title: Estimating Fiber Orientation Distribution Functions in 3D-Polarized Light Imaging

doi: 10.3389/fnana.2016.00040

Figure Lengend Snippet: Real and simulated brain section from the hooded seal. (A) Blockface image of the optic chiasm of the hooded seal before sectioning. (B) Fiber orientation map of a medial section through the optic chiasm. Optic nerves and optic tracts appear as massive and rather homogeneous fiber bundles. Most fiber tracts from the optic nerves decussate to the contralateral optic tract. (C) The decussation zone in the center (i.e., the chiasm) is characterized by a patch pattern produced by small fiber tracts (red and green color; exemplary orientations are indicated by black lines) and fiber crossings characterized by signal attenuation (blue color; exemplary highlighted by white arrow). Based on this FOM, pliODFs were created for super-voxel dimensions of 40 × 40 × 1 native voxels. (D,E) demonstrate different enlargements of the field of pliODFs overlaid with the input FOM. (F) FOM of a simulated section through the optic chiasm and (G) corresponding pliODFs for super-voxel dimensions of 40 × 40 × 1 native voxels. (H) Zoom into the FOM of the fiber decussation zone and (I) corresponding pliODFs. The effects of crossing and bending fibers on the ODF shapes are obvious.

Article Snippet: The established software package to generate pliODFs from 3D-PLI datasets described in this work will be made available through an ICT portal currently being developed by the human brain project consortium.

Techniques: Produced

Journal: Frontiers in Neuroanatomy

Article Title: Estimating Fiber Orientation Distribution Functions in 3D-Polarized Light Imaging

doi: 10.3389/fnana.2016.00040

Figure Lengend Snippet: 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 μm 3 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 μm 3 voxel size. The white arrows indicate a crossing zone of fibers.

Article Snippet: The established software package to generate pliODFs from 3D-PLI datasets described in this work will be made available through an ICT portal currently being developed by the human brain project consortium.

Techniques: Preserving, Comparison, Microscopy, Plasmid Preparation

Journal: Frontiers in Neuroanatomy

Article Title: Estimating Fiber Orientation Distribution Functions in 3D-Polarized Light Imaging

doi: 10.3389/fnana.2016.00040

Figure Lengend Snippet: Coronal section from the central human brain region. (A) Segmented blockface image acquired from the surface of the frozen human brain. (B) Fiber orientation map comprising arcuate fascicle (AF), cingulum bundle (CB), corpus callosum (CC), caudate nucleus (Cd), corona radiata (CR), internal capsule (IC). Fiber orientations are RGB color-coded (see sphere). The white rectangles indicate FOMs (C(1) and D(1)) that were transferred into pliODFs. (C) pliODF representations in the region of CR/IC with super-voxel dimensions of (2) 50 × 50 × 1 and (3) 200 × 200 × 1 native voxels (from different views). Patches of crossing fiber bundles are clearly visible in the FOM and the pliODF maps. (D) pliODF representations in the region of CC with super-voxel dimensions of (2) 50 × 50 × 1 and (3) 200 × 200 × 1 native voxels (from different views). Although a predominant fiber direction is observable, small wriggling fiber bundles cause local inhomogeneities along the CC.

Article Snippet: The established software package to generate pliODFs from 3D-PLI datasets described in this work will be made available through an ICT portal currently being developed by the human brain project consortium.

Techniques:

Journal: Journal of Undergraduate Neuroscience Education

Article Title: Low-Cost Classroom and Laboratory Exercises for Investigating Both Wave and Event-Related Electroencephalogram Potentials

doi: 10.59390/YNPH4485

Figure Lengend Snippet: Results of Alpha Wave Experiment. A. Real-time analysis in Backyard Brains SpikeRecorder software showing alpha waves (10 Hz, arrow) occurring during the eyes closed condition. B. Representative trace of one event, marked by the “closed” event marker (top). The representative trace was filtered and colored to highlight analyzed regions (below). C. Differences in frequency power for eyes open (yellow) and eyes closed (orange) conditions (left). Plot showing the ratio of alpha power in eyes closed/eyes open conditions for all events, shown as dots (middle). Arrow identifies the event shown at left. Average change in alpha power per participant shown as bar. Histogram showing the change in alpha power for all recorded events (right).

Article Snippet: The open-source software package SpikeRecorder (Backyard Brains, Ann Arbor, MI) was used to visualize and analyze the signal in real-time to identify any noise or signal quality issues.

Techniques: Software, Marker

Journal: Journal of Undergraduate Neuroscience Education

Article Title: Low-Cost Classroom and Laboratory Exercises for Investigating Both Wave and Event-Related Electroencephalogram Potentials

doi: 10.59390/YNPH4485

Figure Lengend Snippet: Laboratory P300 Results. A. Real-time analysis of the P300 in Backyard Brains SpikeRecorder software, showing averaged responses to oddball (left) and standard (right) tones. B. All oddball responses were overlaid (black) and averaged (teal) for a single representative session (top). Average responses for standard and oddball tone are plotted together (bottom), where a navy bar indicates regions where the average oddball response is statistically different from the standard tone response. Peak latencies that fall within the significance window are shown with a purple dot. C. Regions of significance and peaks that fall within said region are shown for all 81 recording sessions.

Article Snippet: The open-source software package SpikeRecorder (Backyard Brains, Ann Arbor, MI) was used to visualize and analyze the signal in real-time to identify any noise or signal quality issues.

Techniques: Software