Journal: International Journal of Health Geographics

Article Title: Towards the Atlas of human African trypanosomiasis

doi: 10.1186/1476-072X-8-15

Figure Lengend Snippet: Public-domain databases of geo-referenced named locations. These databases are used to locate HAT cases if geographic coordinates are not available in the epidemiological report.

Article Snippet: EC Joint Research Centre Digital Atlas , .

Techniques:

Journal: NeuroImage

Article Title: A digital 3D atlas of the marmoset brain based on multi-modal MRI

doi: 10.1016/j.neuroimage.2017.12.004

Figure Lengend Snippet: (A) Examples of regional boundaries revealed by different MRI contrasts. From left to right, image contrasts are the fractional anisotropy, the principal direction of the diffusion tensor, the orientation dispersion index (ODI) of the NODDI, and a T2w image. (B) Regional boundaries were manually identified and delineated based on different image contrasts. (C) Each region was then manually labeled using a similar nomenclature as in the Paxinos atlas. (D) The manually-drawn atlas had “jagged” labels and errors. (E) Based on the cellular organization of the cortex, a “columnar anisotropy” can be identified. An example of SMI32-stained image demonstrates the vertically arranged neurons. (F) The principal direction of the diffusion tensor reflects the columnar anisotropy. Labels of the gray matter and the white matter boundaries could be used to relabel the cortex by following the columnar anisotropy. (G) The columnar anisotropy was used to improve cortical labelling. (H) The atlas after the relabeling process based on the columnar anisotropy.

Article Snippet: As the digital Paxinos atlas from the Marmoset Brain Architecture Project ( http://marmoset.braincircuits.org/ ) was licensed under a CC BY-SA 4.0 License ( https://creativecommons.org/licenses/by-sa/4.0/ ), the digital Paxinos atlas registered on our MRI template was included in the release as well under the same license.

Techniques: Diffusion-based Assay, Dispersion, Labeling, Staining

Journal: NeuroImage

Article Title: A digital 3D atlas of the marmoset brain based on multi-modal MRI

doi: 10.1016/j.neuroimage.2017.12.004

Figure Lengend Snippet: (A) Example of voxels that have different (inconsistent) labels (indicated in red) between the MRI atlas (after the columnar-anisotropy relabeling) and the Riken atlas. (B) Cortical areas that show inconsistencies between atlases were refined based on their connectivity profiles. Regions A (red) and B (blue) represent two adjacent areas that have the same (consistent) labels in both MRI and Riken atlases, while the boundary voxels (gray) represent areas with different (inconsistent) labels in the two atlases. Whole-brain tractography was performed for region A, region B, and for each gray voxel to map their connectivity patterns. The gray voxels were then assigned to either region A or B according to similarities of their connectivity patterns to each of the two regions. (C) Inconsistency rates between different atlases. “MRI vs. Histology” bars show inconsistency rates between the MRI atlas and the merged Riken atlas. “Columnar anisotropy” represents the MRI atlas after relabeling by the columnar anisotropy. “Resolving inconsistency” represents the MRI atlas after refining the cortical boundaries based on their connectivity patterns. “Histology vs. Histology” bars show the inconsistency rate between two histological atlases, the Riken atlas and the Paxinos atlas. “Original” represents the original histology atlases (119 cortical regions). “Merged” represents the histology atlases with the number of regions matched with the MRI atlas (54 cortical regions).

Article Snippet: As the digital Paxinos atlas from the Marmoset Brain Architecture Project ( http://marmoset.braincircuits.org/ ) was licensed under a CC BY-SA 4.0 License ( https://creativecommons.org/licenses/by-sa/4.0/ ), the digital Paxinos atlas registered on our MRI template was included in the release as well under the same license.

Techniques: Refining

Journal: NeuroImage

Article Title: A digital 3D atlas of the marmoset brain based on multi-modal MRI

doi: 10.1016/j.neuroimage.2017.12.004

Figure Lengend Snippet: Our MRI-based atlases (MRI), the Riken atlas and the digital Paxinos atlas were spatially transformed to an ex-vivo MTR image (A), an ex-vivo FA image (B), an ex-vivo T2w image (C), an in-vivo T1w image (D), an in-vivo T2w image (E), and an echo planar imaging data (F) from marmosets that were not involved in the atlas construction.

Article Snippet: As the digital Paxinos atlas from the Marmoset Brain Architecture Project ( http://marmoset.braincircuits.org/ ) was licensed under a CC BY-SA 4.0 License ( https://creativecommons.org/licenses/by-sa/4.0/ ), the digital Paxinos atlas registered on our MRI template was included in the release as well under the same license.

Techniques: Transformation Assay, Ex Vivo, In Vivo, Imaging

Journal: Biomaterials

Article Title: Localized Delivery of Low-Density Lipoprotein Docosahexaenoic Acid Nanoparticles to the Rat Brain using Focused Ultrasound

doi: 10.1016/j.biomaterials.2016.01.021

Figure Lengend Snippet: A. Schematic showing the method of achieving localized BBB opening in a rat model using pulsed ultrasound exposures and intravenous microbubbles. B. A close up view of the brain depicts how microbubbles flowing through the brain vasculature respond to the pressure variation produced by the ultrasound exposures to achieve localized BBB opening. C. The target brain location for all animals in this study is overlaid on the transverse brain atlas slice. D. A corresponding brain slice harvested from an animal exposed to ultrasound shows localized leakage of Evans blue into the corresponding brain region.

Article Snippet: A motorized stereotaxic apparatus (51730 M, Stoelting Co., Wood Dale, IL, USA) registered to a digital rat brain atlas (StereoDrive, Neurostar, Tubingen, Germany) was used to register the x, y, z coordinates for skull sutures, bregma and lambda.

Techniques: Produced, Slice Preparation

Journal: Biomaterials

Article Title: Localized Delivery of Low-Density Lipoprotein Docosahexaenoic Acid Nanoparticles to the Rat Brain using Focused Ultrasound

doi: 10.1016/j.biomaterials.2016.01.021

Figure Lengend Snippet: Xenogen IVIS optical imaging was used to track the DiR fluorescence in the brain. A. Whole brain (top) and cross-section (bottom) of brain from rats injected intravenous with LDL-DiR in presence or absence of FUS. B. Fluorescence Microscopy. Digital fluorescent image from coronal cryosection of the brain. Representative areas of interest are expanded from FUS exposed region (left) and contralateral hemisphere (right). Images were captured at 20× magnification. C. Fluorescence Spectrometry. Quantitative measurement of DiR fluorescence in the brain (AU per g of tissue) treated with IV LDL-DiR + FUS and IV LDL-DiR was determined by fluorescence spectrometry at λex and λem of 710 nm and 780 nm respectively (n=3). (**), (***) represent a significant difference from the corresponding groups at p<0.005 and p<0.001 respectively.

Article Snippet: A motorized stereotaxic apparatus (51730 M, Stoelting Co., Wood Dale, IL, USA) registered to a digital rat brain atlas (StereoDrive, Neurostar, Tubingen, Germany) was used to register the x, y, z coordinates for skull sutures, bregma and lambda.

Techniques: Optical Imaging, Fluorescence, Injection, Microscopy