Driftless VesselAtlas

Read this before using it

• One specimen; the measured vessels cover one hemisphere. The other hemisphere shows atlas anatomy only.
• Vessels are graph edges with mean estimated radius of at least 7 µm in connected trees at least 200 µm long. Light-sheet radius estimates run larger than true lumens, so the threshold is relative to this dataset.
• Colors are the dataset’s own artery and vein flags. Pale gray vessels are large but carry neither flag; small vessels and capillaries are not shown.
• Vessel names are tentative, based on position, caliber, and flag.
• The dural sinuses are not in the TubeMap data: they sit in the dura, which is removed with the skull before clearing. The blue translucent sinuses come from a different atlas (MICe, one CBA mouse imaged by micro-CT), registered to the Allen CCF, so their alignment with the TubeMap vessels is approximate to a few hundred micrometres. Hide them or change their opacity in the controls.
• Regions are Allen CCF template anatomy, not this specimen’s boundaries; registration error matters most near region edges. Bregma coordinates are approximate (AP = 5.4 − CCF AP mm, no skull-pitch correction).
• This is an anatomical reference, not a surgical map. Check vessels in the animal you are operating on.

Data and credit

Driftless VesselAtlas is a visualization by the Mohebi & Associates lab of a public dataset. We reanalyzed the released vessel graph; all imaging, reconstruction, and artery/vein labeling are the work of the original authors, who are not affiliated with this viewer. If you use it, please cite the dataset and paper below.

Dataset

Renier N, Kirst C (2020). Dataset for Mapping the fine scale organization of the vasculature (TubeMap Brain-44R). Open Science Framework. osf.io/sa3x8

Method

Kirst C, Skriabine S, Vieites-Prado A, et al. (2020). Mapping the fine-scale organization and plasticity of the brain vasculature. Cell 180:780–795. doi:10.1016/j.cell.2020.01.028

Dural sinuses

Dorr A, Sled JG, Kabani N (2007). Three-dimensional cerebral vasculature of the CBA mouse brain: a magnetic resonance imaging and micro computed tomography study. NeuroImage 35:1409–1423. Atlas files from the Mouse Imaging Centre (MICe), The Centre for Phenogenomics, Toronto; sinus labels registered to the Allen CCF by our lab. doi:10.1016/j.neuroimage.2006.12.040

Atlas

Wang Q, Ding S-L, Li Y, et al. (2020). The Allen Mouse Brain Common Coordinate Framework: a 3D reference atlas. Cell 181:936–953. Annotation volumes via ClearMap. doi:10.1016/j.cell.2020.04.007

Rendering uses three.js. The processing scripts that select the vessels and build these files are kept with the lab's analysis notes.