AtlasesFUS

Hosting of modified atlases for stereotactic navigation for focused ultrasound research

This repository hosts code and the modified Nifti 3D mouse and rat atlases based on the Scalable Brain Atlas:

https://scalablebrainatlas.incf.org

Each atlas was manually inspected to recenter the 0 at Bregma. The size in mm is important to calibrate the area of the SVG scalable templates.

Consult the notebook Atlases/Tools for Atlas preparation/Convert Atlases for Stereotactic navigation.ipynb for details for the conversion.

Citation

When using these atlases in your research, plase be sure of citing the following references

P56 Allen mouse atlas

• Lein ES, Hawrylycz MJ, Ao N, et al. (2007) "Genome-wide atlas of gene expression in the adult mouse brain." Nature 445(7124):168-76. [doi 10.1038/nature05453]

• Rembrandt Bakker, Paul Tiesinga, Rolf Kötter (2015) "The Scalable Brain Atlas: instant web-based access to public brain atlases and related content." Neuroinformatics. http://link.springer.com/content/pdf/10.1007/s12021-014-9258-x (author copy: arXiv:1312.6310)

Walxhom rat atlas

• Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014) "Waxholm Space atlas of the Sprague Dawley rat brain" NeuroImage 97:374-386. [doi 10.1016/j.neuroimage.2014.04.001]

• Kjonigsen LJ, Lillehaug S, Bjaalie JG, Witter MP, Leergaard TB (2015) "Waxholm Space atlas of the rat brain hippocampal region: Three-dimensional delineations based on magnetic resonance and diffusion tensor imaging." NeuroImage 108:441–449. [doi 10.1016/j.neuroimage.2014.12.080]

• Sergejeva M, Papp EA, Bakker R, Gaudnek MA, Okamura-Oho Y, Boline J, Bjaalie JG, Hess A (2015) "Anatomical landmarks for registration of experimental image data to volumetric rodent brain atlasing templates." Journal of Neuroscience Methods 240:161-169. [doi 10.1016/j.jneumeth.2014.11.005]

• Rembrandt Bakker, Paul Tiesinga, Rolf Kötter (2015) "The Scalable Brain Atlas: instant web-based access to public brain atlases and related content." Neuroinformatics. http://link.springer.com/content/pdf/10.1007/s12021-014-9258-x (author copy: arXiv:1312.6310)

VSNetal11 rat atlas

• Valdés-Hernández PA, Sumiyoshi A, Nonaka H, Haga R, Aubert-Vásquez E, Ogawa T, Iturria-Medina Y, Riera JJ, Kawashima R (2011) "An in vivo MRI template set for morphometry, tissue segmentation, and fMRI localization in rats" Front Neuroinform 5(26). [doi 10.3389/fninf.2011.00026]

• Rembrandt Bakker, Paul Tiesinga, Rolf Kötter (2015) "The Scalable Brain Atlas: instant web-based access to public brain atlases and related content." Neuroinformatics. http://link.springer.com/content/pdf/10.1007/s12021-014-9258-x (author copy: arXiv:1312.6310)

Licensing

The code provided in the notebook Atlases/Tools for Atlas preparation/Convert Atlases for Stereotactic navigation.ipynb is distributed under the 3-clause BSD license, see notebook for license. This license does not extend to the atlas data itself (read above)

The svgscale Atlases/Tools for Atlas preparation/svgscale script is provided under the GNU General Public License v3.0

The Walxhom rat atlas (according to Scalable Brain Atlas) is distributed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International