Atlas Examples

We present a set of hands-on examples to illustrate how to manipulate and visualize hierarchical brain atlas ontologies. The full package documentation can be found here

Anatomical Atlases

Below is a list of examples using the ibllib.atlas module

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell. 181(4):936-953.e20. doi: 10.1016/j.cell.2020.04.007. https://www.sciencedirect.com/science/article/pii/S0092867420304025

• Working with IBL atlas object
• Atlas mapping
• Plotting brain region values on histology slices
• Plotting brain region values on cortical flatmap
• Plotting brain region values on circular flatmap
• Plotting cluster locations on histology slices
• Plotting brain region values on the Swanson flat map

Gene expression

• Loading the gene expression atlas

Ng, L., Bernard, A., Lau, C. et al. An anatomic gene expression atlas of the adult mouse brain. Nat Neurosci 12, 356–362 (2009). https://doi.org/10.1038/nn.2281 https://www.nature.com/articles/nn.2281

Lein, E.S. et al. (2007). Genome-wide atlas of gene expression in the adult mouse brain, Nature 445: 168-176. https://doi:10.1038/nature05453