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 <https://int-brain-lab.github.io/iblenv/_autosummary/iblatlas.html#module-iblatlas>`_

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

.. toctree::
   :maxdepth: 1

   notebooks_external/atlas_working_with_ibllib_atlas
   notebooks_external/atlas_mapping
   notebooks_external/atlas_plotting_scalar_on_slice
   notebooks_external/atlas_dorsal_cortex_flatmap
   notebooks_external/atlas_circular_pyramidal_flatmap
   notebooks_external/atlas_plotting_points_on_slice
   notebooks_external/atlas_swanson_flatmap


Gene expression
***************

.. toctree::
   :maxdepth: 1

   notebooks_external/atlas_genomics_load_agea

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


Streamlines
***************

.. toctree::
   :maxdepth: 1

   notebooks_external/atlas_streamlines