Functions for the Allen Institute's Mouse Common Coordinate Framework (CCF) and Mouse Light (Janelia) neurons reconstructions in Python. Check the user guide and the examples notebooks for more information on how to use BrainRender.
Anatomical and projection data is downloaded from the Allen Brain Atlas reference atlas and connectivity atlas using the Allen API (© 2015 Allen Institute for Brain Science. Allen Brain Atlas API. Available from: brain-map.org/api/index.html) ([1], [2]).
An interactive, in-browser 3D structure viewer, the Allen Brain Explorer, is available here.
Streamlines refer to the visualization of efferent projection as determined by local injections of an anterogradely transported virus (see Allen's connectivity atlas). Streamlines reconstructions are made by https://neuroinformatics.nl using the mouse connectome data from Allen (see here for more details).
Neurons morphological data is from Janelia's mouse light database (see the neurons browser). [3]
To create the render BrainRender relies on vtkplotter [see github repo].
If you found BrainRender useful and decided to include a rendering in your talks, posters or article, please acknowledge BrainRender's contribution.
cocoframer is an R library for interacting with the Allen's Mouse CCF github repository.
mouselightr package generates 3D CCF mouse brain plots, along with MouseLight neuron reconstructions github repository
- [1] Lein, E.S. et al. (2007) Genome-wide atlas of gene expression in the adult mouse brain, Nature 445: 168-176. doi:10.1038/nature05453
- [2] Oh, S.W. et al. (2014) A mesoscale connectome of the mouse brain, Nature 508: 207-214. doi:10.1038/nature13186
- [3] Winnubst, J. et al. (2019) Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain, Cell 179: 268-281