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Python scripts to use Allen Brain Map data for analysis and rendering
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README.md

BrainRender

Python scripts to create 3D renderings of mouse brain anatomical and projection data and neurons reconstructions.

Resources

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]). 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 (see the neurons browser). [3]

BrainRender also includes meshes for a reconstruction of the rat brain. These meshes are obtained and modified from
3D-rat-brain from tfiers. Original data from [4] and [5].

BrainRender also comes with meshes for the reconstruction of the brain of Drosophila Melanogaster. Data is from the Virtual Fly Brain Project's adult brain template based on work from Jennet et al 2012.

To create the render BrainRender relies on vtkplotter [see github repo].

Examples

Check the user guide and the examples for more information

Mouse Light neurons morphology rendering

Motor cortex piramidal neuron reconstruction from Mouse Light.

Rendering of different sets of brainstem projecting neurons using MultiScene

Sets of neurons projecting to the brainstem, sorted by brain region.

Allen mouse connectome projection data rendering

Tractography

Projections to the Zona Incerta, colored by projection area.

Streamlines

Efferents from the VAL nucleus of the thalamus.

Ratbrain

The rat and mouse brains side by side.

Referencing Brain Render

If you found BrainRender useful and decided to include a rendering in your talks, posters or article, please aknowledge BrainRender's contribution.

References

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