Using Notebooks

brainrender can be used with Jupyter notebooks in two ways:

1. you can embed a window with your rendered scene

2. you can have your scene be rendered in a pop-up window.

Rendering your scene in a separate window

If you want your scene to be rendered in a new window, then set this option before you create your Scene.

import vedo
vedo.settings.default_backend= 'vtk'

After this everything will work exactly the same as usual, and you will have access to all of brainrender’s features. E.g. to visualise primary visual cortex in the Allen Adult Mouse Brain Atlas:

import vedo
vedo.settings.default_backend= 'vtk'

from brainrender import Scene
popup_scene = Scene(atlas_name='allen_mouse_50um', title='popup')

popup_scene.add_brain_region('VISp')

popup_scene.render()  # press 'Esc' to close

Embedding renderings in Jupyter notebooks

Hint

When embedding renderings in Jupyter Notebook not all of brainrender’s functionality will work! If you want to support all of brainrender’s features you should not embed renderings in the notebooks.

Note that this is due to the backend (k3d) used to embed the renderings not because of brainrender.

If you still need to embed your Scene then brainrender works slightly differently. E.g. to visualise the tectum in the larval zebrafish atlas:

# Set the backend
import vedo
vedo.settings.default_backend= 'k3d'

# Create a brainrender scene
from brainrender import Scene
scene = Scene(atlas_name='mpin_zfish_1um', title='Embedded')  # note the title will not actually display
scene.add_brain_region('tectum')

# Make sure it gets embedded in the window
scene.jupyter = True

# scene.render now will prepare the scene for rendering, but it won't render anything yet
scene.render()

# To display the scene we use `vedo`'s `show` method to show the scene's actors
from vedo import Plotter  # <- this will be used to render an embedded scene 
plt = Plotter()
plt.show(*scene.renderables)  # same as vedo.show(*scene.renderables)

Hint

As with all BrainGlobe tools, if you do not have these atlases locally, the first time you run the commands it may be slow as the data is downloaded.