Visualising your data in brainrender#

3D brainrender visualisation of brainmapper results

To generate 3D figures of your data in atlas space, you can use brainrender. brainmapper automatically exports a file in a brainrender compatible format, which can be found at test_brain/output/points/points.npy.

Once you’ve installed brainrender, you can try something like this:

from brainrender.scene import Scene
from brainrender.actors import Points

cells_path = "test_brain/output/points/points.npy"

# Initialise brainrender scene
scene = Scene()

# Create points actor
cells = Points(cells_path, radius=45, colors="palegoldenrod", alpha=0.8)

# Visualise injection site (retrosplenial cortex)
scene.add_brain_region(["RSPd"], color="mediumseagreen", alpha=0.6)
scene.add_brain_region(["RSPv"], color="purple", alpha=0.6)
scene.add_brain_region(["RSPagl"], color="mediumseagreen", alpha=0.6)

# Add cells
scene.add(cells)

scene.render()

Hint

As the points.h5file contains the detected cells in atlas space, you can load cells from multiple brains (e.g., in a different colour).