Visualising your data in brainrender#

3D brainrender visualisation of cellfinder results

To generate 3D figures of your data in atlas space, you can use brainrender. cellfinder 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_regions(["RSPd"], colors="mediumseagreen", alpha=0.6)
scene.add_brain_regions(["RSPv"], colors="purple", alpha=0.6)
scene.add_brain_regions(["RSPagl"], colors="mediumseagreen", alpha=0.6)

# Add cells



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