Visualising your data in brainrender

Generating 3D renderings of your data
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"
# intialise 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

Alternatively, you can use the brainrender GUI, and use the Add cells button to load the points.npy file. You can use Show structures tree to visualise brain areas.

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