diff --git a/examples/brainmapper.py b/examples/brainmapper.py new file mode 100644 index 00000000..c8891a00 --- /dev/null +++ b/examples/brainmapper.py @@ -0,0 +1,36 @@ +""" +Visualise the output from brainmapper. Cells transformed to atlas space can +be found at brainmapper_output/points/points.npy. + +For more details on brainmapper, please see: +https://brainglobe.info/documentation/brainglobe-workflows/brainmapper/index.html +""" + +from pathlib import Path + +from myterial import orange +from rich import print + +from brainrender.scene import Scene +from brainrender.actors import Points +from brainrender import settings + +settings.SHADER_STYLE = "plastic" + +cells_path = Path(__file__).parent.parent / "resources" / "points.npy" + +print(f"[{orange}]Running example: {Path(__file__).name}") + +# Create a brainrender scene +scene = Scene(title="brainmapper cells") + +# Create points actor +cells = Points(cells_path, radius=45, colors="palegoldenrod", alpha=0.8) + +# Visualise injection site +scene.add_brain_region("VISp", color="mediumseagreen", alpha=0.6) + +# Add cells +scene.add(cells) + +scene.render() diff --git a/resources/points.npy b/resources/points.npy new file mode 100755 index 00000000..de886a2b Binary files /dev/null and b/resources/points.npy differ