Merge pull request #359 from brainglobe/brainmapper

Add brainmapper example script

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()