example to show probe tracks (#313)

* example to show probe tracks * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Standardise script --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Adam Tyson <[email protected]>
brainglobe · Jan 11, 2024 · 52b1ec0 · 52b1ec0
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diff --git a/brainrender/resources/probe_1_striatum.npy b/brainrender/resources/probe_1_striatum.npy
diff --git a/brainrender/resources/probe_2_RSP.npy b/brainrender/resources/probe_2_RSP.npy
diff --git a/examples/probe_tracks.py b/examples/probe_tracks.py
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+"""
+This example visualizes `.npy` files exported from brainglobe-segmentation
+"""
+
+from pathlib import Path
+import numpy as np
+
+from brainrender import Scene
+from brainrender.actors import Points
+
+data_path = Path(__file__).parent.parent / "brainrender" / "resources"
+
+scene = Scene(title="Silicon Probe Visualization")
+
+# Visualise the probe target regions
+cp = scene.add_brain_region("CP", alpha=0.15)
+rsp = scene.add_brain_region("RSP", alpha=0.15)
+
+# Add probes to the scene.
+# Each .npy file should contain a numpy array with the coordinates of each
+# part of the probe.
+scene.add(
+    Points(
+        np.load(data_path / "probe_1_striatum.npy"),
+        name="probe_1",
+        colors="darkred",
+        radius=50,
+    )
+)
+scene.add(
+    Points(
+        np.load(data_path / "probe_2_RSP.npy"),
+        name="probe_2",
+        colors="darkred",
+        radius=50,
+    )
+)
+
+# render
+scene.render()