fix: volume rendering picking issue with other transparent objects

python/tests/volume_rendering_pick_test.py

@@ -0,0 +1,122 @@
+# @license
+# Copyright 2026 Google Inc.
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Test volume rendering picking."""
+
+import threading
+
+import neuroglancer
+import numpy as np
+
+
+def test_volume_rendering_picking_does_not_occlude_mesh(webdriver):
+    """Volume rendering must not steal pick buffer entries from a transparent entry in front of it.
+
+    Scene: a transparent segmentation mesh occupies the near half of the volume (low z,
+    close to the default camera which looks in the +z direction), and an image volume
+    occupies the far half (high z).  Clicking the centre of the 3-D view should pick
+    the mesh, not the image.
+
+    The regression being guarded: before the fix, volume rendering wrote the near-plane
+    depth (≈ 0) to the picking buffer, making it appear closer than any real geometry
+    and stealing pick buffer entries from meshes that were geometrically in front of it.
+    """
+    shape = (20, 20, 20)
+
+    # Image data in the far half of the volume (high z = far from default camera,
+    # which looks in the +z direction so low z is nearest).
+    image_data = np.zeros(shape, dtype=np.uint8)
+    image_data[:, :, 10:20] = 200
+
+    # Segmentation cube in the near half (low z = close to default camera).
+    # The cube must not touch any array boundary so that marching cubes generates
+    # a fully closed mesh rather than an open plane.
+    seg_data = np.zeros(shape, dtype=np.uint64)
+    seg_data[2:18, 2:18, 2:9] = 1
+
+    with webdriver.viewer.txn() as s:
+        s.dimensions = neuroglancer.CoordinateSpace(
+            names=["x", "y", "z"], units="nm", scales=[1, 1, 1]
+        )
+        s.layers.append(
+            name="image",
+            layer=neuroglancer.ImageLayer(
+                source=neuroglancer.LocalVolume(
+                    data=image_data, dimensions=s.dimensions
+                ),
+                volume_rendering_mode="On",
+            ),
+        )
+        s.layers.append(
+            name="seg",
+            layer=neuroglancer.SegmentationLayer(
+                source=neuroglancer.LocalVolume(data=seg_data, dimensions=s.dimensions),
+                segments=[1],
+                object_alpha=0.5,
+            ),
+        )
+        s.layout = "3d"
+        s.show_axis_lines = False
+        s.position = [10, 10, 10]
+        s.projection_scale = 30
+
+    # threading.Event is required because the pick callback fires on a background
+    # thread (browser → Python action dispatch), not on the test's main thread.
+    event = threading.Event()
+    result = [None]
+
+    def pick_action(action_state):
+        result[0] = action_state
+        event.set()
+
+    webdriver.viewer.actions.add("pick-action", pick_action)
+    with webdriver.viewer.config_state.txn() as cs:
+        cs.show_ui_controls = False
+        cs.show_panel_borders = False
+        cs.input_event_bindings.perspective_view["click0"] = "pick-action"
+
+    webdriver.sync()
+
+    webdriver.action_chain().move_to_element(webdriver.root_element).click().perform()
+
+    assert event.wait(timeout=30.0), "Pick action was not triggered"
+    action_state = result[0]
+    assert action_state is not None
+
+    seg_pick = action_state.selected_values.get("seg")
+    assert seg_pick is not None, (
+        "Segmentation mesh was not picked — volume rendering may be incorrectly "
+        "occluding it via a wrong picking depth"
+    )
+    assert seg_pick.value == 1
+
+    # Flip camera 180° around Y so it now looks from +z toward -z.  The image
+    # volume (high z) is now in front of the mesh (low z), so the volume should
+    # be picked instead.
+    event.clear()
+    result[0] = None
+    with webdriver.viewer.txn() as s:
+        s.projection_orientation = [0, 1, 0, 0]
+    webdriver.sync()
+
+    webdriver.action_chain().move_to_element(webdriver.root_element).click().perform()
+
+    assert event.wait(timeout=30.0), "Pick action was not triggered after camera flip"
+    action_state = result[0]
+    assert action_state is not None
+
+    image_pick = action_state.selected_values.get("image")
+    assert (
+        image_pick is not None
+    ), "Image volume was not picked when it is in front of the mesh"
+    # We don't assert the value because currently volume rendering reports 0

src/perspective_view/panel.ts

@@ -231,9 +231,11 @@ function defineMaxProjectionPickCopyShader(builder: ShaderBuilder) {
   builder.addOutputBuffer("highp vec4", "out_z", 1);
   builder.addOutputBuffer("highp vec4", "out_pickId", 2);
   builder.setFragmentMain(`
+vec4 depth = getValue0();
 out_color = vec4(0.0);
-out_z = getValue0();
+out_z = depth;
 out_pickId = getValue1();
+gl_FragDepth = 1.0 - depth.r;
 `);
 }