scverse · timtreis · Jun 22, 2026 · Jun 22, 2026 · Jun 22, 2026
diff --git a/src/spatialdata_plot/pl/_datashader.py b/src/spatialdata_plot/pl/_datashader.py
@@ -730,9 +730,10 @@ def _ax_show_and_transform(
     norm: Normalize | None = None,
     interpolation: str | None = None,
 ) -> matplotlib.image.AxesImage:
-    # ``extent`` uses mpl's pixel-grid convention; world placement happens via
-    # ``set_transform(trans_data)`` afterwards.
-    image_extent = (-0.5, array.shape[1] - 0.5, array.shape[0] - 0.5, -0.5)
+    # Pixel-edge extent [0, W] x [0, H], matching get_extent (which sets the axis limits)
+    # and the affine's data box (placement is via set_transform below). mpl's default
+    # pixel-center extent (-0.5, W-0.5, ...) offsets by half a pixel, amplified by the affine.
+    image_extent = (0.0, array.shape[1], array.shape[0], 0.0)
     # ``alpha`` is applied only when no cmap is set, so RGBA arrays already
     # carrying per-pixel alpha (e.g. datashader output) are not double-attenuated.
     imshow_kwargs: dict[str, Any] = {"zorder": zorder, "extent": image_extent, "norm": norm}

diff --git a/src/spatialdata_plot/pl/render.py b/src/spatialdata_plot/pl/render.py
@@ -2400,7 +2400,16 @@ def _draw_labels(
         # non-linear norm (LogNorm/PowerNorm). Display the RGB without a norm and build the
         # continuous colorbar mappable separately from the resolved norm (mirrors the outline path),
         # so the colorbar reflects the real norm subclass.
-        img = ax.imshow(labels, rasterized=True, alpha=alpha, origin="lower", zorder=render_params.zorder)
+        # Pixel-edge extent (0, W, 0, H) matching get_extent/the affine box; mpl's default
+        # pixel-center extent would offset labels half a pixel. Order follows origin="lower".
+        img = ax.imshow(
+            labels,
+            rasterized=True,
+            alpha=alpha,
+            origin="lower",
+            extent=(0.0, labels.shape[1], 0.0, labels.shape[0]),
+            zorder=render_params.zorder,
+        )
         img.set_transform(trans_data)
         if color_spec.is_categorical:
             return img

diff --git a/tests/_images/ColorbarControls_single_channel_default_channel_name_omits_label.png b/tests/_images/ColorbarControls_single_channel_default_channel_name_omits_label.png
diff --git a/tests/_images/Extent_extent_of_img_is_correct_after_spatial_query.png b/tests/_images/Extent_extent_of_img_is_correct_after_spatial_query.png
diff --git a/tests/_images/Labels_label_centroids_sit_at_pixel_centers.png b/tests/_images/Labels_label_centroids_sit_at_pixel_centers.png
diff --git a/tests/_images/Points_can_annotate_points_with_nan_in_df_categorical_datashader.png b/tests/_images/Points_can_annotate_points_with_nan_in_df_categorical_datashader.png
diff --git a/tests/_images/Points_can_annotate_points_with_nan_in_df_continuous_datashader.png b/tests/_images/Points_can_annotate_points_with_nan_in_df_continuous_datashader.png
diff --git a/...images/Points_can_annotate_points_with_nan_in_table_X_continuous_datashader.png b/...images/Points_can_annotate_points_with_nan_in_table_X_continuous_datashader.png
diff --git a/...ges/Points_can_annotate_points_with_nan_in_table_obs_categorical_datashader.png b/...ges/Points_can_annotate_points_with_nan_in_table_obs_categorical_datashader.png
diff --git a/...ages/Points_can_annotate_points_with_nan_in_table_obs_continuous_datashader.png b/...ages/Points_can_annotate_points_with_nan_in_table_obs_continuous_datashader.png
diff --git a/tests/_images/Points_datashader_can_transform_points.png b/tests/_images/Points_datashader_can_transform_points.png
diff --git a/tests/_images/Points_datashader_can_use_any_as_reduction.png b/tests/_images/Points_datashader_can_use_any_as_reduction.png
diff --git a/tests/_images/Points_datashader_can_use_count_as_reduction.png b/tests/_images/Points_datashader_can_use_count_as_reduction.png
diff --git a/tests/_images/Points_datashader_can_use_max_as_reduction.png b/tests/_images/Points_datashader_can_use_max_as_reduction.png
diff --git a/tests/_images/Points_datashader_can_use_mean_as_reduction.png b/tests/_images/Points_datashader_can_use_mean_as_reduction.png
diff --git a/tests/_images/Points_datashader_can_use_min_as_reduction.png b/tests/_images/Points_datashader_can_use_min_as_reduction.png
diff --git a/tests/_images/Points_datashader_can_use_norm_with_clip.png b/tests/_images/Points_datashader_can_use_norm_with_clip.png
diff --git a/tests/_images/Points_datashader_can_use_norm_without_clip.png b/tests/_images/Points_datashader_can_use_norm_without_clip.png
diff --git a/tests/_images/Points_datashader_can_use_std_as_reduction.png b/tests/_images/Points_datashader_can_use_std_as_reduction.png
diff --git a/tests/_images/Points_datashader_can_use_std_as_reduction_not_all_zero.png b/tests/_images/Points_datashader_can_use_std_as_reduction_not_all_zero.png
diff --git a/tests/_images/Points_datashader_can_use_sum_as_reduction.png b/tests/_images/Points_datashader_can_use_sum_as_reduction.png
diff --git a/tests/_images/Points_datashader_can_use_var_as_reduction.png b/tests/_images/Points_datashader_can_use_var_as_reduction.png
diff --git a/tests/_images/Points_datashader_colors_from_table_obs.png b/tests/_images/Points_datashader_colors_from_table_obs.png
diff --git a/tests/_images/Points_datashader_matplotlib_stack.png b/tests/_images/Points_datashader_matplotlib_stack.png
diff --git a/tests/_images/Points_datashader_norm_vmin_eq_vmax_with_clip.png b/tests/_images/Points_datashader_norm_vmin_eq_vmax_with_clip.png
diff --git a/tests/_images/Points_datashader_norm_vmin_eq_vmax_without_clip.png b/tests/_images/Points_datashader_norm_vmin_eq_vmax_without_clip.png
diff --git a/tests/_images/Points_groups_na_color_none_filters_points_datashader.png b/tests/_images/Points_groups_na_color_none_filters_points_datashader.png
diff --git a/tests/_images/Points_mpl_and_datashader_point_sizes_agree_after_altered_dpi.png b/tests/_images/Points_mpl_and_datashader_point_sizes_agree_after_altered_dpi.png
diff --git a/tests/_images/Shapes_datashader_can_color_by_identical_value.png b/tests/_images/Shapes_datashader_can_color_by_identical_value.png
diff --git a/tests/_images/Shapes_datashader_can_color_by_value.png b/tests/_images/Shapes_datashader_can_color_by_value.png
diff --git a/tests/_images/Shapes_datashader_can_render_colored_shapes.png b/tests/_images/Shapes_datashader_can_render_colored_shapes.png
diff --git a/tests/_images/Shapes_datashader_can_transform_polygons.png b/tests/_images/Shapes_datashader_can_transform_polygons.png
diff --git a/tests/_images/Shapes_datashader_shades_with_linear_cmap.png b/tests/_images/Shapes_datashader_shades_with_linear_cmap.png
diff --git a/tests/_images/Show_user_ax_dpi_preserved.png b/tests/_images/Show_user_ax_dpi_preserved.png
diff --git a/tests/_images/Utils_can_set_zero_in_cmap_to_transparent.png b/tests/_images/Utils_can_set_zero_in_cmap_to_transparent.png
diff --git a/tests/pl/test_render_labels.py b/tests/pl/test_render_labels.py
@@ -61,6 +61,22 @@ def test_plot_labels_render_permutations(self, sdata_blobs: SpatialData):
             sdata_blobs.pl.render_labels("blobs_labels", color="channel_0_sum", colorbar=False, **kw).pl.show(ax=ax)
             ax.set_title(title, fontsize=8)
 
+    def test_plot_label_centroids_sit_at_pixel_centers(self):
+        # Regression for #216: on a tiny grid each data-pixel spans many display pixels, so a
+        # half-pixel image/overlay shift is blatant. Centroids (spatialdata's pixel-edge
+        # convention) must sit dead-center on their label pixels, not on the pixel corners.
+        from spatialdata import get_centroids
+        from spatialdata.models import PointsModel
+        from spatialdata.transformations import Identity
+
+        arr = np.zeros((6, 6), dtype=np.int32)
+        for label, (row, col) in enumerate([(1, 1), (1, 4), (4, 1), (4, 4), (2, 3)], start=1):
+            arr[row, col] = label
+        sdata = SpatialData(labels={"lab": Labels2DModel.parse(arr, dims=("y", "x"))})
+        centroids = get_centroids(sdata["lab"], coordinate_system="global").compute()
+        sdata["centroids"] = PointsModel.parse(centroids[["x", "y"]], transformations={"global": Identity()})
+        sdata.pl.render_labels("lab").pl.render_points("centroids", color="red", size=100).pl.show()
+
     def test_plot_can_render_labels(self, sdata_blobs: SpatialData):
         sdata_blobs.pl.render_labels(element="blobs_labels").pl.show()
 

diff --git a/tests/pl/test_utils.py b/tests/pl/test_utils.py
@@ -1286,3 +1286,64 @@ def test_first_color_per_category_skips_nan_and_handles_numeric_categories():
     source = pd.Categorical([1, None, 2, 1], categories=[1, 2])
     cv = ["#aaaaaa", "#ffffff", "#bbbbbb", "#aaaaaa"]
     assert _first_color_per_category(source, cv) == {1: "#aaaaaa", 2: "#bbbbbb"}
+
+
+def _rendered_image_world_box(im, ax) -> tuple[float, float, float, float]:
+    """World-space (x0, x1, y0, y1) the AxesImage's pixel grid actually occupies."""
+    left, right, bottom, top = im.get_extent()
+    element_affine = im.get_transform() - ax.transData
+    (x0, y0), (x1, y1) = element_affine.transform([(left, bottom), (right, top)])
+    return float(x0), float(x1), float(y0), float(y1)
+
+
+@pytest.mark.parametrize("transform_name", ["identity", "scale"])
+@pytest.mark.parametrize("element", ["image", "labels"])
+def test_rasterized_artist_aligns_with_get_extent(transform_name, element):
+    # Regression test for #216: a rasterized image/labels artist must occupy the
+    # same world box as get_extent (which sets the axis limits). The old pixel-center
+    # extent left it half a pixel off, amplified by the affine (Scale -> hundreds of px).
+    from spatialdata import get_extent
+    from spatialdata.models import Image2DModel
+    from spatialdata.transformations import Identity, Scale
+
+    transform = Identity() if transform_name == "identity" else Scale([1000.0, 1000.0], axes=("x", "y"))
+    if element == "image":
+        el = Image2DModel.parse(np.zeros((1, 4, 8)), dims=("c", "y", "x"), transformations={"global": transform})
+        sdata = SpatialData(images={"el": el})
+        ax = sdata.pl.render_images().pl.show(return_ax=True)
+    else:
+        el = Labels2DModel.parse(
+            np.zeros((4, 8), dtype=np.int32), dims=("y", "x"), transformations={"global": transform}
+        )
+        sdata = SpatialData(labels={"el": el})
+        ax = sdata.pl.render_labels().pl.show(return_ax=True)
+
+    ext = get_extent(sdata["el"], coordinate_system="global")
+    x0, x1, y0, y1 = _rendered_image_world_box(ax.get_images()[0], ax)
+    assert (min(x0, x1), max(x0, x1)) == pytest.approx(ext["x"])
+    assert (min(y0, y1), max(y0, y1)) == pytest.approx(ext["y"])
+    plt.close("all")
+
+
+def test_datashader_points_image_aligns_with_points_extent():
+    # Regression test for #216 (Sonja's case): the rasterized datashader-points image
+    # must occupy the points' world extent, matching where matplotlib scatters them.
+    from spatialdata.models import Image2DModel
+    from spatialdata.transformations import Identity
+
+    sdata = SpatialData(
+        images={"img": Image2DModel.parse(np.full((10, 10, 3), 128, dtype=np.uint8), dims=("y", "x", "c"))},
+        points={
+            "pts": PointsModel.parse(
+                pd.DataFrame({"x": [0.1, 0.9, 0.9, 0.1], "y": [0.1, 0.1, 0.9, 0.9]}),
+                transformations={"global": Identity()},
+            )
+        },
+    )
+    ax = sdata.pl.render_images().pl.render_points("pts", method="datashader", size=40).pl.show(return_ax=True)
+
+    # second image on the axis is the rasterized points (first is the background image)
+    x0, x1, y0, y1 = _rendered_image_world_box(ax.get_images()[1], ax)
+    assert (min(x0, x1), max(x0, x1)) == pytest.approx((0.1, 0.9))
+    assert (min(y0, y1), max(y0, y1)) == pytest.approx((0.1, 0.9))
+    plt.close("all")