napari-spatialdata 0.6.0__tar.gz → 0.7.0__tar.gz

{napari_spatialdata-0.6.0 → napari_spatialdata-0.7.0}/.github/workflows/benchmarks.yml

@@ -8,8 +8,8 @@ name: Benchmarks
 on:
   pull_request:
     types: [labeled]
-  schedule:
-    - cron: "6 6 * * 0" # every sunday
+  #  schedule:
+  #    - cron: "6 6 * * 0" # every sunday
   workflow_dispatch:
     inputs:
       base_ref:
@@ -59,11 +59,11 @@ jobs:
     steps:
       # We need the full repo to avoid this issue
       # https://github.com/actions/checkout/issues/23
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         name: Install Python
         with:
           python-version: "3.11"
@@ -140,7 +140,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           PLATFORM: ${{ matrix.runs-on }}
-          PYTHON: "3.9"
+          PYTHON: "3.11"
           BACKEND: ${{ matrix.benchmark-name }}
           RUN_ID: ${{ github.run_id }}
           TITLE: "[test-bot] Benchmark tests failing"
@@ -170,7 +170,7 @@ jobs:
 
           fi
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         if: always()
         with:
           name: asv-benchmark-results-${{ github.run_id }}-${{ github.run_number }}-${{ github.run_attempt }}-${{ matrix.benchmark-name }}
@@ -182,13 +182,13 @@ jobs:
     if: always()
     steps:
       - name: Download artifact
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v6
         with:
           pattern: asv-benchmark-results*
           path: asv_result
           merge-multiple: true
       - name: Upload artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: asv-benchmark-results-${{ github.run_id }}-${{ github.run_number }}-${{ github.run_attempt }}
           path: asv_result

{napari_spatialdata-0.6.0 → napari_spatialdata-0.7.0}/.github/workflows/benchmarks_report.yml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: "Download artifact"
-        uses: actions/github-script@v7
+        uses: actions/github-script@v8
         with:
           script: |
             let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({
@@ -68,7 +68,7 @@ jobs:
 
       - name: "Comment on PR"
         if: env.PR_NUMBER != ''
-        uses: actions/github-script@v7
+        uses: actions/github-script@v8
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           script: |
@@ -84,7 +84,7 @@ jobs:
 
       - name: "Remove run-benchmarks label"
         if: env.PR_NUMBER != ''
-        uses: actions/github-script@v7
+        uses: actions/github-script@v8
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           script: |

{napari_spatialdata-0.6.0 → napari_spatialdata-0.7.0}/.github/workflows/release.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     if: startsWith(github.ref, 'refs/tags/v')
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - uses: hynek/build-and-inspect-python-package@v2
 
   upload-to-pypi:
@@ -21,7 +21,7 @@ jobs:
 
     steps:
       - name: Download built artifact to dist/
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v6
         with:
           name: Packages
           path: dist

napari_spatialdata-0.7.0/.github/workflows/test.yml

@@ -0,0 +1,72 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: tests
+
+on:
+  push:
+    branches:
+      - main
+      - npe2
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+  pull_request:
+    branches:
+      - main
+      - npe2
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [ubuntu-latest, macos-latest] # [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.11", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # these libraries enable testing on Qt on linux
+      - uses: tlambert03/setup-qt-libs@v1
+
+      # strategy borrowed from vispy for installing opengl libs on windows
+      - name: Install Windows OpenGL
+        if: runner.os == 'Windows'
+        run: |
+          git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
+          powershell gl-ci-helpers/appveyor/install_opengl.ps1
+
+      # note: if you need dependencies from conda, considering using
+      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
+      # and
+      # tox-conda: https://github.com/tox-dev/tox-conda
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install setuptools tox tox-gh-actions
+
+      # this runs the platform-specific tests declared in tox.ini
+      - name: Test with tox
+        uses: coactions/setup-xvfb@v1
+        with:
+          run: python -m tox
+        env:
+          PLATFORM: ${{ matrix.platform }}
+
+      - name: Coverage
+        uses: codecov/codecov-action@v5
+
+      - name: Archive figures generated during testing
+        if: always()
+        uses: actions/upload-artifact@v5
+        with:
+          name: plotting-results-${{ matrix.python-version }}-${{ matrix.platform }}
+          path: /Users/runner/work/napari-spatialdata/napari-spatialdata/tests/plots/generated/*

{napari_spatialdata-0.6.0 → napari_spatialdata-0.7.0}/.gitignore

@@ -117,3 +117,4 @@ tests/plots/generated
 
 # Local temp script for testing user bugs (Luca)
 temp/
+uv.lock

{napari_spatialdata-0.6.0 → napari_spatialdata-0.7.0}/.pre-commit-config.yaml

@@ -7,13 +7,13 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.17.1
+    rev: v1.19.1
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.23]
         exclude: docs
-  - repo: https://github.com/psf/black
-    rev: 25.1.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 25.12.0
     hooks:
       - id: black
         additional_dependencies: [toml]
@@ -45,15 +45,15 @@ repos:
       - id: check-toml
       - id: requirements-txt-fixer
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.19.1
+    rev: 1.20.0
     hooks:
       - id: blacken-docs
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.8
+    rev: v0.14.10
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.20.0
+    rev: v3.21.2
     hooks:
       - id: pyupgrade

{napari_spatialdata-0.6.0 → napari_spatialdata-0.7.0}/.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.11"
 sphinx:
   configuration: docs/conf.py
   fail_on_warning: false

{napari_spatialdata-0.6.0 → napari_spatialdata-0.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-spatialdata
-Version: 0.6.0
+Version: 0.7.0
 Summary: Interactive visualization of spatial omics data with napari
 Home-page: https://github.com/scverse/napari-spatialdata.git
 Author: giovanni palla
@@ -16,23 +16,23 @@ Classifier: Framework :: napari
 Classifier: Topic :: Software Development :: Testing
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Operating System :: OS Independent
 Classifier: License :: OSI Approved :: BSD License
-Requires-Python: >=3.10
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: anndata
+Requires-Dist: anndata>=0.12.0
 Requires-Dist: click
 Requires-Dist: cycler
-Requires-Dist: dask<=2024.11.2,>=2024.4.1
+Requires-Dist: dask>=2025.2.0
 Requires-Dist: geopandas
 Requires-Dist: loguru
 Requires-Dist: matplotlib
 Requires-Dist: napari>=0.6.2
-Requires-Dist: napari-matplotlib
+Requires-Dist: napari-matplotlib>=3.0.2
 Requires-Dist: numba
 Requires-Dist: numpy
 Requires-Dist: packaging
@@ -44,7 +44,7 @@ Requires-Dist: scanpy
 Requires-Dist: scipy
 Requires-Dist: shapely
 Requires-Dist: scikit-learn
-Requires-Dist: spatialdata>=0.2.6
+Requires-Dist: spatialdata>=0.7.0dev1
 Requires-Dist: superqt
 Requires-Dist: typing_extensions>=4.8.0
 Requires-Dist: vispy
@@ -62,8 +62,8 @@ Requires-Dist: pre-commit>=2.9.0; extra == "test"
 Provides-Extra: doc
 Requires-Dist: sphinx>=4.5; extra == "doc"
 Requires-Dist: sphinx-book-theme>=1.0.0; extra == "doc"
-Requires-Dist: myst-parser; extra == "doc"
-Requires-Dist: sphinxcontrib-bibtex>=1.0.0; extra == "doc"
+Requires-Dist: myst-parser>=2.0.0; extra == "doc"
+Requires-Dist: sphinxcontrib-bibtex>=2.5.0; extra == "doc"
 Requires-Dist: sphinx-autodoc-typehints>=1.11.0; extra == "doc"
 Requires-Dist: sphinx-autobuild; extra == "doc"
 Requires-Dist: scanpydoc; extra == "doc"
@@ -71,12 +71,12 @@ Requires-Dist: ipykernel; extra == "doc"
 Requires-Dist: ipython; extra == "doc"
 Requires-Dist: sphinx-copybutton; extra == "doc"
 Requires-Dist: sphinx-qt-documentation; extra == "doc"
-Requires-Dist: myst-nb; extra == "doc"
+Requires-Dist: myst-nb>=1.0.0; extra == "doc"
 Requires-Dist: squidpy; extra == "doc"
 Provides-Extra: readthedocs
 Requires-Dist: pydantic>2; extra == "readthedocs"
 Provides-Extra: pre
-Requires-Dist: spatialdata>=0.1.0-pre0; extra == "pre"
+Requires-Dist: spatialdata>=0.7.0dev0; extra == "pre"
 Provides-Extra: all
 Requires-Dist: napari[pyqt5]; extra == "all"
 Dynamic: license-file

{napari_spatialdata-0.6.0 → napari_spatialdata-0.7.0}/asv.conf.json

@@ -16,7 +16,7 @@
   // Install using default qt install
   "build_command": ["python -V"], // skip build stage
   "install_command": [
-    "in-dir={env_dir} python -m pip install {build_dir}[all,test]"
+    "in-dir={env_dir} python -m pip install --pre {build_dir}[all,test,pre]"
   ],
   "uninstall_command": [
     "in-dir={env_dir} python -m pip uninstall -y {project}"

{napari_spatialdata-0.6.0 → napari_spatialdata-0.7.0}/benchmarks/benchmark.txt

@@ -22,7 +22,7 @@ json5==0.9.25
     # via asv
 mamba==0.11.3
     # via -r benchmark.in
-packaging==24.1
+packaging>=24.2
     # via
     #   asv
     #   build

napari_spatialdata-0.7.0/docs/contributing.md

@@ -0,0 +1,25 @@
+# Contributing guide
+
+Please refer to the [contribution guide from the `spatialdata` repository](https://github.com/scverse/spatialdata/blob/main/docs/contributing.md).
+
+## Debugging napari GUI tests
+
+To visually inspect what a test is rendering in napari:
+
+1. Change `make_napari_viewer()` to `make_napari_viewer(show=True)`
+2. Add `napari.run()` before the end of the test (before the assertions)
+
+Example:
+
+```python
+import napari
+
+
+def test_my_visualization(make_napari_viewer):
+    viewer = make_napari_viewer(show=True)
+    # ... setup code ...
+    napari.run()
+    # assertions...
+```
+
+Remember to revert these changes before committing.

{napari_spatialdata-0.6.0 → napari_spatialdata-0.7.0}/setup.cfg

@@ -19,27 +19,27 @@ classifiers =
 	Topic :: Software Development :: Testing
 	Programming Language :: Python
 	Programming Language :: Python :: 3
-	Programming Language :: Python :: 3.10
 	Programming Language :: Python :: 3.11
 	Programming Language :: Python :: 3.12
+	Programming Language :: Python :: 3.13
 	Operating System :: OS Independent
 	License :: OSI Approved :: BSD License
 
 [options]
 packages = find:
 include_package_data = True
-python_requires = >=3.10
+python_requires = >=3.11
 setup_requires = setuptools_scm
 install_requires = 
-	anndata
+	anndata>=0.12.0
 	click
 	cycler
-	dask>=2024.4.1,<=2024.11.2
+	dask>=2025.2.0
 	geopandas
 	loguru
 	matplotlib
 	napari>=0.6.2
-	napari-matplotlib
+	napari-matplotlib>=3.0.2
 	numba
 	numpy
 	packaging
@@ -51,7 +51,7 @@ install_requires =
 	scipy
 	shapely
 	scikit-learn
-	spatialdata>=0.2.6
+	spatialdata>=0.7.0dev1
 	superqt
 	typing_extensions>=4.8.0
 	vispy
@@ -73,8 +73,8 @@ test =
 doc = 
 	sphinx>=4.5
 	sphinx-book-theme>=1.0.0
-	myst-parser
-	sphinxcontrib-bibtex>=1.0.0
+	myst-parser>=2.0.0
+	sphinxcontrib-bibtex>=2.5.0
 	sphinx-autodoc-typehints>=1.11.0
 	sphinx-autobuild
 	scanpydoc
@@ -82,12 +82,12 @@ doc =
 	ipython
 	sphinx-copybutton
 	sphinx-qt-documentation
-	myst-nb
+	myst-nb>=1.0.0
 	squidpy
 readthedocs = 
 	pydantic>2
 pre = 
-	spatialdata>=0.1.0-pre0
+	spatialdata>=0.7.0dev0
 all = 
 	napari[pyqt5]
 

{napari_spatialdata-0.6.0 → napari_spatialdata-0.7.0}/src/napari_spatialdata/_scatterwidgets.py

@@ -19,14 +19,14 @@ from pyqtgraph.Qt.QtCore import pyqtSignal
 from pyqtgraph.widgets.ColorButton import ColorButton
 from qtpy.QtCore import QSize, Qt, Signal
 from qtpy.QtGui import QColor, QIcon
-from qtpy.QtWidgets import QPushButton
+from qtpy.QtWidgets import QLabel, QPushButton, QSpinBox
 from scipy.spatial import cKDTree
 from shapely.geometry import Point, Polygon
 from spatialdata._types import ArrayLike
 
+import napari_spatialdata.constants.config
 from napari_spatialdata._model import DataModel
 from napari_spatialdata._widgets import AListWidget, ComponentWidget
-from napari_spatialdata.constants.config import POINT_SIZE_SCATTERPLOT_WIDGET
 
 __all__ = [
     "PlotWidget",
@@ -334,6 +334,7 @@ class PlotWidget(GraphicsLayoutWidget):
         self.lut: pg.HistogramLUTItem | None = None
         self.discrete_color_widget: DiscreteColorWidget | None = None
         self.wrapped_widget: QtWidgets.QGraphicsProxyWidget | None = None
+        self._point_size: int = napari_spatialdata.constants.config.POINT_SIZE_SCATTERPLOT_WIDGET
 
         self.scatter_plot = self.addPlot(title="")
         self.scatter_plot.setLabel("bottom", self.x_label)
@@ -344,7 +345,10 @@ class PlotWidget(GraphicsLayoutWidget):
 
         # Create a separate ScatterPlotItem for the highlighted point
         self.hovered_point = pg.ScatterPlotItem(
-            pen=pg.mkPen("r", width=2), symbol="o", size=POINT_SIZE_SCATTERPLOT_WIDGET, brush=pg.mkBrush(255, 0, 0)
+            pen=pg.mkPen("r", width=2),
+            symbol="o",
+            size=self._point_size + 2,
+            brush=pg.mkBrush(255, 0, 0),
         )
         self.scatter_plot.addItem(self.hovered_point)
 
@@ -417,6 +421,19 @@ class PlotWidget(GraphicsLayoutWidget):
         self.rectangle_mode_button.setToolTip("Add rectangular ROIs.")
         self.rectangle_mode_button.move(50, 10)  # Adjust position as needed
 
+        # Point size control
+        self.point_size_label = QLabel("Size:", self)
+        self.point_size_label.setStyleSheet(f"QLabel {{ color: rgb{self.color}; background-color: transparent; }}")
+        self.point_size_label.move(130, 14)
+
+        self.point_size_spinbox = QSpinBox(self)
+        self.point_size_spinbox.setRange(1, 50)
+        self.point_size_spinbox.setValue(self._point_size)
+        self.point_size_spinbox.setFixedWidth(50)
+        self.point_size_spinbox.setToolTip("Adjust point size in scatter plot")
+        self.point_size_spinbox.valueChanged.connect(self._on_point_size_changed)
+        self.point_size_spinbox.move(165, 10)
+
         # Connect mouse events
         self.scatter_plot.setMouseEnabled(x=True, y=True)
         self.scatter_plot.scene().sigMouseMoved.connect(self.mouseMoveEvent)
@@ -461,6 +478,25 @@ class PlotWidget(GraphicsLayoutWidget):
             logger.debug("Updating proximity sensitivity...")
             self.dist_threshold = [x * 15 for x in self.scatter.pixelSize()]  # Adjust this factor as needed
 
+    @property
+    def point_size(self) -> int:
+        """Get the current point size for the scatter plot."""
+        return self._point_size
+
+    @point_size.setter
+    def point_size(self, value: int) -> None:
+        """Set the point size for the scatter plot."""
+        self._point_size = value
+        self.point_size_spinbox.setValue(value)
+
+    def _on_point_size_changed(self, value: int) -> None:
+        """Handle point size spinbox value change."""
+        self._point_size = value
+        # Update hovered point indicator size to be slightly larger
+        self.hovered_point.setSize(value + 2)
+        if self.scatter is not None:
+            self.plot()
+
     def update_hover_highlight(self, x: float, y: float) -> None:
         """Update the hover highlight based on the cursor position."""
         if self.kd_tree is not None and self.x_data is not None and self.y_data is not None:
@@ -759,6 +795,7 @@ class PlotWidget(GraphicsLayoutWidget):
                     pen=None,
                     symbolPen=self.symbolPen,
                     symbol="o",
+                    symbolSize=self._point_size,
                     clear=True,
                     symbolBrush=self.brushes,
                 )
@@ -773,6 +810,7 @@ class PlotWidget(GraphicsLayoutWidget):
                     fillLevel=0,
                     pen=None,
                     symbolPen=self.symbolPen,
+                    symbolSize=self._point_size,
                     symbolBrush=self.brushes,
                     clear=True,
                 )
@@ -785,6 +823,7 @@ class PlotWidget(GraphicsLayoutWidget):
                     fillLevel=0,
                     pen=None,
                     symbolPen=self.symbolPen,
+                    symbolSize=self._point_size,
                     symbolBrush=self.brushes,
                     clear=True,
                 )

{napari_spatialdata-0.6.0 → napari_spatialdata-0.7.0}/src/napari_spatialdata/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.6.0'
-__version_tuple__ = version_tuple = (0, 6, 0)
+__version__ = version = '0.7.0'
+__version_tuple__ = version_tuple = (0, 7, 0)
 
-__commit_id__ = commit_id = 'gc95e3e271'
+__commit_id__ = commit_id = 'g6747bf035'

{napari_spatialdata-0.6.0 → napari_spatialdata-0.7.0}/src/napari_spatialdata/_viewer.py

@@ -18,12 +18,11 @@ from shapely import Polygon
 from spatialdata import get_element_annotators, get_element_instances
 from spatialdata._core.query.relational_query import _left_join_spatialelement_table
 from spatialdata._types import ArrayLike
-from spatialdata.models import PointsModel, ShapesModel, TableModel, force_2d, get_channel_names
+from spatialdata.models import PointsModel, ShapesModel, TableModel, force_2d, get_axes_names, get_channel_names
 from spatialdata.transformations import Affine, Identity
 
 from napari_spatialdata._model import DataModel
 from napari_spatialdata.constants import config
-from napari_spatialdata.constants.config import CIRCLES_AS_POINTS
 from napari_spatialdata.utils._utils import (
     _adjust_channels_order,
     _get_ellipses_from_circles,
@@ -470,7 +469,7 @@ class SpatialDataViewer(QObject):
         if multi:
             original_name = original_name[: original_name.rfind("_")]
 
-        affine = _get_transform(sdata.images[original_name], selected_cs)
+        affine = _get_transform(sdata.images[original_name], selected_cs, include_z=True)
         rgb_image, rgb = _adjust_channels_order(element=sdata.images[original_name])
 
         channels = ("RGB(A)",) if rgb else get_channel_names(sdata.images[original_name])
@@ -517,6 +516,7 @@ class SpatialDataViewer(QObject):
         df = sdata.shapes[original_name]
         affine = _get_transform(sdata.shapes[original_name], selected_cs)
 
+        # 2.5D circles not supported yet
         xy = np.array([df.geometry.x, df.geometry.y]).T
         yx = np.fliplr(xy)
         radii = df.radius.to_numpy()
@@ -541,10 +541,10 @@ class SpatialDataViewer(QObject):
         version = get_napari_version()
         kwargs: dict[str, Any] = (
             {"edge_width": 0.0}
-            if version <= packaging.version.parse("0.4.20") or not CIRCLES_AS_POINTS
+            if version <= packaging.version.parse("0.4.20") or not config.CIRCLES_AS_POINTS
             else {"border_width": 0.0}
         )
-        if CIRCLES_AS_POINTS:
+        if config.CIRCLES_AS_POINTS:
             layer = Points(
                 yx,
                 name=key,
@@ -556,7 +556,7 @@ class SpatialDataViewer(QObject):
             assert affine is not None
             self._adjust_radii_of_points_layer(layer=layer, affine=affine)
         else:
-            if version <= packaging.version.parse("0.4.20") or not CIRCLES_AS_POINTS:
+            if version <= packaging.version.parse("0.4.20") or not config.CIRCLES_AS_POINTS:
                 kwargs |= {"edge_color": "white"}
             else:
                 kwargs |= {"border_color": "white"}
@@ -597,7 +597,8 @@ class SpatialDataViewer(QObject):
             original_name = original_name[: original_name.rfind("_")]
 
         df = sdata.shapes[original_name]
-        affine = _get_transform(sdata.shapes[original_name], selected_cs)
+        include_z = not config.PROJECT_2_5D_SHAPES_TO_2D
+        affine = _get_transform(sdata.shapes[original_name], selected_cs, include_z=include_z)
 
         # when mulitpolygons are present, we select the largest ones
         if "MultiPolygon" in np.unique(df.geometry.type):
@@ -609,7 +610,7 @@ class SpatialDataViewer(QObject):
             df = df.sort_index()  # reset the index to the first order
 
         simplify = len(df) > config.POLYGON_THRESHOLD
-        polygons, indices = _get_polygons_properties(df, simplify)
+        polygons, indices = _get_polygons_properties(df, simplify, include_z=include_z)
 
         # this will only work for polygons and not for multipolygons
         polygons = _transform_coordinates(polygons, f=lambda x: x[::-1])
@@ -662,7 +663,7 @@ class SpatialDataViewer(QObject):
             original_name = original_name[: original_name.rfind("_")]
 
         indices = get_element_instances(sdata.labels[original_name])
-        affine = _get_transform(sdata.labels[original_name], selected_cs)
+        affine = _get_transform(sdata.labels[original_name], selected_cs, include_z=True)
         rgb_labels, _ = _adjust_channels_order(element=sdata.labels[original_name])
 
         adata, table_name, table_names = self._get_table_data(sdata, original_name)
@@ -706,8 +707,10 @@ class SpatialDataViewer(QObject):
         if multi:
             original_name = original_name[: original_name.rfind("_")]
 
+        axes = get_axes_names(sdata.points[original_name])
         points = sdata.points[original_name].compute()
-        affine = _get_transform(sdata.points[original_name], selected_cs)
+        include_z = "z" in axes and not config.PROJECT_3D_POINTS_TO_2D
+        affine = _get_transform(sdata.points[original_name], selected_cs, include_z=include_z)
         adata, table_name, table_names = self._get_table_data(sdata, original_name)
 
         if len(points) < config.POINT_THRESHOLD:
@@ -727,14 +730,16 @@ class SpatialDataViewer(QObject):
             _, adata = _left_join_spatialelement_table(
                 {"points": {original_name: subsample_points}}, sdata[table_name], match_rows="left"
             )
-        xy = subsample_points[["y", "x"]].values
-        np.fliplr(xy)
+        axes = sorted(axes, reverse=True)
+        if not include_z and "z" in axes:
+            axes.remove("z")
+        coords = subsample_points[axes].values
         # radii_size = _calc_default_radii(self.viewer, sdata, selected_cs)
         radii_size = 3
         version = get_napari_version()
         kwargs = {"edge_width": 0.0} if version <= packaging.version.parse("0.4.20") else {"border_width": 0.0}
         layer = Points(
-            xy,
+            coords,
             name=key,
             size=radii_size * 2,
             affine=affine,