brainrender 2.1.19__tar.gz → 2.2.0__tar.gz

{brainrender-2.1.19 → brainrender-2.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brainrender
-Version: 2.1.19
+Version: 2.2.0
 Summary: Visualisation and exploration of brain atlases and other anatomical data
 Author-email: "Federico Claudi, Adam Tyson, Luigi Petrucco" <hello@brainglobe.info>
 License: BSD-3-Clause
@@ -23,12 +23,14 @@ Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: brainglobe-atlasapi>=2.0.1
+Requires-Dist: cloud-volume>=3.11.0
 Requires-Dist: brainglobe-space>=1.0.0
 Requires-Dist: brainglobe-utils>=0.5.0
-Requires-Dist: h5py<3.16.0
+Requires-Dist: h5py
 Requires-Dist: k3d
 Requires-Dist: loguru
-Requires-Dist: morphapi>=0.2.1
+Requires-Dist: meshio
+Requires-Dist: morphapi>=0.3.3
 Requires-Dist: msgpack
 Requires-Dist: myterial
 Requires-Dist: numpy
@@ -55,18 +57,22 @@ Requires-Dist: jupyter; extra == "nb"
 Requires-Dist: k3d; extra == "nb"
 Dynamic: license-file
 
-# brainrender
-
-*A user-friendly python library to create high-quality, 3D neuro-anatomical renderings combining data from publicly available brain atlases with user-generated experimental data.*
-
-[![Python Version](https://img.shields.io/pypi/pyversions/brainrender.svg)](https://pypi.org/project/brainrender)
-[![PyPI](https://img.shields.io/pypi/v/brainrender.svg)](https://pypi.org/project/brainrender)
+[![Docs](https://img.shields.io/badge/Docs-brainrender-blue)](https://brainglobe.info/documentation/brainrender/index.html)
+[![Get in Touch](https://img.shields.io/badge/Get%20in%20Touch-BrainGlobe-blue)](https://brainglobe.info/contact.html)
+[![DOI](https://img.shields.io/badge/DOI-10.7554%2FeLife.65751-green)](https://doi.org/10.7554/eLife.65751)
+[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![tests](https://github.com/brainglobe/brainrender/workflows/tests/badge.svg)](https://github.com/brainglobe/brainrender/actions)
 [![codecov](https://codecov.io/gh/brainglobe/brainrender/graph/badge.svg)](https://codecov.io/gh/brainglobe/brainrender)
+[![Python Version](https://img.shields.io/pypi/pyversions/brainrender.svg)](https://pypi.org/project/brainrender)
+[![PyPI](https://img.shields.io/pypi/v/brainrender.svg)](https://pypi.org/project/brainrender)
 [![Downloads](https://static.pepy.tech/badge/brainrender)](https://pepy.tech/project/brainrender)
-[![image.sc forum](https://img.shields.io/badge/dynamic/json.svg?label=forum&url=https%3A%2F%2Fforum.image.sc%2Ftags%2Fbrainglobe.json&query=%24.topic_list.tags.0.topic_count&colorB=brightgreen&suffix=%20topics&logo=data:image/png;base64,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)](https://forum.image.sc/tag/brainglobe)
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-[![Mastodon](https://img.shields.io/badge/Mastodon-6364FF?logo=mastodon&logoColor=fff)](https://mastodon.online/@brainglobe)
+[![Code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/format.json)](https://github.com/astral-sh/ruff)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-green?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![Contributions Welcome](https://img.shields.io/badge/Contributions-Welcome-green.svg)](https://brainglobe.info/community/developers/index.html)
+
+# brainrender
+
+*A user-friendly python library to create high-quality, 3D neuro-anatomical renderings combining data from publicly available brain atlases with user-generated experimental data.*
 
 &nbsp;
 &nbsp;

{brainrender-2.1.19 → brainrender-2.2.0}/README.md

@@ -1,15 +1,19 @@
-# brainrender
-
-*A user-friendly python library to create high-quality, 3D neuro-anatomical renderings combining data from publicly available brain atlases with user-generated experimental data.*
-
-[![Python Version](https://img.shields.io/pypi/pyversions/brainrender.svg)](https://pypi.org/project/brainrender)
-[![PyPI](https://img.shields.io/pypi/v/brainrender.svg)](https://pypi.org/project/brainrender)
+[![Docs](https://img.shields.io/badge/Docs-brainrender-blue)](https://brainglobe.info/documentation/brainrender/index.html)
+[![Get in Touch](https://img.shields.io/badge/Get%20in%20Touch-BrainGlobe-blue)](https://brainglobe.info/contact.html)
+[![DOI](https://img.shields.io/badge/DOI-10.7554%2FeLife.65751-green)](https://doi.org/10.7554/eLife.65751)
+[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![tests](https://github.com/brainglobe/brainrender/workflows/tests/badge.svg)](https://github.com/brainglobe/brainrender/actions)
 [![codecov](https://codecov.io/gh/brainglobe/brainrender/graph/badge.svg)](https://codecov.io/gh/brainglobe/brainrender)
+[![Python Version](https://img.shields.io/pypi/pyversions/brainrender.svg)](https://pypi.org/project/brainrender)
+[![PyPI](https://img.shields.io/pypi/v/brainrender.svg)](https://pypi.org/project/brainrender)
 [![Downloads](https://static.pepy.tech/badge/brainrender)](https://pepy.tech/project/brainrender)
-[![image.sc forum](https://img.shields.io/badge/dynamic/json.svg?label=forum&url=https%3A%2F%2Fforum.image.sc%2Ftags%2Fbrainglobe.json&query=%24.topic_list.tags.0.topic_count&colorB=brightgreen&suffix=%20topics&logo=data:image/png;base64,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)](https://forum.image.sc/tag/brainglobe)
-[![Bluesky](https://img.shields.io/badge/Bluesky-0285FF?logo=bluesky&logoColor=fff)](https://bsky.app/profile/brainglobe.info)
-[![Mastodon](https://img.shields.io/badge/Mastodon-6364FF?logo=mastodon&logoColor=fff)](https://mastodon.online/@brainglobe)
+[![Code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/format.json)](https://github.com/astral-sh/ruff)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-green?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![Contributions Welcome](https://img.shields.io/badge/Contributions-Welcome-green.svg)](https://brainglobe.info/community/developers/index.html)
+
+# brainrender
+
+*A user-friendly python library to create high-quality, 3D neuro-anatomical renderings combining data from publicly available brain atlases with user-generated experimental data.*
 
  
  

{brainrender-2.1.19 → brainrender-2.2.0}/brainrender/_io.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 
 import requests
-from vedo import load
+from vedo import Mesh, load
 
 
 def connected_to_internet(url="http://www.google.com/", timeout=5):
@@ -85,3 +85,26 @@ def load_mesh_from_file(filepath, color=None, alpha=None):
     actor = load(str(filepath))
     actor.c(color).alpha(alpha)
     return actor
+
+
+def convert_meshio_to_vedo(meshio_mesh, color=None, alpha=None):
+    """
+    Convert a meshio mesh to a vedo mesh.
+
+    Parameters
+    ----------
+    meshio_mesh : meshio.Mesh
+        The meshio mesh to convert.
+    color : str, optional
+        The color to apply to the mesh. Default is None.
+    alpha : float, optional
+        The transparency to apply to the mesh. Default is None.
+
+    Returns
+    -------
+    vedo.Mesh
+        The converted vedo mesh.
+    """
+    actor = Mesh([meshio_mesh.points, meshio_mesh.cells_dict["triangle"]])
+    actor.c(color).alpha(alpha)
+    return actor

{brainrender-2.1.19 → brainrender-2.2.0}/brainrender/_jupyter.py

@@ -43,9 +43,13 @@ class not_on_jupyter:  # pragma: no cover
             return self.func(obj, *args, **kwargs)
         else:
             print(
-                f"[{orange_dark}]Cannot run function [bold {salmon}]{self.func.__name__}[/ bold {salmon}] in a jupyter notebook",
-                f"[{orange_dark}]Try setting the correct backend before creating your scene:\n",
-                Syntax("from vedo import embedWindow", lexer="python"),
-                Syntax("embedWindow(None)", lexer="python"),
+                f"[{orange_dark}]Cannot run function [bold {salmon}]{self.func.__name__}[/bold {salmon}] in a jupyter notebook.",
+                f"[{orange_dark}]To use brainrender in a Jupyter notebook, set the vedo backend to 'k3d' before creating your scene:\n",
+                Syntax("import vedo", lexer="python"),
+                Syntax(
+                    "vedo.settings.default_backend = 'k3d'", lexer="python"
+                ),
+                f"\n[{orange_dark}]Note: some features are not available in the k3d backend.",
+                f"[{orange_dark}]To use all features, run brainrender in a standard Python script or interactive terminal instead.",
             )
             return None

{brainrender-2.1.19 → brainrender-2.2.0}/brainrender/_video.py

@@ -30,7 +30,7 @@ class Video(VtkVideo):
         if self.size:
             fmt += f" -s {self.size}"
 
-        command = f"ffmpeg -hide_banner -loglevel panic -y -r {fps} -start_number 0 -i {fld} {fmt} {name}"
+        command = f'ffmpeg -hide_banner -loglevel panic -y -r {fps} -start_number 0 -i "{fld}" {fmt} "{name}"'
         out = os.system(command)
         self.tmp_dir.cleanup()
         return out, command

{brainrender-2.1.19 → brainrender-2.2.0}/brainrender/actor.py

@@ -1,5 +1,9 @@
+"""Actor class and label utilities for brainrender scenes."""
+
+from __future__ import annotations
+
 from io import StringIO
-from typing import Optional
+from typing import Any, Self
 
 import numpy as np
 import numpy.typing as npt
@@ -7,8 +11,8 @@ import pyinspect as pi
 from brainglobe_atlasapi import BrainGlobeAtlas
 from brainglobe_space import AnatomicalSpace
 from myterial import amber, orange, salmon
-from rich.console import Console
-from vedo import Sphere, Text3D
+from rich.console import Console, ConsoleOptions, RenderResult
+from vedo import Mesh, Sphere, Text3D
 
 from brainrender._utils import listify
 
@@ -17,27 +21,44 @@ label_mtx = [[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 1, 0], [0, 0, 0, 1]]
 
 
 def make_actor_label(
-    atlas,
-    actors,
-    labels,
-    size=300,
-    color=None,
-    radius=100,
-    xoffset=0,
-    yoffset=-500,
-    zoffset=0,
-):
+    atlas: BrainGlobeAtlas,
+    actors: Actor | list[Actor],
+    labels: str | list[str],
+    size: int = 300,
+    color: str | list[float] | None = None,
+    radius: int | None = 100,
+    xoffset: int = 0,
+    yoffset: int = -500,
+    zoffset: int = 0,
+) -> list[Text3D | Sphere]:
     """
-    Adds a 2D text anchored to a point on the actor's mesh
-    to label what the actor is
-
-    :param kwargs: keyword arguments can be passed to determine
-            text appearance and location:
-                - size: int, text size. Default 300
-                - color: str, text color. A list of colors can be passed
-                        if None a gray color is used. Default None.
-                - xoffset, yoffset, zoffset: integers that shift the label position
-                - radius: radius of sphere used to denote label anchor. Set to 0 or None to hide.
+    Create 3D text labels anchored to actor meshes.
+
+    Parameters
+    ----------
+    atlas
+        Atlas used for hemisphere queries and point mirroring.
+    actors
+        Actors to label.
+    labels
+        Label string(s) for each actor.
+    size
+        Text size. Default 300.
+    color
+        Label colour. Defaults to dark grey if None.
+    radius
+        Radius of the anchor sphere. Set to None to hide. Default 100.
+    xoffset
+        Positional offset along x. Default 0.
+    yoffset
+        Positional offset along y. Default -500.
+    zoffset
+        Positional offset along z. Default 0.
+
+    Returns
+    -------
+    list
+        Flat list of vedo Text3D and Sphere objects.
     """
     offset = [-yoffset, -zoffset, xoffset]
     default_offset = np.array([0, -200, 100])
@@ -79,40 +100,50 @@ def make_actor_label(
 
 
 class Actor:
-    _needs_label = False  # needs to make a label
-    _needs_silhouette = False  # needs to make a silhouette
-    _is_transformed = False  # has been transformed to correct axes orientation
-    _is_added = False  # has the actor been added to the scene already
+    """
+    Represents any object displayed in a brainrender scene.
+
+    Wraps a vedo Mesh with a name and class type, and provides helpers
+    for creating silhouettes and 3D labels. Unknown attribute lookups
+    are delegated to the underlying mesh.
+
+    Parameters
+    ----------
+    mesh
+        The 3D mesh for this actor.
+    name
+        Actor name. Default ``"Actor"``.
+    br_class
+        Brainrender class type. Default ``"None"``.
+    is_text
+        Whether this actor is a 2D text annotation. Default False.
+    color
+        Colour to apply to the mesh on construction.
+    alpha
+        Transparency to apply to the mesh on construction.
+    """
+
+    _needs_label: bool = False  # needs to make a label
+    _needs_silhouette: bool = False  # needs to make a silhouette
+    _is_transformed: bool = (
+        False  # has been transformed to correct axes orientation
+    )
+    _is_added: bool = False  # has the actor been added to the scene already
 
-    labels = []
-    silhouette = None
+    labels: list[Actor] = []
+    silhouette: Actor | None = None
 
     def __init__(
         self,
-        mesh,
-        name=None,
-        br_class=None,
-        is_text=False,
-        color=None,
-        alpha=None,
-    ):
-        """
-        Actor class representing anything shown in a brainrender scene.
-        Methods in brainrender.actors are used to creates actors specific
-        for different data types.
-
-        An actor has a mesh, a name and a brainrender class type.
-        It also has methods to create a silhouette or a label.
-
-        :param mesh: instance of vedo.Mesh
-        :param name: str, actor name
-        :param br_class: str, name of brainrender actors class
-        :param is_text: bool, is it a 2d text or annotation?
-        :param color: str, name or hex code of color to assign to actor's mesh
-        :param alpha: float, transparency to assign to actor's mesh
-        """
+        mesh: Mesh,
+        name: str | None = None,
+        br_class: str | None = None,
+        is_text: bool = False,
+        color: str | None = None,
+        alpha: float | None = None,
+    ) -> None:
         self.mesh = mesh
-        self.name = name or "Actor"
+        self.name = name or Actor
         self.br_class = br_class or "None"
         self.is_text = is_text
 
@@ -121,10 +152,14 @@ class Actor:
         if alpha:
             self.mesh.alpha(alpha)
 
-    def __getattr__(self, attr):
+    def __getattr__(self, attr: str) -> Any:
         """
-        If an unknown attribute is called, try `self.mesh.attr`
-        to get the mesh's attribute
+        Delegate unknown attribute lookups to the underlying mesh.
+
+        Raises
+        ------
+        AttributeError
+            If the attribute is not found on any mesh object.
         """
         if "mesh" not in self.__dict__.keys():
             raise AttributeError(
@@ -148,10 +183,10 @@ class Actor:
             f"Actor does not have attribute {attr}"
         )  # pragma: no cover
 
-    def __repr__(self):  # pragma: no cover
+    def __repr__(self) -> str:  # pragma: no cover
         return f"brainrender.Actor: {self.name}-{self.br_class}"
 
-    def __str__(self):
+    def __str__(self) -> str:
         buf = StringIO()
         _console = Console(file=buf, force_jupyter=False)
         _console.print(self)
@@ -159,23 +194,50 @@ class Actor:
         return buf.getvalue()
 
     @property
-    def center(self):
+    def center(self) -> npt.NDArray[np.float64]:
         """
-        Returns the coordinates of the mesh's center
+        Return the mesh's centre of mass coordinates.
+
+        Returns
+        -------
+        numpy.ndarray
+            Array of shape (3,) with (x, y, z) coordinates.
         """
         return self.mesh.center_of_mass()
 
     @classmethod
-    def make_actor(cls, mesh, name, br_class):
+    def make_actor(cls, mesh: Mesh, name: str, br_class: str) -> Self:
         """
-        Make an actor from a given mesh
+        Construct an Actor from an existing mesh.
+
+        Parameters
+        ----------
+        mesh
+            Mesh to wrap.
+        name
+            Actor name.
+        br_class
+            Brainrender class type.
+
+        Returns
+        -------
+        Actor
         """
         return cls(mesh, name=name, br_class=br_class)
 
-    def make_label(self, atlas):
+    def make_label(self, atlas: BrainGlobeAtlas) -> list[Actor]:
         """
-        Create a new Actor with a sphere and a text
-        labelling this actor
+        Create 3D label actors anchored to this actor's mesh.
+
+        Parameters
+        ----------
+        atlas
+            Atlas used for hemisphere queries and mirroring.
+
+        Returns
+        -------
+        list of Actor
+            Label actors (text and optional sphere markers).
         """
         labels = make_actor_label(
             atlas, self, self._label_str, **self._label_kwargs
@@ -188,9 +250,14 @@ class Actor:
         self.labels = lbls
         return lbls
 
-    def make_silhouette(self):
+    def make_silhouette(self) -> Actor:
         """
-        Create a new silhouette actor outlining this actor
+        Create a silhouette actor outlining this actor's mesh.
+
+        Returns
+        -------
+        Actor
+            Silhouette actor with brainrender class ``"silhouette"``.
         """
         lw = self._silhouette_kwargs["lw"]
         color = self._silhouette_kwargs["color"]
@@ -208,19 +275,25 @@ class Actor:
     def mirror(
         self,
         axis: str,
-        origin: Optional[npt.NDArray] = None,
-        atlas: Optional[BrainGlobeAtlas] = None,
-    ):
+        origin: npt.NDArray | None = None,
+        atlas: BrainGlobeAtlas | None = None,
+    ) -> None:
         """
-        Mirror the actor's mesh around the specified axis, using the
-        parent_center as the center of the mirroring operation. The axes can
-        be specified using an abbreviation, e.g. 'x' for the x-axis, or anatomical
-        convention e.g. 'sagittal'. If an atlas is provided, then the anatomical
-        space of the atlas is used, otherwise `asr` is assumed.
-
-        :param axis: str, axis around which to mirror the mesh
-        :param origin: np.ndarray, center of the mirroring operation
-        :param atlas: BrainGlobeAtlas, atlas object to use for anatomical space
+        Mirror the actor's mesh across the given axis.
+
+        Accepts Cartesian axes (``'x'``, ``'y'``, ``'z'``) or anatomical
+        plane names (``'sagittal'``, ``'vertical'``, ``'frontal'``).
+        If an anatomical name is used without an atlas, ``'asr'`` space
+        is assumed. The mesh is updated in place.
+
+        Parameters
+        ----------
+        axis
+            Axis or anatomical plane to mirror across.
+        origin
+            Centre of the mirroring operation. Default None.
+        atlas
+            Atlas used to resolve anatomical axis names. Default None.
         """
         if axis in ["sagittal", "vertical", "frontal"]:
             anatomical_space = atlas.space if atlas else AnatomicalSpace("asr")
@@ -230,7 +303,9 @@ class Actor:
 
         self.mesh = self.mesh.mirror(axis, origin)
 
-    def __rich_console__(self, *args):
+    def __rich_console__(
+        self, console: Console, options: ConsoleOptions
+    ) -> RenderResult:
         """
         Print some useful characteristics to console.
         """

{brainrender-2.1.19 → brainrender-2.2.0}/brainrender/atlas.py

@@ -1,24 +1,36 @@
+"""Atlas subclass adding region and plane Actor support for scenes."""
+
+from typing import Any
+
 import numpy as np
+import numpy.typing as npt
 from brainglobe_atlasapi.bg_atlas import BrainGlobeAtlas
 from loguru import logger
 from vedo import Plane
 
 from brainrender import settings
-from brainrender._io import load_mesh_from_file
+from brainrender._io import convert_meshio_to_vedo
 from brainrender._utils import return_list_smart
 from brainrender.actor import Actor
 
 
 class Atlas(BrainGlobeAtlas):
-    def __init__(self, atlas_name=None, check_latest=True):
-        """
-        Brainrender's Atlas class subclasses BrainGlobeAtlas
-        to add methods to get regions meshes as Actors
-        and to get a plane at a given point and normal.
-
-        :param atlas_name: str, atlas name from brainglobe's atlas API atlases
-        :param check_latest: bool, if True checks that the atlas is the latest version
-        """
+    """
+    Subclass of BrainGlobeAtlas with helpers for rendering.
+
+    Parameters
+    ----------
+    atlas_name
+        Falls back to ``settings.DEFAULT_ATLAS`` if None.
+    check_latest
+        Check for the latest atlas version. Default True.
+    """
+
+    def __init__(
+        self,
+        atlas_name: str | None = None,
+        check_latest: bool = True,
+    ) -> None:
         atlas_name = atlas_name or settings.DEFAULT_ATLAS
         self.atlas_name = atlas_name
         logger.debug(f"Generating ATLAS: {atlas_name}")
@@ -30,9 +42,9 @@ class Atlas(BrainGlobeAtlas):
             super().__init__(atlas_name=atlas_name, check_latest=check_latest)
 
     @property
-    def zoom(self):
+    def zoom(self) -> float:
         """
-        Returns the best camera zoom given the atlas resolution
+        Return a reasonable camera zoom given the atlas resolution.
         """
         res = np.max(self.metadata["resolution"])
 
@@ -44,20 +56,44 @@ class Atlas(BrainGlobeAtlas):
         else:
             return 40 / res
 
-    def _get_region_color(self, region):
+    def _get_region_color(self, region: str | int) -> list[float]:
         """
-        Gets the rgb color of a region in the atlas
+        Get the rgb color of a region in the atlas.
+
+        Parameters
+        ----------
+        region
+            Region acronym or ID.
+
+        Returns
+        -------
+        list of float
         """
         return [
             x / 255 for x in self._get_from_structure(region, "rgb_triplet")
         ]
 
-    def get_region(self, *regions, alpha=1, color=None):
+    def get_region(
+        self,
+        *regions: str | int,
+        alpha: float = 1,
+        color: str | list[float] | None = None,
+    ) -> Actor | list[Actor] | None:
         """
-        Get brain regions meshes as Actors
-        :param regions: str with names of brain regions in the atlas
-        :param alpha: float
-        :param color: str
+        Get brain regions meshes as Actors.
+
+        Parameters
+        ----------
+        *regions
+            Region acronyms or IDs.
+        alpha
+            Mesh transparency. Default 1.
+        color
+            Uses atlas RGB colour if None.
+
+        Returns
+        -------
+        Actor or list of Actor or None
         """
         if not regions:
             return None
@@ -75,12 +111,14 @@ class Atlas(BrainGlobeAtlas):
                 continue
 
             # Get mesh
-            obj_file = str(self.meshfile_from_structure(region))
             try:
-                mesh = load_mesh_from_file(obj_file, color=color, alpha=alpha)
+                meshio_mesh = self.mesh_from_structure(region)
+                mesh = convert_meshio_to_vedo(
+                    meshio_mesh, color=color, alpha=alpha
+                )
             except FileNotFoundError:
                 print(
-                    f"The region {region} is in the onthology but does not have a corresponding volume in the atlas being used: {self.atlas_name}. Skipping"
+                    f"The region {region} is in the ontology but does not have a corresponding volume in the atlas being used: {self.atlas_name}. Skipping"
                 )
                 continue
 
@@ -99,25 +137,45 @@ class Atlas(BrainGlobeAtlas):
 
     def get_plane(
         self,
-        pos=None,
-        norm=None,
-        plane=None,
-        sx=None,
-        sy=None,
-        color="lightgray",
-        alpha=0.25,
-        **kwargs,
-    ):
+        pos: npt.ArrayLike | None = None,
+        norm: npt.ArrayLike | None = None,
+        plane: str | None = None,
+        sx: float | None = None,
+        sy: float | None = None,
+        color: str = "lightgray",
+        alpha: float = 0.25,
+        **kwargs: Any,
+    ) -> Actor:
         """
         Returns a plane going through a point at pos, oriented
-        orthogonally to the vector norm and of width and height
+        orthogonally to the ``norm`` vector and of width and height
         sx, sy.
 
-        :param pos: 3-tuple or list with x,y,z, coords of point the plane goes through
-        :param norm: 3-tuple with plane's normal vector (optional)
-        :param sx, sy: int, width and height of the plane
-        :param plane: "sagittal", "horizontal", or "frontal"
-        :param color, alpha: plane color and transparency
+        Parameters
+        ----------
+        pos
+            (x, y, z) the plane passes through. Defaults to root centre of mass.
+        norm
+            Normal vector. Derived from *plane* if not given.
+        plane
+            ``"sagittal"``, ``"horizontal"``, or ``"frontal"``.
+        sx
+            Width. Inferred from root bounds if None.
+        sy
+            Height. Inferred from root bounds if None.
+        color
+            Default ``"lightgray"``.
+        alpha
+            Default 0.25.
+
+        Returns
+        -------
+        Actor
+
+        Raises
+        ------
+        ValueError
+            If *plane* has no matching normal in the atlas space.
         """
         axes_pairs = dict(sagittal=(0, 1), horizontal=(2, 0), frontal=(2, 1))