siibra 1.0.1a1__tar.gz → 1.0.1a2__tar.gz

{siibra-1.0.1a1/siibra.egg-info → siibra-1.0.1a2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: siibra
-Version: 1.0.1a1
+Version: 1.0.1a2
 Summary: siibra - Software interfaces for interacting with brain atlases
 Home-page: https://github.com/FZJ-INM1-BDA/siibra-python
 Author: Big Data Analytics Group, Forschungszentrum Juelich, Institute of Neuroscience and Medicine (INM-1)
@@ -59,6 +59,14 @@ It aims to facilitate programmatic and reproducible incorporation of brain parce
 It supports both discretely labelled and statistical (probabilistic) parcellation maps, which can be used to assign brain regions to spatial locations and image signals, to retrieve region-specific neuroscience datasets from multiple online repositories, and to sample information from high-resolution image data. 
 The datasets anchored to brain regions address features of molecular, cellular and architecture as well as connectivity, and are complemented with live queries to external repositories as well as dynamic extraction from "big" image volumes such as the 20 micrometer BigBrain model.
 
+``siibra`` hides much of the complexity that would be required to collect and interact with the individual parcellations, templates and data repositories.
+By encapsulating many aspects of interacting with different maps and reference templates spaces, it also minimizes common errors like misinterpretation of coordinates from different reference spaces, confusing label indices of brain regions, or using inconsistent versions of parcellation maps. 
+It aims to provide a safe way of using maps defined across multiple spatial scales for reproducible analysis.
+
+.. intro-end
+
+.. about-start
+
 ``siibra`` was developed in the frame of the `Human Brain Project <https://humanbrainproject.eu>`__ for accessing the `EBRAINS
 human brain atlas <https://ebrains.eu/service/human-brain-atlas>`__. 
 It stores most of its contents as sustainable and open datasets in the `EBRAINS Knowledge Graph <https://kg.ebrains.eu>`__, and is designed to support the `OpenMINDS metadata standards <https://github.com/HumanBrainProject/openMINDS_SANDS>`__. 
@@ -67,11 +75,7 @@ In fact, the viewer is a good resource for exploring ``siibra``\ ’s core funct
 Feature queries in ``siibra`` are parameterized by data modality and anatomical location, while the latter could be a brain region, brain parcellation, or location in reference space. 
 Beyond the explorative focus of ``siibra-explorer``, the Python library supports a range of data analysis functions suitable for typical neuroscience workflows.
 
-``siibra`` hides much of the complexity that would be required to collect and interact with the individual parcellations, templates and data repositories.
-By encapsulating many aspects of interacting with different maps and reference templates spaces, it also minimizes common errors like misinterpretation of coordinates from different reference spaces, confusing label indices of brain regions, or using inconsistent versions of parcellation maps. 
-It aims to provide a safe way of using maps defined across multiple spatial scales for reproducible analysis.
-
-.. intro-end
+.. about-end
 
 .. getting-started-start
 

{siibra-1.0.1a1 → siibra-1.0.1a2}/README.rst

@@ -20,6 +20,14 @@ It aims to facilitate programmatic and reproducible incorporation of brain parce
 It supports both discretely labelled and statistical (probabilistic) parcellation maps, which can be used to assign brain regions to spatial locations and image signals, to retrieve region-specific neuroscience datasets from multiple online repositories, and to sample information from high-resolution image data. 
 The datasets anchored to brain regions address features of molecular, cellular and architecture as well as connectivity, and are complemented with live queries to external repositories as well as dynamic extraction from "big" image volumes such as the 20 micrometer BigBrain model.
 
+``siibra`` hides much of the complexity that would be required to collect and interact with the individual parcellations, templates and data repositories.
+By encapsulating many aspects of interacting with different maps and reference templates spaces, it also minimizes common errors like misinterpretation of coordinates from different reference spaces, confusing label indices of brain regions, or using inconsistent versions of parcellation maps. 
+It aims to provide a safe way of using maps defined across multiple spatial scales for reproducible analysis.
+
+.. intro-end
+
+.. about-start
+
 ``siibra`` was developed in the frame of the `Human Brain Project <https://humanbrainproject.eu>`__ for accessing the `EBRAINS
 human brain atlas <https://ebrains.eu/service/human-brain-atlas>`__. 
 It stores most of its contents as sustainable and open datasets in the `EBRAINS Knowledge Graph <https://kg.ebrains.eu>`__, and is designed to support the `OpenMINDS metadata standards <https://github.com/HumanBrainProject/openMINDS_SANDS>`__. 
@@ -28,11 +36,7 @@ In fact, the viewer is a good resource for exploring ``siibra``\ ’s core funct
 Feature queries in ``siibra`` are parameterized by data modality and anatomical location, while the latter could be a brain region, brain parcellation, or location in reference space. 
 Beyond the explorative focus of ``siibra-explorer``, the Python library supports a range of data analysis functions suitable for typical neuroscience workflows.
 
-``siibra`` hides much of the complexity that would be required to collect and interact with the individual parcellations, templates and data repositories.
-By encapsulating many aspects of interacting with different maps and reference templates spaces, it also minimizes common errors like misinterpretation of coordinates from different reference spaces, confusing label indices of brain regions, or using inconsistent versions of parcellation maps. 
-It aims to provide a safe way of using maps defined across multiple spatial scales for reproducible analysis.
-
-.. intro-end
+.. about-end
 
 .. getting-started-start
 

siibra-1.0.1a2/siibra/VERSION

@@ -0,0 +1 @@
+1.0.1-alpha.2

{siibra-1.0.1a1 → siibra-1.0.1a2}/siibra/__init__.py

@@ -13,35 +13,29 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import os as _os
+
 from .commons import (
     logger,
     QUIET,
     VERBOSE,
     MapType,
-    MapIndex,
     set_log_level,
     __version__
 )
-
+from . import configuration, features, livequeries
+from .configuration import factory
 from .core import (
     atlas as _atlas,
     parcellation as _parcellation,
     space as _space
 )
 from .volumes import parcellationmap as _parcellationmap
-from .retrieval.requests import (
-    EbrainsRequest as _EbrainsRequest,
-    CACHE as cache
-)
+from .retrieval.requests import CACHE as cache
 from .retrieval.cache import Warmup, WarmupLevel
+from .locations import Point, PointCloud, Plane, BoundingBox
 
-from . import configuration
-from . import experimental
-from .configuration import factory
-from . import features, livequeries
-from siibra.locations import Point, PointCloud
 
-import os as _os
 logger.info(f"Version: {__version__}")
 logger.warning("This is a development release. Use at your own risk.")
 logger.info(
@@ -49,8 +43,6 @@ logger.info(
 )
 
 # forward access to some functions
-set_ebrains_token = _EbrainsRequest.set_token
-fetch_ebrains_token = _EbrainsRequest.fetch_token
 find_regions = _parcellation.find_regions
 from_json = factory.Factory.from_json
 
@@ -151,10 +143,9 @@ def __dir__():
         "MapType",
         "Point",
         "PointCloud",
+        "BoundingBox",
         "QUIET",
         "VERBOSE",
-        "fetch_ebrains_token",
-        "set_ebrains_token",
         "vocabularies",
         "__version__",
         "cache",

{siibra-1.0.1a1 → siibra-1.0.1a2}/siibra/commons.py

@@ -17,24 +17,26 @@
 import os
 import re
 from enum import Enum
-from nibabel import Nifti1Image
-from nilearn.image import resample_to_img
 import logging
-from tqdm import tqdm
-import numpy as np
-import pandas as pd
-from typing import Generic, Iterable, Iterator, List, TypeVar, Union, Dict, Generator, Tuple
-from skimage.filters import gaussian
 from dataclasses import dataclass
 from hashlib import md5
 from uuid import UUID
 import math
+from typing import Generic, Iterable, Iterator, List, TypeVar, Union, Dict, Generator, Tuple
 try:
     from typing import TypedDict
 except ImportError:
     # support python 3.7
     from typing_extensions import TypedDict
 
+from tqdm import tqdm
+import numpy as np
+import pandas as pd
+from nibabel import Nifti1Image
+from nilearn.image import resample_to_img
+from skimage.filters import gaussian
+
+
 logging.addLevelName(21, "INFO_WO_PROGRESS_BARS")
 logger = logging.getLogger(__name__.split(os.path.extsep)[0])
 ch = logging.StreamHandler()

{siibra-1.0.1a1 → siibra-1.0.1a2}/siibra/configuration/factory.py

@@ -13,6 +13,15 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from os import path
+import json
+from typing import List, Dict, Callable
+from io import BytesIO
+from functools import wraps
+
+import numpy as np
+import pandas as pd
+
 from ..commons import logger, Species
 from ..features import anchor, connectivity
 from ..features.tabular import (
@@ -29,14 +38,6 @@ from ..retrieval import datasets, repositories
 from ..volumes import volume, sparsemap, parcellationmap
 from ..volumes.providers.provider import VolumeProvider
 
-from os import path
-import json
-import numpy as np
-from typing import List, Dict, Callable
-import pandas as pd
-from io import BytesIO
-from functools import wraps
-
 
 _registered_build_fns: Dict[str, Callable] = {}
 

{siibra-1.0.1a1 → siibra-1.0.1a2}/siibra/core/__init__.py

@@ -12,5 +12,5 @@
 # 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.
-""":ref:`Main siibra concepts<mainconcepts>`"""
+"""Core concepts behind siibra, :ref:`see glossary <glossary>` for details."""
 from . import atlas, parcellation, space

{siibra-1.0.1a1 → siibra-1.0.1a2}/siibra/core/assignment.py

@@ -17,6 +17,7 @@
 from enum import Enum
 from dataclasses import dataclass
 from typing import Dict, Generic, TypeVar, TYPE_CHECKING
+
 if TYPE_CHECKING:
     from .structure import BrainStructure
 

{siibra-1.0.1a1 → siibra-1.0.1a2}/siibra/core/concept.py

@@ -13,6 +13,10 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """Parent class to siibra main concepts."""
+
+import re
+from typing import TypeVar, Type, Union, List, TYPE_CHECKING, Dict
+
 from ..commons import (
     create_key,
     clear_name,
@@ -23,8 +27,6 @@ from ..commons import (
 )
 from ..retrieval import cache
 
-import re
-from typing import TypeVar, Type, Union, List, TYPE_CHECKING, Dict
 
 T = TypeVar("T", bound="AtlasConcept")
 _REGISTRIES: Dict[Type[T], InstanceTable[T]] = {}

{siibra-1.0.1a1 → siibra-1.0.1a2}/siibra/core/region.py

@@ -14,9 +14,18 @@
 # limitations under the License.
 """Representation of a brain region."""
 
-from . import concept, structure, space as _space, parcellation as _parcellation
-from .assignment import Qualification, AnatomicalAssignment
+import re
+from typing import List, Union, Iterable, Dict, Callable, Tuple, Set
+from difflib import SequenceMatcher
+import json
+from functools import wraps, reduce
+from concurrent.futures import ThreadPoolExecutor
+from functools import lru_cache
+
+import anytree
+from ebrains_drive import BucketApiClient
 
+from . import concept, structure, space as _space, parcellation as _parcellation, assignment
 from ..retrieval.cache import cache_user_fn
 from ..locations import location, pointcloud, boundingbox as _boundingbox
 from ..volumes import parcellationmap, volume
@@ -29,16 +38,6 @@ from ..commons import (
 )
 from ..exceptions import NoMapAvailableError, SpaceWarpingFailedError
 
-import re
-import anytree
-from typing import List, Union, Iterable, Dict, Callable, Tuple, Set
-from difflib import SequenceMatcher
-from ebrains_drive import BucketApiClient
-import json
-from functools import wraps, reduce
-from concurrent.futures import ThreadPoolExecutor
-from functools import lru_cache
-
 
 REGEX_TYPE = type(re.compile("test"))
 
@@ -128,7 +127,7 @@ class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
 
         Yields
         ------
-        Qualification
+        assignment.Qualification
 
         Example
         -------
@@ -595,7 +594,7 @@ class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
             except NoMapAvailableError:
                 return False
 
-    def assign(self, other: structure.BrainStructure) -> AnatomicalAssignment:
+    def assign(self, other: structure.BrainStructure) -> assignment.AnatomicalAssignment:
         """
         Compute assignment of a location to this region.
 
@@ -609,8 +608,8 @@ class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
 
         Returns
         -------
-        AnatomicalAssignment or None
-            None if there is no Qualification found.
+        assignment.AnatomicalAssignment or None
+            None if there is no assignment.Qualification found.
         """
         if (self, other) in self._ASSIGNMENT_CACHE:
             return self._ASSIGNMENT_CACHE[self, other]
@@ -659,17 +658,17 @@ class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
         else:  # other is a Region
             assert isinstance(other, Region)
             if self == other:
-                qualification = Qualification.EXACT
+                qualification = assignment.Qualification.EXACT
             elif self.__contains__(other):
-                qualification = Qualification.CONTAINS
+                qualification = assignment.Qualification.CONTAINS
             elif other.__contains__(self):
-                qualification = Qualification.CONTAINED
+                qualification = assignment.Qualification.CONTAINED
             else:
                 qualification = None
             if qualification is None:
                 self._ASSIGNMENT_CACHE[self, other] = None
             else:
-                self._ASSIGNMENT_CACHE[self, other] = AnatomicalAssignment(self, other, qualification)
+                self._ASSIGNMENT_CACHE[self, other] = assignment.AnatomicalAssignment(self, other, qualification)
         return self._ASSIGNMENT_CACHE[self, other]
 
     def tree2str(self):
@@ -926,7 +925,7 @@ def get_related_regions(region: Region) -> Iterable["RegionRelationAssessments"]
 
     Yields
     ------
-    Qualification
+    assignment.Qualification
 
     Example
     -------
@@ -968,7 +967,7 @@ def _register_region_reference_type(ebrain_type: str):
     return outer
 
 
-class RegionRelationAssessments(AnatomicalAssignment[Region]):
+class RegionRelationAssessments(assignment.AnatomicalAssignment[Region]):
     """
     A collection of methods on finding related regions and the quantification
     of the relationship.
@@ -1110,7 +1109,7 @@ class RegionRelationAssessments(AnatomicalAssignment[Region]):
                 yield cls(
                     query_structure=src,
                     assigned_structure=found_target,
-                    qualification=Qualification.parse_relation_assessment(overlap)
+                    qualification=assignment.Qualification.parse_relation_assessment(overlap)
                 )
 
             if "https://openminds.ebrains.eu/sands/ParcellationEntity" in target.get("type"):
@@ -1124,7 +1123,7 @@ class RegionRelationAssessments(AnatomicalAssignment[Region]):
                         yield cls(
                             query_structure=src,
                             assigned_structure=reg,
-                            qualification=Qualification.parse_relation_assessment(overlap)
+                            qualification=assignment.Qualification.parse_relation_assessment(overlap)
                         )
 
     @classmethod
@@ -1178,7 +1177,7 @@ class RegionRelationAssessments(AnatomicalAssignment[Region]):
                     yield cls(
                         query_structure=src,
                         assigned_structure=region,
-                        qualification=Qualification.OTHER_VERSION
+                        qualification=assignment.Qualification.OTHER_VERSION
                     )
 
             # homologuous

{siibra-1.0.1a1 → siibra-1.0.1a2}/siibra/core/space.py

@@ -14,18 +14,16 @@
 # limitations under the License.
 """A particular brain reference space."""
 
+from typing import List, TYPE_CHECKING, Union
 
-from .concept import AtlasConcept
-
+from . import concept
 from ..commons import logger, Species
 
-from typing import List, TYPE_CHECKING, Union
-
 if TYPE_CHECKING:
     from ..volumes import volume
 
 
-class Space(AtlasConcept, configuration_folder="spaces"):
+class Space(concept.AtlasConcept, configuration_folder="spaces"):
 
     def __init__(
         self,
@@ -66,7 +64,7 @@ class Space(AtlasConcept, configuration_folder="spaces"):
                 Key: EBRAINS KG schema, value: EBRAINS KG @id
         """
 
-        AtlasConcept.__init__(
+        concept.AtlasConcept.__init__(
             self,
             identifier=identifier,
             name=name,

{siibra-1.0.1a1 → siibra-1.0.1a2}/siibra/features/anchor.py

@@ -14,8 +14,9 @@
 # limitations under the License.
 """Handles the relation between study targets and BrainStructures."""
 
-from ..commons import Species, logger
+from typing import Union, List, Dict, Iterable
 
+from ..commons import Species, logger
 from ..core.structure import BrainStructure
 from ..core.assignment import AnatomicalAssignment, Qualification
 from ..locations.location import Location
@@ -23,11 +24,8 @@ from ..core.parcellation import Parcellation, find_regions
 from ..core.region import Region
 from ..core.space import Space
 from ..exceptions import SpaceWarpingFailedError
-
 from ..vocabularies import REGION_ALIASES
 
-from typing import Union, List, Dict, Iterable
-
 
 class AnatomicalAnchor:
     """

{siibra-1.0.1a1 → siibra-1.0.1a2}/siibra/features/connectivity/regional_connectivity.py

@@ -14,11 +14,18 @@
 # limitations under the License.
 
 from zipfile import ZipFile
-from ..feature import Feature, Compoundable
-from ..tabular.tabular import Tabular
+from typing import Callable, Union, List, Tuple, Iterator
+try:
+    from typing import Literal
+except ImportError:  # support python 3.7
+    from typing_extensions import Literal
 
-from .. import anchor as _anchor
+import numpy as np
+import pandas as pd
 
+from .. import anchor as _anchor
+from ..feature import Feature, Compoundable
+from ..tabular.tabular import Tabular
 from ...commons import logger, QUIET, siibra_tqdm
 from ...core import region as _region
 from ...locations import pointcloud
@@ -26,16 +33,6 @@ from ...retrieval.repositories import RepositoryConnector
 from ...retrieval.requests import HttpRequest
 
 
-import pandas as pd
-import numpy as np
-from typing import Callable, Union, List, Tuple, Iterator
-
-try:
-    from typing import Literal
-except ImportError:  # support python 3.7
-    from typing_extensions import Literal
-
-
 class RegionalConnectivity(Feature, Compoundable):
     """
     Parcellation-averaged connectivity, providing one or more matrices of a

{siibra-1.0.1a1 → siibra-1.0.1a2}/siibra/features/feature.py

@@ -14,12 +14,6 @@
 # limitations under the License.
 """Handles multimodal data features and related queries."""
 
-from . import anchor as _anchor
-
-from ..commons import logger, InstanceTable, siibra_tqdm, __version__
-from ..core import concept, space, region, parcellation, structure
-from ..volumes import volume
-
 from typing import Union, TYPE_CHECKING, List, Dict, Type, Tuple, BinaryIO, Any, Iterator
 from hashlib import md5
 from collections import defaultdict
@@ -28,6 +22,11 @@ from abc import ABC, abstractmethod
 from re import sub
 from textwrap import wrap
 
+from . import anchor as _anchor
+from ..commons import logger, InstanceTable, siibra_tqdm, __version__
+from ..core import concept, space, region, parcellation, structure
+from ..volumes import volume
+
 if TYPE_CHECKING:
     from ..retrieval.datasets import EbrainsDataset
     TypeDataset = EbrainsDataset
@@ -130,23 +129,22 @@ class Feature:
         # allows subclasses to implement lazy loading of an anchor
         return self._anchor_cached
 
-    def __init_subclass__(cls, configuration_folder=None, category=None, do_not_index=False, **kwargs):
+    def __init_subclass__(cls, configuration_folder=None, category=None, **kwargs):
 
         # Feature.SUBCLASSES serves as an index where feature class inheritance is cached. When users
         # queries a branch on the hierarchy, all children will also be queried. There are usecases where
         # such behavior is not desired (e.g. ProxyFeature, which wraps livequery features id to capture the
         # query context).
-        # do_not_index flag allow the default index behavior to be toggled off.
-
-        if do_not_index is False:
+        if "ProxyFeature" in cls.__name__:
+            return
 
-            # extend the subclass lists
-            # Iterate over all mro, not just immediate base classes
-            for BaseCls in cls.__mro__:
-                # some base classes may not be sub class of feature, ignore these
-                if not issubclass(BaseCls, Feature):
-                    continue
-                cls._SUBCLASSES[BaseCls].append(cls)
+        # extend the subclass lists
+        # Iterate over all mro, not just immediate base classes
+        for BaseCls in cls.__mro__:
+            # some base classes may not be sub class of feature, ignore these
+            if not issubclass(BaseCls, Feature):
+                continue
+            cls._SUBCLASSES[BaseCls].append(cls)
 
         cls._live_queries = []
         cls._preconfigured_instances = None
@@ -156,6 +154,9 @@ class Feature:
             cls._CATEGORIZED[category].add(cls.__name__, cls)
         return super().__init_subclass__(**kwargs)
 
+    def __repr__(self) -> str:
+        return f"<{self.__class__.__name__}(id='{self.id}', name='{self.name}')>"
+
     @classmethod
     def _get_subclasses(cls):
         return {Cls.__name__: Cls for Cls in cls._SUBCLASSES}
@@ -625,7 +626,9 @@ class Feature:
 
         See docstring of serialize_query_context for further context.
         """
-        class ProxyFeature(feature.__class__, do_not_index=True):
+
+        # if you change the name of this class, change the string in Feature.__init_subclass__
+        class ProxyFeature(feature.__class__):
 
             # override __class__ property
             # some instances of features accesses inst.__class__

{siibra-1.0.1a1 → siibra-1.0.1a2}/siibra/features/image/__init__.py

@@ -22,6 +22,8 @@ from .volume_of_interest import (
     XPCTVolumeOfInterest,
     LSFMVolumeOfInterest,
     DTIVolumeOfInterest
-    # SegmentedVolumeOfInterest
 )
-from .sections import CellbodyStainedSection
+from .sections import (
+    CellbodyStainedSection,
+    BigBrain1MicronPatch
+)

{siibra-1.0.1a1 → siibra-1.0.1a2}/siibra/features/image/image.py

@@ -14,15 +14,13 @@
 # limitations under the License.
 """Base type of features in volume format and related anatomical anchor."""
 
+from typing import List, TYPE_CHECKING
 from zipfile import ZipFile
-from .. import feature
 
+from .. import feature
 from .. import anchor as _anchor
-
 from ...volumes import volume as _volume
 
-from typing import List, TYPE_CHECKING
-
 if TYPE_CHECKING:
     from ...locations.boundingbox import BoundingBox
     from ...volumes.providers import provider

siibra-1.0.1a2/siibra/features/image/sections.py

@@ -0,0 +1,105 @@
+# Copyright 2018-2025
+# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
+
+# 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.
+"""Multimodal data features in 2D section."""
+
+from typing import TYPE_CHECKING
+
+from . import image
+
+if TYPE_CHECKING:
+    from ...locations import AxisAlignedPatch, Contour
+    from ...features.anchor import AnatomicalAnchor
+
+
+class CellbodyStainedSection(
+    image.Image,
+    configuration_folder="features/images/sections/cellbody",
+    category="cellular",
+):
+    def __init__(self, **kwargs):
+        image.Image.__init__(self, **kwargs, modality="cell body staining")
+
+
+class BigBrain1MicronPatch(image.Image, category="cellular"):
+
+    _DESCRIPTION = """Sample approximately orthogonal cortical image patches
+    from BigBrain 1 micron sections, guided by an image volume
+    in a supported reference space providing. The image
+    volume is used as a weighted mask to extract patches
+    along the cortical midsurface with nonzero weights in the
+    input image.
+    An optional lower_threshold can be used to narrow down
+    the search. The weight is stored with the resulting features."""
+
+    def __init__(
+        self,
+        patch: "AxisAlignedPatch",
+        profile: "Contour",
+        section: CellbodyStainedSection,
+        vertex: int,
+        relevance: float,
+        anchor: "AnatomicalAnchor",
+    ):
+        self._patch = patch
+        self._profile = profile
+        self._section = section
+        self.vertex = vertex
+        self.relevance = relevance
+        image.Image.__init__(
+            self,
+            name=f"Cortical patch in {section.name}",
+            modality=section.modality,
+            space_spec=section._space_spec,
+            providers=list(section._providers.values()),
+            region=None,
+            datasets=section.datasets,
+            bbox=patch.boundingbox,
+            id=None,
+        )
+        self._anchor_cached = anchor
+        self._description_cached = self._DESCRIPTION
+
+    def __repr__(self):
+        return (
+            f"<{self.__class__.__name__}(space_spec={self._space_spec}, "
+            f"name='{self.name}', "
+            f"section='{self._section.get_boundingbox().minpoint.bigbrain_section()}', "
+            f"vertex='{self.vertex}', providers={self._providers})>"
+        )
+
+    @property
+    def section(self) -> CellbodyStainedSection:
+        return self._section
+
+    def get_boundingbox(self, **fetch_kwargs):
+        """Enforce that the bounding box spans the full section thickness."""
+        bbox_section = self._section.get_boundingbox(**fetch_kwargs)
+        bbox = self._patch.boundingbox
+        bbox.minpoint[1] = bbox_section.minpoint[1]
+        bbox.maxpoint[1] = bbox_section.maxpoint[1]
+        return bbox
+
+    @property
+    def profile(self) -> "Contour":
+        return self._profile
+
+    @property
+    def bigbrain_section(self):
+        return self.get_boundingbox().minpoint.bigbrain_section()
+
+    def fetch(self, flip: bool = False, resolution_mm: float = -1, **kwargs):
+        assert len(kwargs) == 0
+        p = self._patch.flip() if flip else self._patch
+        return p.extract_volume(self._section, resolution_mm=resolution_mm).fetch()