Index A | B | C | D | F | G | I | J | L | M | N | P | Q | R | S | T | U | V | W A add_image() (spatialdata.SpatialData method) add_labels() (spatialdata.SpatialData method) add_points() (spatialdata.SpatialData method) add_shapes() (spatialdata.SpatialData method) Affine (class in spatialdata.transformations) aggregate() (in module spatialdata) (spatialdata.SpatialData method) align_elements_using_landmarks() (in module spatialdata.transformations) are_extents_equal() (in module spatialdata) array_type (spatialdata.models.Image2DModel attribute) (spatialdata.models.Image3DModel attribute) (spatialdata.models.Labels2DModel attribute) (spatialdata.models.Labels3DModel attribute) assert_elements_are_identical() (in module spatialdata.testing) assert_elements_dict_are_identical() (in module spatialdata.testing) assert_spatial_data_objects_are_identical() (in module spatialdata.testing) attrs (spatialdata.models.Image2DModel attribute) (spatialdata.models.Image3DModel attribute) (spatialdata.models.Labels2DModel attribute) (spatialdata.models.Labels3DModel attribute) ATTRS_KEY (spatialdata.models.PointsModel attribute) (spatialdata.models.ShapesModel attribute) (spatialdata.models.TableModel attribute) B BaseTransformation (class in spatialdata.transformations) bounding_box_query() (in module spatialdata) C checks (spatialdata.models.Image2DModel attribute) (spatialdata.models.Image3DModel attribute) (spatialdata.models.Labels2DModel attribute) (spatialdata.models.Labels3DModel attribute) chunks (spatialdata.models.Image2DModel attribute) (spatialdata.models.Image3DModel attribute) (spatialdata.models.Labels2DModel attribute) (spatialdata.models.Labels3DModel attribute) compose_with() (spatialdata.transformations.Affine method) (spatialdata.transformations.BaseTransformation method) (spatialdata.transformations.Identity method) (spatialdata.transformations.MapAxis method) (spatialdata.transformations.Scale method) (spatialdata.transformations.Sequence method) (spatialdata.transformations.Translation method) concatenate() (in module spatialdata) coordinate_systems (spatialdata.SpatialData attribute) coords (spatialdata.models.Image2DModel attribute) (spatialdata.models.Image3DModel attribute) (spatialdata.models.Labels2DModel attribute) (spatialdata.models.Labels3DModel attribute) D deepcopy() (in module spatialdata) dims (spatialdata.models.Image2DModel attribute) (spatialdata.models.Image3DModel attribute) (spatialdata.models.Labels2DModel attribute) (spatialdata.models.Labels3DModel attribute) dtype (spatialdata.models.Image2DModel attribute) (spatialdata.models.Image3DModel attribute) (spatialdata.models.Labels2DModel attribute) (spatialdata.models.Labels3DModel attribute) F FEATURE_KEY (spatialdata.models.PointsModel attribute) filter_by_coordinate_system() (spatialdata.SpatialData method) force_2d() (in module spatialdata.models) from_elements_dict() (spatialdata.SpatialData static method) from_ngff() (spatialdata.transformations.Affine class method) (spatialdata.transformations.BaseTransformation class method) (spatialdata.transformations.Identity class method) (spatialdata.transformations.MapAxis class method) (spatialdata.transformations.Scale class method) (spatialdata.transformations.Sequence class method) (spatialdata.transformations.Translation class method) G gen_elements() (spatialdata.SpatialData method) gen_spatial_elements() (spatialdata.SpatialData method) GEOMETRY_KEY (spatialdata.models.ShapesModel attribute) GEOS_KEY (spatialdata.models.ShapesModel attribute) get() (spatialdata.SpatialData method) get_annotated_regions() (spatialdata.SpatialData static method) get_axes_names() (in module spatialdata.models) get_centroids() (in module spatialdata) get_channels() (in module spatialdata.models) get_dask_backing_files() (in module spatialdata) get_extent() (in module spatialdata) get_instance_key_column() (spatialdata.SpatialData static method) get_model() (in module spatialdata.models) get_region_key_column() (spatialdata.SpatialData static method) get_spatial_axes() (in module spatialdata.models) get_transformation() (in module spatialdata.transformations) get_transformation_between_coordinate_systems() (in module spatialdata.transformations) get_transformation_between_landmarks() (in module spatialdata.transformations) get_values() (in module spatialdata) I Identity (class in spatialdata.transformations) Image2DModel (class in spatialdata.models) Image3DModel (class in spatialdata.models) images (spatialdata.SpatialData attribute) ImageTilesDataset (in module spatialdata.dataloader) init_from_elements() (spatialdata.SpatialData class method) INSTANCE_KEY (spatialdata.models.PointsModel attribute) (spatialdata.models.TableModel attribute) inverse() (spatialdata.transformations.Affine method) (spatialdata.transformations.BaseTransformation method) (spatialdata.transformations.Identity method) (spatialdata.transformations.MapAxis method) (spatialdata.transformations.Scale method) (spatialdata.transformations.Sequence method) (spatialdata.transformations.Translation method) is_backed() (spatialdata.SpatialData method) J join_spatialelement_table() (in module spatialdata) json (spatialdata.models.Image2DModel attribute) (spatialdata.models.Image3DModel attribute) (spatialdata.models.Labels2DModel attribute) (spatialdata.models.Labels3DModel attribute) L labels (spatialdata.SpatialData attribute) Labels2DModel (class in spatialdata.models) Labels3DModel (class in spatialdata.models) locate_element() (spatialdata.SpatialData method) M MapAxis (class in spatialdata.transformations) match_element_to_table() (in module spatialdata) match_table_to_element() (in module spatialdata) module spatialdata N name (spatialdata.models.Image2DModel attribute) (spatialdata.models.Image3DModel attribute) (spatialdata.models.Labels2DModel attribute) (spatialdata.models.Labels3DModel attribute) NAME_KEY (spatialdata.models.ShapesModel attribute) NPARTITIONS (spatialdata.models.PointsModel attribute) P parse() (spatialdata.models.Image2DModel class method) (spatialdata.models.Image3DModel class method) (spatialdata.models.Labels2DModel class method) (spatialdata.models.Labels3DModel class method) (spatialdata.models.PointsModel class method) (spatialdata.models.ShapesModel class method) (spatialdata.models.TableModel class method) path (spatialdata.SpatialData attribute) points (spatialdata.SpatialData attribute) points_dask_dataframe_to_geopandas() (in module spatialdata.models) points_geopandas_to_dask_dataframe() (in module spatialdata.models) PointsModel (class in spatialdata.models) polygon_query() (in module spatialdata) Q query (spatialdata.SpatialData attribute) R RADIUS_KEY (spatialdata.models.ShapesModel attribute) rasterize() (in module spatialdata) read() (spatialdata.SpatialData static method) read_zarr() (in module spatialdata) REGION_KEY (spatialdata.models.TableModel attribute) REGION_KEY_KEY (spatialdata.models.TableModel attribute) remove_transformation() (in module spatialdata.transformations) remove_transformations_to_coordinate_system() (in module spatialdata.transformations) rename_coordinate_systems() (spatialdata.SpatialData method) S save_transformations() (in module spatialdata) Scale (class in spatialdata.transformations) Sequence (class in spatialdata.transformations) set_table_annotates_spatialelement() (spatialdata.SpatialData method) set_transformation() (in module spatialdata.transformations) shape (spatialdata.models.Image2DModel attribute) (spatialdata.models.Image3DModel attribute) (spatialdata.models.Labels2DModel attribute) (spatialdata.models.Labels3DModel attribute) shapes (spatialdata.SpatialData attribute) ShapesModel (class in spatialdata.models) spatialdata module SpatialData (class in spatialdata) SpatialElement (in module spatialdata.models) subset() (spatialdata.SpatialData method) T table (spatialdata.SpatialData attribute) TableModel (class in spatialdata.models) tables (spatialdata.SpatialData attribute) to_affine() (spatialdata.transformations.Affine method) (spatialdata.transformations.BaseTransformation method) (spatialdata.transformations.Identity method) (spatialdata.transformations.MapAxis method) (spatialdata.transformations.Scale method) (spatialdata.transformations.Sequence method) (spatialdata.transformations.Translation method) to_affine_matrix() (spatialdata.transformations.Affine method) (spatialdata.transformations.BaseTransformation method) (spatialdata.transformations.Identity method) (spatialdata.transformations.MapAxis method) (spatialdata.transformations.Scale method) (spatialdata.transformations.Sequence method) (spatialdata.transformations.Translation method) to_circles() (in module spatialdata) to_json() (spatialdata.models.Image2DModel method) (spatialdata.models.Image3DModel method) (spatialdata.models.Labels2DModel method) (spatialdata.models.Labels3DModel method) to_ngff() (spatialdata.transformations.Affine method) (spatialdata.transformations.BaseTransformation method) (spatialdata.transformations.Identity method) (spatialdata.transformations.MapAxis method) (spatialdata.transformations.Scale method) (spatialdata.transformations.Sequence method) (spatialdata.transformations.Translation method) to_scale_vector() (spatialdata.transformations.Scale method) to_translation_vector() (spatialdata.transformations.Translation method) transform() (in module spatialdata) transform_element_to_coordinate_system() (spatialdata.SpatialData method) TRANSFORM_KEY (spatialdata.models.PointsModel attribute) (spatialdata.models.ShapesModel attribute) transform_to_coordinate_system() (spatialdata.SpatialData method) Translation (class in spatialdata.transformations) TYPE_KEY (spatialdata.models.ShapesModel attribute) U unpad_raster() (in module spatialdata) update_annotated_regions_metadata() (spatialdata.SpatialData static method) V validate() (spatialdata.models.Image2DModel method) (spatialdata.models.Image3DModel method) (spatialdata.models.Labels2DModel method) (spatialdata.models.Labels3DModel method) (spatialdata.models.PointsModel class method) (spatialdata.models.ShapesModel class method) (spatialdata.models.TableModel method) validate_axes() (spatialdata.transformations.Affine static method) (spatialdata.transformations.BaseTransformation static method) (spatialdata.transformations.Identity static method) (spatialdata.transformations.MapAxis static method) (spatialdata.transformations.Scale static method) (spatialdata.transformations.Sequence static method) (spatialdata.transformations.Translation static method) validate_table_in_spatialdata() (spatialdata.SpatialData method) W write() (spatialdata.SpatialData method)