API

SpatialData

The SpatialData class.

SpatialData([images, labels, points, ...])

The SpatialData object.

Operations

Operations on SpatialData objects.

bounding_box_query(element, axes, ...)	Perform a bounding box query on the SpatialData object.
polygon_query(sdata, polygons, ...[, ...])	Query a spatial data object by a polygon, filtering shapes and points.
get_values(value_key[, element, sdata, ...])	Get the values from the element, from any location: df columns, obs or var columns (table).
match_table_to_element(sdata, element_name)	Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.
concatenate(sdatas[, region_key, instance_key])	Concatenate a list of spatial data objects.
rasterize(data, axes, min_coordinate, ...[, ...])	Rasterize a SpatialData object or a SpatialElement (image, labels, points, shapes).
transform(data, transformation[, ...])	Transform a SpatialElement using this transformation and returns the transformed element.
aggregate(values, by[, values_sdata, ...])	Aggregate values by given region.

Utilities

unpad_raster(raster)

Remove padding from a raster type that was eventually added by the rotation component of a transformation.

Models

The elements (building-blocks) that consitute SpatialData.

Image2DModel(*args, **kwargs)
Image3DModel(*args, **kwargs)
Labels2DModel(*args, **kwargs)
Labels3DModel(*args, **kwargs)
ShapesModel()
PointsModel()
TableModel()

Utilities

get_model(e)	Get the model for the given element.
SpatialElement	alias of Union[SpatialImage, MultiscaleSpatialImage, GeoDataFrame, DataFrame]
get_axes_names(e)	Get the dimensions of a SpatialElement.
get_spatial_axes(axes)	Get the spatial axes of interest.
points_geopandas_to_dask_dataframe(gdf[, ...])	Convert a GeoDataFrame which represents 2D or 3D points to a Dask DataFrame that passes the schema validation.
points_dask_dataframe_to_geopandas(points[, ...])	Convert a Dask DataFrame to a GeoDataFrame.

Transformations

The transformations that can be defined between elements and coordinate systems in SpatialData.

BaseTransformation()	Base class for all transformations.
Identity()
MapAxis(map_axis)
Translation(translation, axes)
Scale(scale, axes)
Affine(matrix, input_axes, output_axes)
Sequence(transformations)

Utilities

get_transformation(element[, ...])	Get the transformation/s of an element.
set_transformation(element, transformation)	Set a transformation/s to an element, in-memory or to disk.
remove_transformation(element[, ...])	Remove a transformation/s from an element, in-memory or from disk.
get_transformation_between_coordinate_systems(...)	Get the transformation to map a coordinate system (intrinsic or extrinsic) to another one.
get_transformation_between_landmarks(...)	Get a similarity transformation between two lists of (n >= 3) landmarks.
align_elements_using_landmarks(...[, ...])	Maps a moving object into a reference object using two lists of (n >= 3) landmarks.

DataLoader

Input/output

read_zarr(store[, selection])	Read a SpatialData dataset from a zarr store (on-disk or remote).
save_transformations(sdata)	Save all the transformations of a SpatialData object to disk.