Extended Data Fig. 1: Illustration of the SpatialData query function.

To facilitate analyses on large datasets, SpatialData enables the selection of distinct regions within a dataset. The spatial query interface allows users to request the data contained in a query region, which can be specified both as a bounding box or a polygonal region. The query region can be specified using any of the coordinate systems present in the SpatialData object. The query operator returns a derived SpatialData object that contains the data within the query region for all layers, including the corresponding table annotations. The bounding box spatial query can be performed in 2D for all elements or in 3D for raster elements (that is, Image and Labels) and points; extended discussion on 3D queries is presented in Supplementary Note 6. Shown are code excerpts from the spatial query tutorial. This specific tutorial explains how a region of interest can be specified, such as rectangular bounding boxes or defined via polygonal shapes, and how the data underlying the specified query region can be retrieved. The full example can be found in the ‘spatial query’ notebook in the online documentation (https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/spatial_query.html).