Large data sets can be stored and processed in real time by combining and registering the large data sets into a single data set. The data can be stored in a data tree structure formed of layers of spatially organized blocks of data. Such storage allows portions of the data to be viewed efficiently, displaying actual point data at an acceptable resolution for the viewing mechanism. Density limited queries can be executed that allow sub-sampling to be done directly and evenly without geometric constraint, to provide a subset of points that is limited in size and includes a spatially-even decomposition of that set of points. This allows the system as a whole to support arbitrarily large point sets while allowing full partitioning functionality, which is efficient to use in both time and space.