The algorithm walks the tree recursively. At each node, it checks: does this node's bounding box overlap with the query rectangle? If not, the entire subtree gets pruned (skipped). If it does overlap, it tests the node's points against the query and recurses into the children.
It is not for lack of trying. In some cases, microbiologists have ditched the Petri dish altogether, using microfluidics for manipulating and growing cells. However, these approaches aren’t likely to be adopted at scale as they require less common, less practical, and more expensive devices. So, what about other growth media?
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