It’s also worth noting that even if alternatives superior to agar were found, scientists are reluctant to abandon established protocols (even when microbiologists do use other jellies, they often still add agar to the mix, for example, to increase the gel strength of the solid media). As agar has been the standard gelling agent in microbiology for around 150 years, an enormous infrastructure of standardized methods, reference values, and quality control procedures has emerged around its specific properties. Switching to a different medium (even a superior one) means results may not be directly comparable to decades of published literature or to other laboratories’ findings.
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The efficiency depends on the query size relative to the data distribution. A small query in a sparse region prunes almost everything. A query that covers the whole space prunes nothing (because every node overlaps), degenerating to a brute-force scan. The quadtree gives you the most benefit when your queries are spatially local, which is exactly the common case for map applications, game physics, and spatial databases.