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In large biological systems, direct counting (meaning literally looking at and counting one by one every animal) is not always a realistic possibility. There may be too many animals spread over too large an area making it difficult to locate and count them. Or the animals may be hidden underground and therefore difficult to locate. Or you may be counting the number of bacterial cells on a specimen plate and there are simply too many and they are too small (and all moving around) to count directly. In these cases, indirect counting methods are used to estimate populations. In the case of bacteria, you could measure with a spectrophotometer the amount of light that passes through the speciment plate. The more bacteria that are present, the less light will pass through the sample. With enough data points, a reliable estimation can be made. Another example is studying animal tracks and movements to and from common water sources to estimate the population of a particular animal in a region. In the case of pests or insects, counting the numbers of nests and measuring their sizes can estimate that insect's population in or around a structure.
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