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In situ is a Latin phrase meaning in the place. It is used in many different contexts.
In biology, in situ means to examine the phenomenon exactly in place where it occurs (i.e. without moving it to some special medium). This usually means something intermediate between in vivo and in vitro. For example, examining a cell within a whole organ intact and under perfusion may be in situ investigation. This would not be in vivo as the donor is sacrificed before experimentation, but it would not be the same as working with the cell alone (a common scenario in in vitro experiments).
In genetics, in situ can also mean 'in the chromosome.' For example, fluorescent in situ hybridization (FISH) can be done with chromosomes in cells or in a karyotype, such as with spectral karyotyping. In each case, the target sequence(s) is observed in the chromosome.
In linguistics, specifically syntax, an element may be said to be in situ if it is pronounced in the position where it is interpreted. For example, questions in languages such as Chinese have in-situ wh-elements, with structures comparable to "John bought what?" while English wh-elements are not in-situ: "What did John buy?"