text: FISH is a very general technique.  The differences between the various FISH techniques are usually due to variations in the sequence and labeling of the probes; and how they are used in combination.  Probes are divided into two generic categories: cellular and acellular. In fluorescent "in situ" hybridization refers to the cellular placement of the probe
  Probe size is important because shorter probes hybridize less specifically than longer probes, so that long enough strands of DNA or RNA (often 10–25 nucleotides) which are complementary to a given target sequence are often used to locate a target. The overlap defines the resolution of detectable features. For example, if the goal of an experiment is to detect the breakpoint of a translocation, then the overlap of the probes — the degree to which one DNA sequence is contained in the adjacent probes — defines the minimum window in which the breakpoint may be detected.
  The mixture of probe sequences determines the type of feature the probe can detect.  Probes that hybridize along an entire chromosome are used to count the number of a certain chromosome, show translocations, or identify extra-chromosomal fragments of chromatin. This is often called "whole-chromosome painting." If every possible probe is used, every chromosome, (the whole genome) would be marked fluorescently, which would not be particularly useful for determining features of individual sequences.   However, it is possible to create a mixture of smaller probes that are specific to a particular region (locus) of DNA; these mixtures are used to detect deletion mutations.  When combined with a specific color, a locus-specific probe mixture is used to detect very specific translocations.  Special locus-specific probe mixtures are often used to count chromosomes, by binding to the centromeric regions of chromosomes, which are distinctive enough to identify each chromosome (with the exception of Chromosome 13, 14, 21, 22.)
  A variety of other techniques uses mixtures of differently colored probes. A range of colors in mixtures of fluorescent dyes can be detected, so each human chromosome can be identified by a characteristic color using whole-chromosome probe mixtures and a variety of ratios of colors.  Although there are more chromosomes than easily distinguishable fluorescent dye colors, ratios of probe mixtures can be used to create secondary colors.  Similar to comparative genomic hybridization, the probe mixture for the secondary colors is created by mixing the correct ratio of two sets of differently colored probes for the same chromosome.  This technique is sometimes called M-FISH.
  The same physics that make a variety of colors possible for M-FISH can be used for the detection of translocations.  That is, colors that are adjacent appear to overlap; a secondary color is observed.  Some assays are designed so that the secondary color will be present or absent in cases of interest.  An example is the detection of BCR/ABL translocations, where the secondary color indicates disease.   This variation is often called double-fusion FISH or D-FISH.  In the opposite situation—where the absence of the secondary color is pathological—is illustrated by an assay used to investigate translocations where only one of the breakpoints is known or constant.  Locus-specific probes are made for one side of the breakpoint and the other intact chromosome.  In normal cells, the secondary color is observed, but only the primary colors are observed when the translocation occurs.  This technique is sometimes called "break-apart FISH".