Limitations
Just as any technique, Brainbow has a number of limitations that stem from the methods required to perform it. For example, the process of breeding at least two strains of transgenic animals from embryonic stem cells is both time consuming and complex. Even if two transgenic species are successfully created, not all of their offspring will show the recombination. Thus, this requires extensive planning prior to performing an experiment.
In addition, due to the random nature in the expression of the fluorescent proteins, scientists are unable to precisely control the labeling of neural circuitry, which may result in the poor identification of specific neurons.
The use of brainbow in mammalian populations is also hampered by the incredible diversity of neurons of the central nervous system. The sheer density of neurons coupled with the presence of long tracts of axons make viewing larger regions of the CNS with high resolution difficult. Brainbow is most useful when examining single cell resolution against the background of a complex multicellular environment. However, due to the resolution limits of optical microscopy, conclusive identification of synaptic connections between neurons is not easily accomplished. This issue is somewhat avoided by the use of synaptic markers to supplement the use of optical microscopy in viewing synaptic connections.
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