active gene expression, in terms of mRNA rather than protein. This allows identification histologically (in situ) of the cells involved in the production of genetically-coded molecules, which often represent differentiation or functional traits, as well as the molecular boundaries separating distinct brain domains or cell populations. Genetically encoded markers By expressing variable amounts of red, green, and blue fluorescent proteins in the brain, the so-called "brainbow" mutant mouse allows the combinatorial visualization of many different colors in neurons. This tags neurons with enough unique colors that they can often be distinguished from their neighbors with fluorescence microscopy, enabling researchers to map the local connections or mutual arrangement (tiling) between neurons. Optogenetics uses transgenic constitutive and site-specific expression (normally in mice) of blocked markers that can be activated selectively by illumination with a light beam. This allows researchers to study axonal connectivity in the nervous system in a very discriminative way. Non-invasive brain imaging Magnetic resonance imaging has been used extensively to investigate brain structure and function non-invasively in healthy human subjects. An important example is diffusion tensor imaging, which relies on the restricted diffusion of water in tissue in order to produce axon images. In particular, water moves more quickly along the direction aligned with the axons, permitting the inference of their structure. Viral-based methods Certain viruses can replicate in brain cells and cross synapses. So, viruses modified to express markers (such as fluorescent proteins) can be used to trace connectivity between brain regions across multiple synapses. Two tracer viruses which replicate and spread transneuronal/transsynaptic are the Herpes simplex virus type1 (HSV) and the Rhabdoviruses. Herpes simplex virus was used to trace the connections between the brain and the stomach, in order to examine the brain areas involved in viscero-sensory processing. Another study injected herpes simplex virus into the eye, thus allowing the visualization of the optical pathway from the retina into the visual system. An example of a tracer virus which replicates from the synapse to the soma is the pseudorabies virus. By using pseudorabies viruses with different fluorescent reporters, dual infection models can parse complex synaptic architecture. Dye-based methods Axonal transport methods use a variety of dyes (horseradish peroxidase variants, fluorescent or radioactive markers, lectins, dextrans) that are more or less avidly absorbed by neurons or their processes. These molecules are selectively transported anterogradely (from soma to axon terminals) or retrogradely (from axon terminals to soma), thus providing