I have used India Ink for a number of purposes including tracing of vessels and brain ventricles. I have also used it extensively for marking specimens pre-processing. For example, if I need to keep track of which end of an isolated nerve is proximal and which is distal, I mark one end with India Ink. The advantage of the method is that the colorant is essentially carbon particles, and is therefore chemically inert, and is therefore not removed by any of the organic solvents used in tissue processing. Also, the ink doesn't penetrate into the tissue, but just marks the surface. Therefore the black color appears in the section as a thin black line on the surface, with no effect on internal structures. But, I find it hard to envision how it might be used to trace nerves, since nerves have no internal space that the ink can flow through, and as I said, the ink doesn't penetrate into the tissue because the colorant is particulate, not molecular in size. I wonder if your supervisor is confusing vessel-tracing techniques with nerve-tracing techniques?
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