I frequently observed labeling of pericytes (macrophage-like cells along blood vessels) in the motor cortex and along the spinal cord after FluoroRuby injections in the lumbar spinal cord, even 3 weeks after the injection. I think there is a good possibitlity that this dye is transcytosed from neurons to glial cells and it in theory it could also end up in another neuron though I would expect to encounter it in the lysosomal compartment rather than in axons. I hardly observed this extensive labelling in glial cells and pericytes after we switched to cholera toxin subunit B (CTB)- conjugated Alexa dyes as a retrograde tracer. This dye is more expensive though but I achieved superior retrograde labeling on injection in the non-injured spinal cord.

Thansk a lot Manfred

If your goal is anterograde labeling of CST axons, you might consider switching to BDA. There is a lot of literature on this tracer in models of spinal cord injury. I cannot comment specifically on the labeling patterns that you see with FR outside the CST axons. Perhaps pericytes or activated microglia responding to axonal die-back at the site of injury with subsequent incorporation of the dye. This is not something that is observed with BDA. I would recommend checking out PMID: 18596159

I have seen the same phenomenon with FR labeling the walls of blood vessels after cortical injections. At one point I had thought that an excessive injection volume might lead to tracer entry to the blood vessels.  We now utilize very small injection volumes at multiple points, and the background label around vessels is much less. I agree with Dr. Popovich that BDA is useful, but mainly when reacted for study with light microscopy.