It actually depends more on your equipment. Biocytine labeling is
suitable for light microscopy whereas Lucifer yellow implies the use a
Biocytine labeling is a much more older (and classic) method, which
demands fixing overnight, developing with peroxidase, etc.. whose
conditions are well-described in the literature,and don't vary too much
for different cell types. The dendritic arbourization is easily visible
through the staining, and provides a good morphology description.
Lucifer yellow does not need to be developed, and has the advantage of
the plausible use of the high-resolution fluorescence techniques
(confocal, two-photon...) and posterior digitalization and imaging.
Moreover, Lucifer yellow is essential if you want to label your tissue
with fluorescence antibodies, to describe certain protein localization
(i.e somatic vs. dendritic) . However, I find the morphology is not that
clear as this showed by Biocytine, unless you use confocal-microscopy.
Depending on the tissue and on your experience you can get a good by
both staining methods. I saw wonderful 3D pictures reconstruction with
Lucifer yellow, but I have to admit that Biocytine labeling of the
dendritic arbourization is better.
For Lucifer yellow you should work in darkness, to avoid the fluorophore
I guess you're filling the cells with patch-micropipettes. For both
methods, you should take care of forming the outside-out configuration
after filling the cell (10-20 min), to avoid the diffusion of your
marker into the slice (this is specially unpleasant with Biocitin).
Biocitin solution concentrations are in the range of 1-2% and Lucifer
yellow is about 0.6%.
I checked you're writing from Germany... I'm electrophysiologist working
for the medical faculty of the University of Leipzig, we have some
experience here for such labeling (also in cortex), so if you have any
question, please contact me!