It is common to get a granular, brown precipitate (or at least it has the
appearance of a precipitate) and sometimes glossy black nuclei in H&E stained
sections when the sections are allowed to dry between the xylene and
coverslipping steps. I would suggest removing the coverslip and backing the
slide up to absolute alcohol, or even 95% alcohol, and then re-clearing and
coverslipping - taking care that the slides do not dry.
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