Aggregated plateletts may be discriminated to some extent by plotting
Forward Scatter intergral against Forward Scatter Peak; aggregates fall away
from the line of linear relation between the two parameters. However I
imagine this may be of little use as you are performing a selection which
may exclude the very particles you wish to analyse.
It may be possible to (as you suggest) to merely base your analysis on the
mean cell fluorescence of the total platelette population, this however
makes some assumptions on the ability of the cytometer to acurately measure
the anexin V signal from aggregates.
If you looking at annexin V binding as a function of an activation event
then it may be inappropriate to inhibit aggregation. If this is the case I
think that I might look into the possibility of analysing these samples on
a fluorimeter
Best wishes.
Arnold.