My understanding is that these cross-correlograms have mostly
been used to uncover underlying connections between neurons rather
than for examining stimulus-dependent response patterns. This is
the reason that the shuffling is done; to weed out those nasty
stimulus-driven synchronies. But what if the stimulus-driven
synchronies are what the system uses to encode edges and
spatial intervals between edges? One has thrown out the most
important aspects of the neural response.
I think it depends on what you want to include as
a representation of the stimulus. One could argue
that there are neural responses to stimuli which
do not contribute to the representation of what
matters about the stimulus to the perceiver, and
one could argue that all response is part of
the representation, but we selectively attend
to part of it. If we do not have a way to eliminate
that which we choose to call noise, we are unable
to learn how the part of the neural response that
we care about is represented apart from that noise.
Jim Kroger
Center for the Study of Brain, Mind, and Behavior
Princeton University