Vincent,
I may be wrong, but it looks like you could use a weighted histogramdd (see other thread where I sent a patch to do so).
You run it once to find the number of sample in each bin, then again with weights=value, normed=False to find the total weight in each bin, then you can divide each bin by the number of samples to find the average.
N, d = histogramdd(cells)
W, d = histogramdd(cells, weights = value)
average = W/N
David
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