One of the limitations of IsoDen is that there are several parameters
whose value is somewhat arbitrary: 
, 
, and the
``significance'' parameter n.
The parameter is particularly important
since it determines how much smoothing is done to the particle density field.
In particular, IsoDen is unlikely to detect halos which have fewer particles
than .
Also, the peak densities and overlap densities, which are
used in the noise suppression method, will be affected by changing .
Notice that only enters the density estimation step. An
alternative density estimator might have different parameters, but
generally, some free parameter(s) in the density estimator will govern
the minimum size of peaks that are discovered in the density field.
The parameter has an effect similar to .
If, is too large, then a bona fide peak whose central particle
is an -neighbor of a higher density particle
will be overlooked by the method.
If is too small, then overlaps are not detected at all, and
halos are detected in isolation rather than as part of a hierarchy.
Our limited experience is that the results are
not strongly sensitive to in the range 12 to 24.
The ``significance'' parameter, n, represents a tradeoff between failing to detect small halos and wrongly ``detecting'' spurious halos. Since the test is not actually a rigorous statistical test, an appropriate value of n needs to be empirically determined, and the best value may depend in a subtle way on the other parameters. It is even possible that the best value could vary for different simulations or for different spatial or temporal regions of a single simulation. One option could be to use the evaporative method, which is motivated by the discipline-specific knowledge about the problem, to determine an appropriate value of n in various circumstances.
Both methods for noise suppression make some assumptions about the nature of the particle position and velocity distributions in N-body simulations -- e.g. specific sorts of randomness. While these assumptions are based on experience with the simulation data, and seem reasonable, it is possible that they could be violated under some conditions.
The method used by IsoDen to estimate densities has been chosen from a practical point of view as an effective way to deal with resolution in regions of vastly different density. However there are alternative methods available for density estimation which we have not examined, and would could ultimately prove even more effective.