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pwalter> For my natural light stacks I almost always go out very early in the morning when the bugs are still relatively inactive. With a sturdy tripod it is usually not so much harder to take a series of shots with different focus rather than just one. I do handheld, flash lit stacks too and these tend to demand a little more work in post processing (i.e. careful pre-alignment of the frames prior to stacking)

For focus stacking I use a free app called CombineZP (Lightroom + Photoshop for the rest).