The technique Nate describes is also known as multi-plane scanning. Sidney Ray's Applied Photographic Optics gives a brief description, as well as several other references.
Another alternative is software combination of images at various focus distances. It doesn't need a sophisticated setup, but it's obviously more of a chore with LF than with small- or medium-format digital. And it benefits from a stationary subject, which can be tough with flowers.
I've not personally used either technique, so I can't offer much additional comment.
Perhaps after providing a lot more information than the OP may have wanted, an attempt at practical answer to his question might be appropriate. Let's assume that DoF as well as sharpness in the plane of focus is important, and consider an example at 1.0 magnification, and for which the focus spread is 10 mm. Using my formula for optimal f-number at the DoF limits,
N = 20 sqrt(10) / (1 + 1) = 32 .
There's no point in using a smaller aperture because the image will get less sharp, even at the DoF limits. Assuming the standard 4x5 CoC of 0.1 mm, the conventional geometrical formula gives
N = 10 / [2 x 0.1 x (1 + 1)] = 25 ,
so it should be possible to get the desired DoF. The geometrical formula ignores diffraction, and probably underestimates the minimum f-number, so a better value might be 32, the same as given for the optimal f-number.
What happens if the minimum f-number is greater than the optimal? Use the optimal, because using a greater f-number will make the image less sharp. When this happens, you can't get the desired DoF, and you also may be getting sharpness at the DoF limits at the expense of that in the plane of focus, and may need to decide which is more important.
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