In this article we're going to look at a couple of techniques to improve the output beyond what stacking software can currently manage under normal circumstances;
This technique is used to overcome a problem commonly experienced when focus stacking insects. It's common for two elements of the subject to both be in focus at the same position in the picture at different depths in the stack. In this case the software cannot necessarily do a perfect job of showing what you want. A good example of this occurs with antennae which overlap as in this shot;
This is a two frame animated gif which should toggle between the original untouched image and the image which has had a sub-stack overlaid on the left antenna
You can see that some of the texture of top of the insects head shows through some parts of the antenna at the front which do not contain detail. Unfortunately it seems there is no obvious way to fix this automatically in the stacking software, so a way to fix this is to use 'sub stacks'.
You need to go through the input images and find the range of images which contain the front antenna in focus. You then stack just those images in a separate stack to the full stack (the one you ran originally which contains all input images). You then load both the full stack and the sub stack into an image editor like Photoshop or Paint Shop Pro, and clone over the area you want cleaned up. So in this case you would just clone the area marked in the image above from the sub stack which just contains the front antenna in focus.
In some cases you may need to do several sub stacks. Hairy subjects with complex overlapping hairs can be a nightmare!
Note Zerene stacker can do this all without an external image editor, and with some advantages (namely automated image alignment). Simply run a full stack, then select the range you want sub stacked and tell the software to stack selected images. Then use the built in touch up tools to copy from the sub stack back to the main stack. See this tutorial for more information.
This technique is really quite simple and can make a big difference in making very high magnification stacks look more natural. It is used to mitigate the 'DOF falling off a cliff' problem which can occur with focus stacking at high magnification especially with wide apertures.
Note 1. This tip is only worth trying if you do not attempt to get every piece of the subject which is visible in the frame in focus. If you do that then this will not achieve anything. Personally my style often involves leaving some of the subject out of focus, as that's my preferred look. I think the out of focus elements help hint to the human eye/brain that the subject is small.
Note 2. You obviously need a lens with variable aperture to do this. Most of the high magnification lenses I use are microscope objectives which do not contain adjustable apertures, they are always 'wide open'. See the Lenses article for some high powered macro lenses which can go to high magnification and do have variable apertures.
This technique involves adjusting the aperture (and shutter speed/flash power to compensate) at the beginning and/or end of the stack so that rather than going suddenly from in focus to out of focus in a micron you can achieve a more natural look with the subject going gradually out of focus.
At it's most simple, shoot a stack starting from the front of the subject. Progress through to the rear most detail you want to maintain in sharp focus, then when you get to the end of the stack, close the aperture down 2 or 3 stops and either decrease the shutter speed or increase flash power to compensate, and take a final shot. This will result in an image which is likely to suffer from diffraction to some degree but as it will be used for out of focus areas of the subject this doesn't really matter.
Just include this shot as a normal one at the end of the stack when combining in software. The software will choose all the detail from the wide aperture shots where it exists, and then will use most of the last image to make up the rest of the picture, as although it will be out of focus, it will be less out of focus than the same areas shot with wider aperture. This will result in a much more natural looking DOF falloff in the shot.
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I did not know this kind of detail was available to someone with some what ordinary equipment. If I could spell it I would say incredable.