Focus stack blurring parts of image

[jespera84579981]

So, I experimented a little with a macro lens, taking 6 photos of a flower, and then focus stacking them in Photoshop CC.

I was very dissappointed to find that parts of the image is blurred at the edges. Notice for instance around the leaf of the lilly, how there is a space of a few milimeters that is completely blurred. What to do?

/Jesper

[Chuck Uebele · Accepted solution]

That, unfortunately is plain optics. There is a transition area between two objects of different distances that a camera can't record things in focus. For example, when the leaf is in focus, the background is blurred. They the bg is in focus, the leaf blurs out into the bg. If you camera can't record a sharp image in that fine area, PS can't create it.

[jespera84579981]

Thank you Chuck, makes sense.

Well, that seems to be a bit of a setback with regard to focus stacking. I used a wide open aperture, F3.2 I think. Perhaps usung a higher DOF by increasing to, say, F8 could reduce the blur?

[Chuck Uebele]

Yes, a smaller f-stop will help. I know some software like Helicon focus says to use a wide f-stop, but I've found that I get less that pleasant results. It all depends on what you're shooting. If you really want a bg to go blurry, then use a wide aperture. You might even try using both a wide and small aperture and see how that works. or do two stacks and blend them with mask.

[Rafael Aviles]

I think you are missing the point of focus stacking. In this case, there would be two images available: one with the leaf in focus, one with the background in focus. The software selects the parts in focus, and masks out the parts out of focus, when stacking the images and creating the output.

I believe that in the OP's case, one problem is that the focus shifting was not fine enough (or there weren't enough images) to make sure that all elements of the composition appeared in focus in at least one image.

It could also be that Photoshop is very good but not great at focus stacking. As others mentioned, there are specialized software packages that do a better job.

[D Fosse · Accepted solution]

Chuck is right about the optical laws. No software can do anything about that, short of inventing sharp pixels where there aren't any.

But there is one thing that will at least reduce the problem. Instead of focusing the lens with the camera fixed, use a focusing rail to move the camera with fixed focus. The problem with focusing just the lens is that it changes the distance between lens optical center and subject. This changes the whole angle of view slightly. In addition, many lenses are so constructed that focal length varies with focus distance. This is strictly a flaw, but so expensive to fully correct that it's usually not done.

If you move the whole rig, on a focusing rail, none of this happens.

Even more effective is a bellows system where only the camera body is moved, and the lens stays fixed. That's pretty specialized equipment, though.

A focusing rail can also be used to eliminate parallax error in panos, so it's a very useful investment.

[Chuck Uebele]

As Dag said, camera rails are really nice - bellows even better.

[davescm]

Looking closely at your image , I'm not sure that this is a case of simple optics and no sharp pixels available. Go through and view each layer individually with the masks temporarily disabled and check if one of them is sharp in the circled area. Sometimes I find I have to tweak the masks a bit after focus stacking to address any small areas like this.

Dave

[Chuck Uebele]

Photoshop also doesn't do the best job at stacking. It does have a hard time with areas of similar color and density with fine detail. I was shooting a job with hundreds of stacked images and PS was leaving blurred areas where there was good detail. I ended up buying Zerene Stacker, which did a much better job.

[waynee61264534]

I know it's 6 years on, but I will agree with the idea that it's a limit with optics. 6 images just isn't enough for such a limited area of focus a macro lens may have provided at this distance from subject. 20 would have given plenty of focal range.

..... and it could be a limit of PS at the time and now (2025)

Having done quite a bit of stacking over the years, PS doesn't always get it right, even with enough images. 

For instance: today I was working on a 20 image stack of a subject and it to had blurred areas. I went back to look at my original images and they were sharp at every point. PS was just getting it wrong! I stacked the images in smaller groups and then stacked the stacks and the final image it turned out fine. 

[Chuck Uebele]

Years ago, I worked on a large stacking project of wave guides. Photoshop did a horrible job. We ended up using Zerene stacker, which worked much better. We were getting blurred areas in some of the flat metal areas where PS couldn't seem to pick the right area from the sharpest exposure. 

[davescm]

It may be six years on but it is still relevant advice. Incidentally, I now use Zerene Stacker, mentioned above by Chuck, for stacking microscope images. It enables both the grouping you mention, called slabbing, as well as retouching from original images,, slabs or from alternative stacks mafe with different settings. 

Dave