Focus Stacking (using Zerene Stacker)

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w7ptt
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Focus Stacking (using Zerene Stacker)

Post by w7ptt »

Hello,

I am currently photographing with a Fuji GFX 100 medium format camera.

Last night I did 3 different sequences (40 frames, 60 frames, and 100 frames). As far as the GFX 100, my settings were: (Frames = 40, 60, or 100), (Step = 5), (Interval = 2). I am using Zerene Focus Stacker, and what I find interesting I am getting more haloing on the 100 frame stack vs. the 60 frame stack (yet of course the depth of field is better on the 100 frame stack vs. the 60 frame stack).The haloing (fuzzy looking) only goes out a few millimeters on then, then the image is clear (and the object is at the same distance where the haloing is vs. where it is not). Are you thinking that maybe I should lower my step setting from 5 to 4? I seem to be getting enough depth of field from the near object in the frame vs. the far object. This is a macro shot (120mm lens, shot at F11). I did check each individual frame and none of the frames had something tack sharp in that area. Also I ran the stacks as PMax and DMap.

See attached file of one of the problem areas of the photo.

Any thoughts?
Halo.jpg

rjlittlefield
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Re: Focus Stacking (using Zerene Stacker)

Post by rjlittlefield »

w7ptt, welcome aboard!

I replied a few minutes ago to your support request email about the same issue.

Sticking that reply here so that it can be read by others...
Thanks for writing.

Regarding the halos, please read my (long) explanations at http://www.photomacrography.net/forum/v ... 557#102557 and http://www.photomacrography.net/forum/v ... 42#p135042 , both in the thread titled "What causes halo?"

Let me include here a screen capture of the second post:

p135042.jpg

So, I hate to sound depressing, but at this moment what I'm seeing looks like you may have an impossible problem.

Your comment that "I did check each individual frame and none of the frames had something tack sharp in that area" is pretty strong confirmation of my fears.

If this is correct, then you can mitigate the problem to some extent by using a smaller aperture. The halos will remain, but they will shrink in width, in proportion to the aperture diameter. Unfortunately this approach is limited because at some point stopping down causes too much loss of resolution from diffraction.

All that said, I have been wrong before and perhaps I'm misunderstanding your situation.

Please study the explanations in the forum, then get back to me with your own thoughts. Thanks!
--Rik

joshmacro
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Re: Focus Stacking (using Zerene Stacker)

Post by joshmacro »

Rik: Is providing consistent lighting for the background and foreground a mitigating remedy for this issue ?
Thanks.

w7ptt
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Re: Focus Stacking (using Zerene Stacker)

Post by w7ptt »

FYI, the lighting for that photo is very even, and flat.

bobfriedman
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Re: Focus Stacking (using Zerene Stacker)

Post by bobfriedman »

I have had a similar issue and I think that Rik's explanation makes logical sense to me with the downside that it is almost impossible to mitigate... in this example it is self-evident,

Nikon D800E ,Mitutoyo M Plan APO 20x NA 0.42 200/0
275 stack
Image

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Re: Focus Stacking (using Zerene Stacker)

Post by rjlittlefield »

joshmacro wrote:
Tue Oct 06, 2020 10:51 am
Rik: Is providing consistent lighting for the background and foreground a mitigating remedy for this issue ?
In general, the problem is worse with bright foreground and dark background.

So, if you are lucky enough to have independent control of foreground and background brightness, and aesthetics would not be messed up by changing the relative brightness, then you can mitigate by making the background brighter or the foreground darker. This will not change the width of the halos, but will improve the amount of background contrast that is retained in the contaminated regions.
bobfriedman wrote:downside that it is almost impossible to mitigate... in this example it is self-evident
Yes, the loss of contrast when looking through a forest of hairs cannot be avoided by any method that I know.

With enough patience, it's possible to use a localized levels adjustment to restore contrast and brightness in contaminated areas. But I don't know any way to do that automatically, only by laborious hand work.

One last comment, this thread is misplaced in the Nature forum. I'll move it to Technique and Technical Discussions after people have had a little time to read this.

--Rik

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lothman
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Re: Focus Stacking (using Zerene Stacker)

Post by lothman »

Rik how would a telecentric lens compare? This should eliminate such problems, shouldn't it?

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Re: Focus Stacking (using Zerene Stacker)

Post by rjlittlefield »

lothman wrote:
Wed Oct 07, 2020 4:42 am
how would a telecentric lens compare? This should eliminate such problems, shouldn't it?
No, a telecentric lens has exactly the same problem, at least at the center of the image.

I suspect you're thinking that a telecentric lens only looks straight forward, so it won't experience the problem caused by the slanted rays.

But in fact a telecentric lens has entrance cones with slanted rays just like any other lens. The only difference is that with a telecentric lens, the central axes of the cones are all looking straight forward.

In the explanatory diagram copied above, notice that the central axis of the Entrance Cone is aligned straight up and down. If all the other entrance cones have the same alignment, then what's diagrammed is a telecentric lens!

--Rik

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Re: Focus Stacking (using Zerene Stacker)

Post by MarkSturtevant »

Could the problem be helped in some circumstances by also taking some pictures of the background without the foreground subject? I was wondering if adding that to the stack might then give the program (and the human who does touching up) information about what to put into the background adjacent to the subject.
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Re: Focus Stacking (using Zerene Stacker)

Post by rjlittlefield »

MarkSturtevant wrote:
Wed Oct 14, 2020 5:56 am
Could the problem be helped in some circumstances by also taking some pictures of the background without the foreground subject? I was wondering if adding that to the stack might then give the program (and the human who does touching up) information about what to put into the background adjacent to the subject.
In principle, yes. In practice, not so much.

First, it will be challenging to get the background alone properly aligned with the background in normal pictures that include the subject. Certainly Zerene Stacker is not going to do that part automatically.

Second, the added information would be very likely to mess up an automatic stacking process, not help it. This is because having unobstructed background available across the entire frame would make the entire subject vulnerable to the dreaded "transparent foreground" artifact. So, for most subjects, I think you would have to exclude the just-background image from automatic stacking. Perhaps a stack-all that includes the just-background would give a better rendering of visible background, and then the subject area could be retouched if necessary using a stack-selected that excludes the just-background image.

Once upon a time, I did read about some photographer who avoided halos by methodically dissecting his subject as he shot from front to back, so that the in-focus portions were always seen without obstruction. But I only read that once, and as I recall his entire process was manual, combining images by brushing in Photoshop.

--Rik

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Re: Focus Stacking (using Zerene Stacker)

Post by MarkSturtevant »

I was anticipating that the idea suggested would still produce artifacts and work. But to add to this: Would slabbing help in reducing the work load of painting a solid foreground over the subject-less background? That way you would have maybe 10 slabs to use to paint in the foreground over the transparent subject, rather than 100 frames to paint in.

A 2nd question related to slabbing (sorry to intrude into this thread, but it may be relevant): Is slabbing supposed to help ease the pain of halos? I am using ZS Pro (free trial) and in what little chance I've had to actually use it, it seemed I had about as much halo artifact in the slabbed hairy spider that I recently stacked, as the same spider stacked without slabbing. But I am hoping the chore of touching up halos will be less in the slabbed stack, since there are fewer slabs than original frames to draw from. Not sure if I'm making sense...
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Re: Focus Stacking (using Zerene Stacker)

Post by rjlittlefield »

MarkSturtevant wrote:
Wed Oct 14, 2020 12:48 pm
Is slabbing supposed to help ease the pain of halos? I am using ZS Pro (free trial) and in what little chance I've had to actually use it, it seemed I had about as much halo artifact in the slabbed hairy spider that I recently stacked, as the same spider stacked without slabbing. But I am hoping the chore of touching up halos will be less in the slabbed stack, since there are fewer slabs than original frames to draw from. Not sure if I'm making sense...
Yes, slabbing can help with halos in a couple of different ways, depending on exactly what you're doing.

First, as you note, if you do need to retouch then it's simpler to retouch from the slabs versus the more numerous original frames.

Second, if you slab with PMax but make the final result with DMap, you may end up with far less annoying halos than by processing the entire stack at once using either approach. For example this is a powerful technique for handling subjects that are covered by short hair, seen against uniform background. PMax is then able to generate clean slabs that can be cleanly combined by DMap, eliminating both small halos around the hairs (which would be left by DMap alone) and large halos around the subject (which would be left by PMax alone).

PMax followed by DMap also greatly reduces the time needed to try different contrast selection thresholds, which is another method to reduce or eliminate halos.

Would slabbing help in reducing the work load of painting a solid foreground over the subject-less background? That way you would have maybe 10 slabs to use to paint in the foreground over the transparent subject, rather than 100 frames to paint in.
Slabbing would help, but for this special purpose it seems even better to do a Stack Selected of the entire subject, leaving out the subject-less background. This is analogous to the original use of Stack Selected, as discussed on Zerene's website as "Using Stack Selected to Retouch Transparent Foreground".

--Rik

MarkSturtevant
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Re: Focus Stacking (using Zerene Stacker)

Post by MarkSturtevant »

Thank you! It looks like I've some researching to do when I can get to it. 8)
Mark Sturtevant
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