Focus Stacking

Rather than continue to hijack Ann Louise’s Orange Petals thread with our stacking sidebar, I thought it might be polite to take it to a separate discussion.

Our Weekly Challenge moderator, Mark Seaver, does a lot with stacking and has done some webinars for NPN on the subject, but I thought maybe a catch-all thread could be helpful no matter if you’re an experienced stacker, just starting or even only thinking about it.

Since moving from a manual (legacy 35mm) macro lens to a system lens, I’ve gotten into stacking in a major way and have written two articles about it on my blog. It might be helpful to start there if you’re curious about stacking.

I think all of us have our different methods and techniques and so please feel free to comment, ask questions or point us to more information on the subject.

Here are some photo critiques that have had stacking sidebars or discussions -

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Kris, thanks for posting this in the Discussion thread. I will follow with great interest. I read your two blog articles. Well done and very informative. I use Helicon Focus for stacking. Zerene is also very good. Photoshop is the worst…

In the last 3 years I have spent a lot of time in our Portland Japanese Garden shooting with a 100-200mm lens. Much of the time I used focus stacking to ensure front to back sharpness. A couple of things I learned along the way:

  1. Wind is not you friend–hard to get a good stack.
  2. Moving water is also a challenge–this can be fixed in retouching
  3. Objects in the foreground can end up with blurry halos around them. This is because at wider apertures the foreground objects become larger as they go out of focus, blocking some of the background. Most stacking software can’t deal with that. The only real option in these cases is to close down to a smaller aperture. I generally shoot stacks at f/11, f/16, and even f/22 to minimize the halos. Japanese Maple trees are the worst for this…

I look forward to learning more from others.

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Thanks so much. I’m glad you found them useful. I think Zerene & Helicon work in similar ways.

Wind is a pain and if I’m determined to get a shot of something with a breeze present I don’t use focus bracketing, but instead use the cable release and wait it out. The end result isn’t as smooth sometimes as a bracketed shot would be since I’m touching focus points on the screen, but in a pinch it can work pretty well.

@Ed_McGuirk can talk about the moving water blend better than I can since I’ve never done it, but I think he uses Photoshop to blend images with masking, not a real stacking program.

I haven’t tried stopping down as much as you you mention, but I always can give it a go if I can get a clean background. I think I’d have to use one of my longer lenses since my macro is 45mm which is 90mm in 35mm terms. Experimenting is all part of the process.

Yes, for moving water I use multiple exposures, which I blend manually using layer masks in Photoshop. Generally for landscapes I do this in a non-focus stacking situation, and do it primarily for two things, exposure and “look” in the water. With waterfalls, the water itself often requires a darker exposure than the land/rocks around it. Or I might vary the shutter speed to get the “best” look and texture in the waterfall, while still getting a good exposure in the land.

I generally do not use focus stacking for landscapes, unless I am using a long focal length (less inherent DOF), or if its impossible to align the plane of the sensor with the subject. Think shooting lily pads in water with a telephoto from the shore of a pond. In this case I do use focus stacking. Generally the water is calm is this case and focus stacking usually works fine. I usually have more probelm with wind moving the lily pads, that can create ghosting in a stack.

But generally focus stacking and moving water is not a good combination. I suppose you could do a pure focus stack, then take an additional exposure not in the focus stack for the look of the water and manually blend it with masks. That might be a pain to align and blend though.

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Thanks for starting this dedicated discussion, @Kris_Smith. I’ve had a hard time focus stacking for macros, I think because I don’t really appreciate (or even believe!) just how small the depth of field is! The physics of optics continually amazes me. I’ll look forward to reading your articles, and finally getting around to Mark’s webinar.

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Two questions:

  1. I haven’t heard the distinction between "manual macro lens” and “system lens” before. Can you explain the difference?
  2. My Nikon D750 is ancient :grin: in that it doesn’t have in-camera focus bracketing or stacking. I can’t imagine being able to slightly shift focus by so little that I can get 20 images in a half inch object, for example. Am I limited in what I can do with macro focus stacking because my camera doesn’t have the in-camera feature?
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Hi Mark,
One possibility could be to mount your camera on a focusing rail. Instead of changing the focus in the camera you move the camera slightly between each of the shots


Until recently I never had in-camera focus bracketing and have done a lot of it the hard way, by incrementing focus with the focus ring on the lens. I read somewhere that (at least with Zerene) not to use a rail, as the software can’t compensate for the size changes of the image with varying lens distance, but it will compensate for focus breathing, which is a change of size as the focus point shifts.

Now I have recently discovered focus bracketing is a feature in my Canon R5. It’s wonderful because it will shoot a stack of 20 in about a second, which can help somewhat with slower subject movement. So I’m going to be doing a lot of it. I also finally installed the Zerene plug-in to LR, which saves some tedious steps.

I had wondered if the plug-in would use develop adjustments when it created its TIFFs and I found an old bracket sequence where I had not deleted the source files and tested it – and yes, it does. (It would be hard to believe it wouldn’t, but I’m always the skeptic.)

I shot several sequences yesterday and will be working them up today. It was a bit too breezy and there may not be much usable, but I’ll be having fun anyway. And I’ll be trying the Zerene editing for the first time. I had never taken time to check it out but I think it is a lot easier than it looks at first glance, and is a fantastic tool.

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And now I have another question, which has plagued me from the start – how do I best choose the slider position for DMax, and the settings for Estimation and Smoothing radius?

Sorry for creating any mysteries, Mark. I will explain. No that will take too long, I will sum up.

For years my macro lens was one I used with my 35mm film rig back in the day. An adapter fit it to either my Olympus DSLR or Panasonic mirrorless cameras. It would meter fine, but I had to focus and manipulate the aperture ring. Ah, memories. But it was literally being used to death. It’s old, rare and impossible to find parts for so I gave up and got a lens that will autofocus and all the other stuff that system lenses do.

My older GH3 doesn’t have focus bracketing either so I occasionally tried to choose focus points on the back screen in order to have a wider DOF. It works ok so long as you’re careful and can really see what’s in which plane of focus. You can do the same and still use the images in a stacker like Zerene or Helicon. A hand lens might help if you have an especially dense subject with lots of parts .

Does that make sense?

Oh boy, I wrestled with this for months. Basically now I crank it until it starts to mask (put black on) my subject. Sometimes it’s 0 and sometimes it’s 30%. It really depends. I’ve noticed that the background comes out less goopy (a seriously technical term, I hope you aren’t lost, lol…) if I mask a lot of it. If it does start to mask out some of my subject, I back it off unless that area is better served by masking. You can always ‘paint’ in a crisp version from a source file if it looks weird.

That’s odd – I’m usually at 85-95%, but my subjects are generally more isolated from the BG than your little critters. I’ve read that it’s OK to have black areas on the subject if they are surrounded by clear areas, but that may apply more to a rose petal than a warty little toad.

Goopy is standard terminology.

Yes, that makes sense Kristen. Thanks for elaborating. The hardest part for me is really seeing what’s in which plane of focus, and the micro-adjustments of the focus ring. Figuring these out makes for some absorbing time!

New guy here:

I do my stacking using command-line tools (specifically enfuse) and automate the daylights out of it. Once I have my images aligned, a point a script at them and let it rip, using a whole range of different settings. Probably not immediately helpful for you, but the point is to simply bracket things. It helps to make a matrix of all the different settings, and just plug them in. If you have a way to script it, do that, and walk away for a while.

Once you have a bunch of candidates, just pick what you like best. On my system (3.6GHz i9-9900K CPU) a full run takes at most an hour or so, even with 80+ images to stack.

I have about 10 sets of settings that I run, BTW. After you’ve had a chance to see what all the variants are, you get a feel for what’s going to work well. It’s a great way to learn. Not too efficient in terms of workflow, perhaps, but I’m retired and have time to burn.

One of the main reasons I purchased a Nikon Z6 was for the built in focus stacking. I usually focus on the nearest point and then use the focus ring to bring the first focus point to just out of focus, keeps me from missing the close focus point as I have done on occasion. The Z6 puts each set of images in a separate folder making it easy to know which ones go together. I look through them and delete those on the front and back to get the focus range I want and use Affinity to do the stack. The latest version of Affinity seems to do a real good job.

Seems like a nice way to do things. Does it actually combine the images in camera? That’s stacking, but what you describe here seems to be focus bracketing. I wish that my G9 would put them in a folder or something, but it doesn’t. Maybe in a new firmware version.

When I have the camera do a bracket set, I use the old panorama trick of sticking my hand in front of the lens for a shot, bracket away then to the same hand thing. Then in LR I can easily see each set.

Combining the frames in-camera will give a JPEG with its limited quality. I want to use the raw converter to adjust the first frame, sync the settings to the others and process in stacking software – Zerene Stacker or Helicon Focus seem to be the most sophisticated.

Kristen, Nikon does refer to it as focus shift and does not stack them in camera. Here is a stack where I eliminated some of the front and back shots that were in focus.

Gotcha. Focus shift and/or bracketing is the same thing - meaning the camera makes multiple images with different focus points as directed by the photographer.

I sometimes use the hand separation method too, @Diane_Miller - I’m annoyed that something can’t be done with firmware to be sure those images used to make a bracketed set aren’t corralled in some way. I notice my G9 will denote an exposure bracket group in camera, but not when it hits Lightroom. Annoying.

When I do focus stacking, I’m usually shooting about 20 frames via the stacking in the Olympus system so the images are all captured in a second or two depending on shutter speed. Once imported into LR, I just go to Photo / Stacking / Auto Stack by Capture Time and set the Time Between Stacks slider to 2 or 3 seconds and I have all my stacks in nice convenient logical stacks.

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