Stacking for Macro – Part 2 – Editing

Welcome to Part 2. I hope you enjoyed Part 1 which was about best practices to use while you’re taking the pictures. This post is all about processing. This part is also tech dependent, but not camera dependent.

A lotta ins, a lotta outs – processing workflow

Lightroom is my primary editor as well as my photo management software so all the RAW files go there first. Usually I compile each stack sequence into a group by selecting the photos that go together then using a right mouse click and choosing stack. When you do this Lr shows one image in the grid view and in the corner the number of images in the stack. If you do a lot of sequences it keeps things neat. Unstack to see individual shots and to edit the group.

Process one to your liking – hit it with basically everything you want aside from cropping and a lot of sharpening (do some, but don’t add noise, reduce noise, but don’t lose detail). Once you have it the way you want it, sync those settings to the rest in the sequence. Then export them as TIFs to a folder on your hard drive. Open Zerene and drag them to the workspace. Zerene cannot use RAW files of any kind. There is an option to create a Lightroom plug-in right from the Zerene menu. It works well, but has its own quirks. More on that below!

Do your stacking and retouching and save your final image. If you’re not using the plug-in put it in the same folder as the source images. From there import just that one image back into the correct folder in Lr. This is when I do final cropping, sharpening and any other edits I need. Sometimes, particularly if I use PMax (a file type produced by Zerene, details below), I have to do some work with color or white balance and exposure. Be sure that you create a 16-bit TIF from whichever photo you export from Zerene. A TIF gives you more color and detail than a jpeg.

If you need to bring it into Photoshop or any other external editor from here it will make the round trip just like any other file. When you’re done you can export as a jpeg for web sharing as usual.

10 image stack of felt horn lichen. 45mm macro @ f/5.6 which left the background nicely blurred, but it needs retouching. Soupy and goopy. Ah, lessons learned.

Bloodroot is one of my favorite flowers, but it’s really difficult to get the wrapped leaves and the bud in focus in one photo. One is always slightly blurry.

This is a 10 image stack using focus bracketing and now the raindrops, the petals, the stem and the leaf are crisp and clear.

But look at the background. This is a very early stack, before I mastered retouching and it’s pretty awful. Goopy, banded and grainy. A do-over candidate.

Here it is cleaned up. Better!

This next photo is from an Eastern leatherwood bush in my front yard. After it rained it was still a little breezy so I took only five images, focus points selected manually, and I waited for it to be still before firing the cable release. It’s not quite as perfect, but it works for me.

And look a that background in comparison to the bloodroot shot. So much smoother. I went to a lot of trouble to paint in a soft background to emphasize the crisp leaves & flowers. That little dark bit between the flowers against the leaf is a spider. It moved around as I shot, but it got included in the final where it was most in focus – against that leaf.


What to do with all those shots after the stack is done.

This applies twofold – the TIFs and the RAW files. If you aren’t using a plug-in for Zerene, you will have to export TIFs to a separate folder and then bring them into the software. They stay there with any finished shots and boy are they big files. No need to keep those unless you have limitless storage. Delete them. And the RAW files. Yes, I wrote that.

Unless you’re going to use one of them for a shallow DOF image, what’s the point? Save that one and kill the rest once you have your final stacked photo. The final pictures are the keepers, the goal of the whole process. So be brave and delete. Otherwise you’ll just have folders full of files you’ve already made use of and won’t do again. The clutter is unnecessary.

Also – delete stacks that don’t work. If I notice an area of focus I missed that ruins the shot I delete the whole sequence (usually it’s the closest part that I failed to see). Not only are they not useful for stacking, they confuse me when I come back to the folder after the time I shot them. I can’t remember that I tried stacking them already and that they didn’t work. If something is still in my catalog it is something I want to work with so by deleting I know that what I have is worth looking at. Also deleting means I’m done with that image and have produced my final shot. If they’re sill in there I haven’t. Does that make sense?

Seriously, if you do a lot of this you’re going to have literally hundreds or thousands of images that you’ll never look at again once you’ve done the final stacked image. In an hour or so outside working with lichen and a few other things, I came away with over 500 shots. Be ruthless.

Concentric boulder lichen – 40+ shot stack because the rock curved downwards quite a bit (2cm across)

Zerene file types & the importance of retouching.

There are many videos out there (some from Zerene directly) that show how to use the software and I’m not going to try to do that. Instead I’ll just write about how I use it. It’s pretty simple in terms of stacking – you can do either PMax or DMap or both at once. I do the latter then choose which I want to have for my final photo. After a few times you’ll get a feel for which will probably work best. I find that Pyramid Max sometimes gives me grainy halos around crisp objects with clean backgrounds, but usually renders overlapped detail better. Depth Map images tend to be better in terms of color, but sometimes don’t have as much contrast as a PMax image. Because of the way DMaps are made, you can select how much of the out of focus areas to exclude in the stack. I generally go under 30% and in almost all cases have to do a lot of retouching to get the background right. Many times it comes out goopy and has to be fixed, but to me it’s much easier to correct than the grainy halos PMax sometimes produces. For a technical explanation of the difference between the two methods, click here for the Zerene site.

Which brings me to retouching. That’s the real icing on the cake. In the right panel select the version you want to use as the basis for your final (PMax or DMap). Then under the edit menu choose start retouching. When you do that, select a source image and it will appear in the left panel. I use 100 or 200 % enlargement when I’m retouching. Place your cursor on the left to sample – click and literally paint the pixels from that one onto your final image. The cursor position in each image is matched exactly. Be careful about the cursor’s size – it’s a circle similar to brushes in Photoshop and Lightroom, but without any feathering or density (in the Personal edition). You can choose any of your source images or the other output style to correct your retouched shot.

The Zerene workspace – with the last source image chosen, but you can choose any of those or the DMap image which is the other stacked output. I’m retouching the PMax image.

And here it is finished. Since it was a PMax, I had to re-edit for color and overall contrast –

Among the fallen – 24 shot stack, PMax – finished in Ps for some clone stamping – IRL it’s about 2 cm wide and I think it’s common greenshield lichen.

That’s right – any image can be selected so take your time to evaluate where you are in the stack relative to the output image. When I have a bit of crisp detail with some halo or goop, I choose the image that is the source of that crisp detail. This way when you paint over an area the sharpness is retained, but now you get the background you want. If I want the same out of focus background throughout, I’ll choose one to source from and paint it onto the final. This way the background is smooth and uniform. Sometimes detail is missing in one output style and is present in another – just paint the detail into the one you’re retouching. It works a treat. Once I had a tiny springtail move from shot to shot. I didn’t even see it IRL, but I placed it in the final photo by selecting the one it showed best in. Like a microscopic pink bunny that you can only see on a very large version.

You do have to watch out and be precise with brush size and source image, but when you let go of the mouse it becomes a step you can undo by ctrl-Z. Another nice thing is that you can save projects and keep retouching even after you’ve committed.

I kind of like the contrast between the green and red –

Another tiny flake of lichen – this one about 1/2 inch wide. It’s a 27 shot stack out of 31 images taken and was a PMax image I believe. My first try was only a 21 shot sequence which wasn’t enough to get the base of the formation in focus. With tiny subjects like this, I can place it on almost anything I want for a background.

About that Plug-in…

When I first started writing this post I wasn’t using it, but decided to try it since I was doing so much stacking and the process is long enough as it is. Why not cut down on some steps or at least some time? Zerene covers a few different ways to get photos in and out of Lightroom, but for me the plug-in method is the best. It works via the Export menu versus the Edit in menu. Setting up Zerene as a side-car editing software is possible, but is limited to 30 images and I often work with deeper stacks so that’s a deal-breaker.

The plug-in exports TIFFs to Zerene directly. When you are done with your final image click Save final image(s) and the dialog box that opens will show your original Lightroom folder. Don’t forget the final step! You need to go into Lightroom and right click on the folder and choose Synchronize folder. That imports your DMap or PMax image into the catalog. It’s similar to saving into a folder on your hard drive and importing from there, but done within Lightroom’s catalog function.


So that’s my experience with Zerene and focus stacking so far. I’ve only touched the surface and am using it in a very simple way. There are settings and menu items I haven’t explored yet. Also, I think I’m using the most basic of the license levels. If I find things are too limited, I’ll see about upgrading. Moving forward I think this will be a regular feature of my nature photography, especially macro. All my life I’ve been fascinated with very small things and now I get to show them off with even more clarity and detail. So exciting. And I’ll have to remember this technique with slices and other smaller scenes that could use some added depth.

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