The second task is to combine (or stack) all the pictures from the series into one image. While there are lots of good stacking software out there, I’ve chosen to show how it’s done using Photoshop. It’s far from being the best in this department, but it is undoubtedly the best known editing program. Stacking might sound difficult, but Photoshop gives us automatic tools that make it surprisingly easy and fast.

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I’ll show the process with a series of 4 images of a robber fly I’d like to stack. The series was taken with Canon's MP-E 65mm macro lens, at about 4X magnification and an aperture value of f/10. As is clearly visible, with these magnification and aperture settings, the depth of field in each image is, by far, too small for it to be useable on its own, at least if I want to show all the detail on this fly. Image number 1 is focused on the front of the fly’s proboscis, leaving its eyes (the part whose sharpness is the most critical in wildlife photography), the front of its head and everything else out of focus. Image 2 shows the hairs on the front of the face in focus, as well as those near the antenae. Image 3 and 4 have different parts of the eyes in focus. All in all, we have all the desired parts of the fly’s head in focus, each in different shots.

Here are four images of a robber fly I’d like to focus stack. All shot at 1.3sec, ISO 100, f/10. Canon EOS 40D, Canon MP-E 65mm f/2.8 1-5X macro lens.

To obtain the image series, I shot using a tripod and after every shot I gently changed the lens' focal distance, to get sharp focus on different parts of the fly's head: on the first image the proboscis is focused, and so on until the last picture is focused on the farthest body part I need focused. It’s very important to mention that I usually do not strive to have all parts of a subject in focus, even when I focus stack. The reason is that shots of tiny subjects all focused appear very strange to the eye and lack the “natural” macro look I desire. Therefore I usually leave a small part of the subject out of focus, to maintain a natural look.

Note how the front of this orange tip butterfly’s left-side antenna remains out of focus, and so does its right wing. This is intentional, and done to give the image the ‘natural’ macro look, where not all the subject is in focus.

Canon EOS 7D, Canon MP-E 65mm f/2.8 1-5X macro lens, 8 shots all at 1/5 sec, ISO 100, f/8.

Now we can start combining all the pictures into one.

There are a few ways of applying the stacking in Adobe Photoshop. I’ll show the simplest one.

We go to File -> Automate -> Photomerge and get the following menu:

In this menu we select the pictures we want to stack or a folder that contains them. We should also deselect the 'Blend Images Together' option. Next we press OK.

We have to wait for the operation to finish (the process duration depends on the number of pictures, their size and format and your computer's processing power), but when it does, we get a new Photoshop project with all the images arranged in layers and aligned in relation to one another. Photoshop compensates for slight movement and even for the difference in magnification resulting from focus shifting in extreme magnifications. Pretty impressive stuff.

By the way, if you find it more convenient, blending can be done manually in Photoshop by loading all the pictures into layers (with the Adobe Bridge software, for example), selecting all the layers and using Edit -> Auto-Align Layers. After that you can keep working as described.

When we have the stack series on different layers, all that’s left to do is to select all the layers and go to Edit -> Auto Blend Layers (making sure the 'Stack Images' option is selected), press OK and wait again.

When we apply auto layer blending, Photoshop detects the focused regions of every picture and unites the best-focused parts into one layered project. But now, the layers are masked to only show the focused parts selected by Photoshop. When we merge the layers, we get a focus-stacked image.

The final, focus stacked and processed result. See how all the interesting parts of the head are in sharp focus, from the front of the proboscis to the eyes. I saw no need to continue the stack to include the further parts of the fly: it would just look unnatural and draw attention from the more important parts of the portrait.

Usually, the result isn’t perfect. Sometimes you have to crop white edges resulting from automatic alignment or fix places where the software couldn’t recognize the layer it should have used, but after a few adjustments we can achieve a shots with a depth of field unobtainable in any other way. After stacking, we can apply all the post-processing we usually do on our macro images.

Some final notes:

  1. You might find that it’s better to change the focal point by moving the lens physically back and forth rather than using the focus ring. This is because changing the focal distance in extreme magnification ranges will affect subject magnification drastically, resulting in compositional changes across the series. Note though, that a focusing rail isn't always sturdy enough to allow sufficient stability in field conditions (especially when shooting at extreme magnifications), so use it with great caution. Nowadays, I personally prefer focus-shifting to using a rail, for both convenience and stability reasons. Photoshop’s auto align option makes up for all shifts in magnification and composition.
  2. One can rightfully think of focus stacking as an equivalent to the HDR technique, with focus bracketing instead of exposure bracketing. I agree, and consider these techniques to be members of the image-combination family, so prevalent in the digital photography process today. I even use both simultaneously in landscape photography, when very high contrast appears in conjunction with near and far subjects, requiring focus stacking.

    This robber fly was warming its flight-muscles. To obtain this shot I had to combine two different captures: one with the fly buzzing its wings, one with the wings still, since the fly’s head was constantly vibrating during the shot with the moving wings. This is not exactly focus-stacking, but my point is that we sometimes need to combine different exposures to get a more natural-looking, more appealing result.
  1. Many people ask me if I think focus stacking is 'natural'. I’ve thought quite a bit about this question, and I can now say that I do think it’s natural, at least as much as flash photography, high-ISO shooting or any other kind of digital photography technique is natural. Your camera sensor never sees like your eye does, and I suppose if the eye had the same close-focusing abilities as the macro lenses, it might have been able to see something close to the results we get through focus stacking. 

For more information on macro photography take a look at Erez's other articles:

Erez Marom is a professional nature photographer and photography guide based in Israel.
In July 2013, Erez will lead his 'Macro and More' Costa Rica workshop, where he'll share his techniques and experience to help you shoot incredible macro, wildlife and landscapes in one of the most fascinating and biodiverse locations on earth. See Erez' amphibian gallery here.
You can follow Erez on his Facebook page, 500px and deviantArt.