Macro Focus Stacking

While live music is still my primary photographic activity, over the past 18 months I have started dabbling in the world of macro nature photography. It happened to coincide with my switch to Olympus digital cameras, which I’ve written about previously. It wasn’t a field I was overly interested in, but a friend of the wife asked if I would photograph the wildflowers on the local common for a book she wanted to write. It was at the end of pandemic lockdowns, summer was on its way, and live music was only just starting to happen again. Always being up for a challenge, I said, why not? So I purchased a used macro lens (M.Zuiko 30mm f/3.5), put it on the camera and off I headed, with little to no idea of what I was doing or what I was looking for.

I’d occasionally passed the common in question, an expansive piece of public land in south London, while on the bus and thought it was simply a weed-strewn wasteland. However, after my first foray I began to have a completely different opinion. What I had been led to believe were weeds were, in fact, wildflowers, and what I had perceived as barren wasteland was alive with them. Hundreds of different varieties in assorted sizes and colours.

It was a complete contrast to the dark, noisy, crowded environs I usually frequented. This was sunshine, solitude and silence (well, relatively, the noise of traffic was still audible). I was out in nature, discovering new things, including shooting macro/close-up photography. Strictly, it wasn’t true macro photography because I rarely went for the 1:1 that defines it as I needed to show the whole flower and the leaves to help with identification, which was the purpose of the book.

I covered a lot of the common, which is divided into seven distinct areas, but did not do it as comprehensively as the project required. The intention was to restart in the spring of the following year and get whatever I had missed and reshoot some of the ones from my earliest attempts. However, nature had other plans (if nature indulges in that peculiarly human activity) and we experienced one of the UK’s hottest, driest summers on record, which resulted in a severe lack of the usual abundance of blooms. 

My new interest in taking a closer look at nature also coincided with a rekindling of my interest in fungi that began at the end of the 1970s. It turns out that Mitcham Common has an abundance on fungi – around 130 identified species according to an ecological survey carried out in 1984 – and with the arrival of autumn they would be fruiting into mushrooms. So while there were no flowers, as such, the heavy rainfalls we’d been having, along with the falling leaves was encouraging the mushrooms to appear and do their work. I made half a dozen visits, scouring the undergrowth for mushrooms and other fungi, and found many, most of which I couldn’t identify, from ones the size of pinheads growing on leaves up to saucer size. 

On my first couple of visits I was only using single focus shots with my Olympus OM-D EM-1iii and 30mm macro lens, stopping down the lens as much as practically possible for maximum depth of field. Using a Micro Four Thirds camera for this is ideal because of the shorter focal length lenses allowing for greater depth of field, and the fantastic in-body image stabilisation (IBIS) making it possible to hand hold shots at much slower shutter speeds than would be with larger format systems. The camera’s weather sealing also meant there was never any worries about putting the camera in damp grass. After watching some YouTube videos about macro photography I found out that Olympus cameras are very adept at focus bracketing and in-camera focus stacking, even handheld. Unfortunately my hands aren’t as steady as they used to be (I blame the cold), so I added a small desktop tripod to my kit for more stable bracketed shots, along with a small LED photo light for the fungi hidden in undergrowth. I already had a cable release. And so began my first attempts at focus bracketing. I opted for that method over focus stacking as it was not only quicker but also offers more control. However, the images need to be composited afterwards. 

Setting up focus bracketing is easy enough and is available on most pro and semi-pro M4/3 cameras (Lumix and Olympus/OM System). In the menu, it’s under bracketing in the camera settings, but that can differ slightly, depending on the camera model. When you dig your way through the settings you just need to set two things, the number of shots (up to 999) and the differential (the amount of space between each shot/focus change), which will depend on what you are shooting, the lens focal length and the aperture used. This automated bracketing only works with autofocus lenses. Focus bracketing can be done with manual lenses, but the focus will, of course, have to be adjusted manually. While the focus bracketing can be done handheld, thanks to the amazing IBIS in Olympus cameras, whenever possible I prefer to use a tripod and cable release to avoid any unnecessary camera movement. This makes the job of compositing afterwards a lot simpler for the computer. Olympus/OM System cameras also offer the option of in-camera focus stacking. This is essentially the same as focus bracketing except the camera produces a final JPEG composited image as well as giving you all the individual files. It also works slightly differently in that, with bracketing you select the focus point nearest the camera and it shoots however many frames you set, moving the focus point away from the camera. With the focus stacking option, you set the starting focus point about one-third of the way into your finished image and the camera then starts closer to the camera and moves out. Focus stacking also only works with certain Zuiko lenses, whereas bracketing will work with any autofocus lens, ideally a M4/3 one.

Because the compositing is being done in-camera, it takes longer than bracketing and is prone to errors when it can’t align the images if the camera moved slightly or the lighting changed during exposure. For these reasons I much prefer to just use bracketing and composite afterwards. However, the advantage of using stacking is you can tell at the time if there was an issue during exposure and either reshoot, or simply composite manually later leaving out the offending frame.

I have set focus bracketing to one of the custom settings buttons on my EM-1iii, and while I can adjust the two parameters before each shot sequence, I tend to use the same settings all time. That way I know how many shots and which shots to composite. If you do a reshoot or alter the number of frames, it is a good idea to take a blank shot between each sequence, but remember to switch off bracketing, hence the use of a custom setting so that it can be easily done with the turn of the dial.

I always shoot everything in RAW format, because of the increased exposure latitude and the ability to make non-destructive adjustments afterwards. However, I would recommend making sure you get the exposure and white balance correct in camera, and not use auto settings for these. This is to save time when it comes to compositing, especially if you have a large number of frames. While most of the standard image editing software will composite RAW files, you don’t end up with a RAW file. This means that you will have to batch edit all the RAW files before compositing.

I have tried a variety of popular and readily available image editing programs to composite the bracketed images and will run through each of them giving their pros and cons.

OM Workspace

Workspace is free from OM Systems for Olympus/OM System users. You do need a camera serial number to download it. The price is one of its major positive aspects. You select the images you want to composite and can batch process any adjustments you want to make to the RAW files. It’s then simply a matter of selecting Tools > Composite Images > Focus Stacking, then highlight Adjust Image Position, especially if it was handheld sequence, and letting it do its thing. The results are very good. OM Workspace isn’t the speediest of RAW processors, even on Apple’s new M1 and M2 chips, although the composite is reasonably fast. The main downside is it has the same restrictions as doing in-camera focus stacking and will only work with the same specific lenses. 

Affinity Photo 2

Next along the price scale is Affinity Photo 2. This is the updated version of the very popular alternative to Photoshop. Until January 25 2023 it is selling for only £35.99 (normally £59.99). Or you can buy a universal licence (Mac, Windows, iPadOS) for the whole suite of Photo, Designer and Publisher for £89.99, which is fantastic value for artists and designers. That’s a one time purchase that includes free updates until version 3. The RAW processing tools of Affinity Photo are still fairly rudimentary compared with dedicated RAW processors, and there’s no straightforward way to batch process RAW files, or copy the settings from one image to the next. However, when it comes to focus stacking it is very easy. You select File > New Focus Merge, choose the images you want to merge and it automatically aligns and composites them quickly and well. Although the final image is no longer a RAW file, Photo does non-destructive adjustments as layers, which you can either delete, hide or re-edit. You can then save the file in the native .afphoto format for further editing at a later moment, or you can export to JPEG or another format. This is an excellent option for focus stacking, and image editing in general. 

ON1 Photo RAW

ON1 positions itself as the Lightroom/Photoshop alternative, combining both programs into one affordable package. The basic software is £102, but they are always have sales and offers. The program has a new version every year, but whatever version licence you buy will not expire, and includes free updates for that version. It is packed with AI enhancements such as NoNoise, masking, resizing, HDR and more, as well cataloguing like Lightroom. Stacking the images is simply a matter of highlighting the images, clicking the Focus icon in the righthand size of the software, which brings up a window with several options. These can be adjusted on a trial and error basis, however using the default settings does seem to leave a lot of artefacts in the final image, which none of the other programs I tried did. Although it is packed with features for a great price, I’ve never been really satisfied with the results I got from anything I’ve done with it, stacking or otherwise. Other people love it. So each to their own.

Adobe Photoshop/Lightroom

I have a bit of a love/hate relationship with the grandaddy of image editors. Where newcomers such as Affinity Photo shine is they have constructed new architectures from fresh code on the foundations built by Adobe. However, that long history does mean it has a lot of baggage and is not as streamlined as the others. There is no doubt that Adobe Camera RAW (ACR) is a solid RAW processor, and Photoshop is a powerhouse image editor. The subscription model is questionable, but the Photoshop/Lightroom Plan for a tenner a month isn’t excessive, except that you have nothing to use at the end of the first year’s contract, unless you continue to pay, whereas, for an extra £20 you could buy the whole Affinity suite to use for as long as you want (or for £30 less at the moment). When a software becomes a verb you know that it is well established. But this isn’t supposed to be a whinge about Adobe, and I still haven’t been able to cut the ties as ACR is the best option of editing my live music photos, as I’ve outlined in a previous blog post. This is about focus stacking, and unfortunately the Adobe way it is a rather convoluted process.

Firstly, you have to open the RAW files in Lightroom, it is even more complicated if you use ACR directly in Photoshop. Batch adjusting the files, if needed, is easy with Lightroom, but from there on it is a bit of a juggle. In the Lightroom menu, go to Photo > Edit In > Open as Layers in Photoshop, which will take you to Photoshop (obviously). Select all the layers and then Edit > Auto-Align Layers, followed by Edit > Auto-Blend Layers, which will create the merged composite image on a separate layer. You can then save this file as a TIFF or PSD. To export it, you will want to convert it from 16 bit to 8 bit then Save a Copy as JPEG or whatever format and size you want. There’s no doubt the finished image is good, but what a faff to get there.

Helicon Focus

This is a dedicated focus stacking software. It’s a simple-to-use, very fast one-trick pony. If you do a lot of focus stacking then it may be worth having, but you will still need another image editor for anything else. It does require an additional RAW processor, such as Adobe DNG or Apple’s built-in one, to work with RAW files. It’s a paid shareware that has annual licences from $30 to $65, or lifetime ones from $115 to $240, depending on the feature set. Even the cheapest option is more expensive than Affinity Photo, which, for my money is far better value. However, a lot macro shooters use it. Again, each to their own. 

There are other dedicated focus stacking programs that I didn’t investigate, and the other two popular RAW processors, DxO PhotoLab and Capture One, don’t appear to be able to focus stack.

All the options I’ve outlined will do the job. I wouldn’t bother with ON1 because of the artefacts issue. My first choice is Affinity Photo, with its match of excellent image editing and great price. OM Workspace is free, but limited to Olympus/OM System users and specific Zuiko lenses. If you’re already a Photoshop/Lightroom user then it will do a good job in its own convoluted way.

As someone new to macro photography, finding out about focus bracketing has taken it to a new level, especially with these great software solutions taking all the hard work out of compositing them. I’m looking forward to further exploring the world through a macro lens, and hope this article will help if you are also new to it.

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