I've been running into the limitations of Photoshop when processing focus-stacked images for my greenhouse blog. Focus stacking involves taking a series of images focused on different parts of a scene, usually from near to far, and using software to combine the in-focus parts of the various images. Newer cameras have this function built in; older cameras you need to select the focus points manually. After some internet research I found five practical ways to do focus stacking with my particular setup, which is a Canon R5 Mark II camera (Canon's flagship) with a 100mm RF macro lens.
- Photoshop (my current method)
- Canon in-camera Depth Compositing
- Canon Digital Photo Professional program version 4, Depth Compositing
- Zerene Stacker program
- Helicon Focus program
To start the testing, I shot two new sequences of my plants that I thought would provide a good workout for each of the methods. All of the images were shot in AV mode at f/8, ISO 100, exposure time set by the camera. I shot the images in our kitchen using the countertop as a background and didn't use any supplemental light, so exposures were several seconds and a tripod was mandatory. If anyone happens to read this and they are wondering "Why didn't you...?" then they can do their own testing. Most of my focus-stacked images are macro images of plants, and I don't want the bother of setting up lighting. This is real world testing for me and I don't know or care what anyone else's needs are. Zerene and Helicon both have 31-day trial programs, DPP comes included with Canon cameras, and I'm guessing Nikon and Sony have something similar to DPP. Figure out what works for you. The subjects are:
- An Echeveria Neon Breakers. I figured the overlapping leaves and crinkly edges would provide a real challenge. I shot 48 exposures with focus steps of 2.
- A little Powder Puff cactus with a flower. Photoshop chokes on the flower, I think because the background has higher contrast. I shot 18 exposures with focus steps of 3.
The focus steps are the amount of change the camera lens does between images as it moves focus from near to far. A lower number means the images are closer together in focus, and a higher number potentially means there would be bands of the image that are out of focus. I usually set it at 3 or 4 and that has always worked.
The in-camera method is quickest because it produces an image immediately. But the output is only JPG. Also, there is no opportunity to select which images to use. All of the images in the stack are included. In the first test image, there was extensive haloing around the Neon Breakers leaves. I wasn't sure how many images to take using steps of only 2, and it turns out that 48 was way too many. Fourteen was the right number, omitting the first image (the front of the pot) and the last 33 (the background).
DPP took 21 minutes to process the 48 images of Neon Breakers. There are only a couple of parameters to fiddle with and it is a hands-off process after that. I would call the result identical to the in-camera processing, which makes sense since they both use Canon algorithms. Reducing the number of images to the 14 which were actually needed cut the processing time to six minutes, and eliminated much of the haloing. There is none around the back leaves with a distant background, but still some around front leaves where they are close to other leaves. I'm actually impressed. I exported it as JPG but I found later it can be saved as 16-bit TIF. (And yes, the plant is that blue.)
Photoshop required a few more mouse clicks, but only took four minutes to process the 14 source images. Alas, in my opinion the image was inferior to the DPP version. There was stronger haloing around the front leaves.
Next up was Zerene Stacker. It can't handle RAW CR3 files so I used JPG. It took three minutes to stack and save two images using different algorithms, PMax and DMap. According to the documentation, "PMAX excels in preserving fine detail and sharpness, while DMAP is ideal for smooth transitions and natural results." In my opinion, PMax produced the better image of the two. Both methods have weird artifacts scattered around the image in the form of short lines. Except for these artifacts, Zerene produced the best image overall. (How was the play, Mrs. Lincoln?) Condescending interweb twits claim these are dust spots that somehow become trails as the focus changes, ignoring the fact that dust spots are dark and fuzzy. Or maybe they are stuck pixels that trail. In my admittedly brief experience, the stacked images taken using a tripod vary much less than the length of these artifacts, the trails follow different angles, and they only show up in Zerene and not in the other methods. Just look at the image. The two trails are at different angles, which to my way of thinking would be impossible if they were stuck pixels trailing due to camera movement. Just say it out loud, "It's a bug."
Later I went back and converted the CR3 files to TIF, processed them through Zerene, and exported the result as 16-bit TIF. I think this helped with color and detail incrementally, but I'm not 100% sure. The streaks were less apparent but were still there. For the supposed benefit of using TIF over JPG, that means a couple extra steps for me and more files to clean up at the end.
Finally, Helicon Focus took only three minutes to process and save the images using three different algorithms, Weighted Average, Depth Map and Pyramid. I loaded the CR3 images and the output was DNG, which according to my way of thinking gives Helicon an advantage over Zerene. In my opinion, the Weighted Average was the best of the three, and in fact produced the best image of any of the methods. (And didn't have any streaks.) Pyramid produced a similar result, but from the description of Depth Map I would not use that one for my typical subjects.
I already had a winner in mind, but I wanted to see how the various programs handled the cactus flower. I determined that it was appropriate to use all 18 of the images that I shot so I just looked at the in-camera processing and did not use DPP. The flower is not in focus and that is all I will say about that. Same with Photoshop. Let's move on to the contenders.
In Helicon, all three algorithms almost got the flower into focus, with some haloing. I really couldn't pick which of the three I preferred, but none of them were as good as the Zerene image. Or should I say, most of the Zerene image.
Zerene got the flower into focus with almost no haloing with the PMax algorithm, but the little streaks in the background remain. In my limited use of the program, PMax always seems preferable to DMap for my subject matter, and both are afflicted by the streaks. Here is the Zerene 16-bit TIF image with the streaks cleaned up.
Using the Photoshop Remove tool to hunt down the streaks reminded me of the old days when my Canon 1D Mark I sensor would get so dirty that I would spend hours cloning out dust spots. Real dust spots. One of the last images I shot with that camera was "Little Brothers" in 2004, and it required quite a bit of cleanup before I sent it off to the publisher. I don't want to start doing that again on every image.
These are my conclusions:
- Zerene and Helicon produced the best results. DPP took third place (surprisingly) ahead of Photoshop. But for each stacked image DPP produces, it leaves a folder of large (~25Mb) .bin files, something which needs to be cleaned up when you are done. In-camera processing is identical to DPP and is quicker since there is no user-involved processing, but you have to know ahead of time how many images to shoot. That's often not easily determined.
- Helicon did the best on the Neon Breakers.
- Zerene did the best on the cactus flower, but those streaks are annoying.
- Both commercial programs have different levels of licensing, and the cost is similar enough that it is not a factor in which one to choose. Zerene calls their tiers Student, Personal, Prosumer and Professional for $39, $89, $189 and $289 for lifetime licenses (no yearly option). Helicon calls its levels Lite, Pro and Premium costing $30, $55 and $65 for one year; $115, $200 and $240 for lifetime.
- Helicon can handle Canon CR3 files and can output DNG files. Zerene only deals with JPG and TIF files.
- Helicon's interface is cleaner and appears to give more customization options which I did not fully explore. I just want something that works.
Note: All of the images produced by the various stacking methods were run through the Photoshop RAW filter for the usual color and contrast adjustments, then were cropped and saved as JPG. This is part of my workflow and is not affected by which program produced the stacked file. I'm not dumping Photoshop, just its focus stacking function.
In conclusion: Helicon nailed it on the Neon Breakers but didn't do great on the flower. There are a lot of settings in the program and maybe there is a combination that would handle it better. Zerene did the best job on the flower, but I had to clean up the streaks. I want to like Zerene, BUT, those streaks. I have a month to decide. This is something I've gotten by without for my 28 years of digital photography, but I am shooting lots of macro images of my succulents now. I'm leaning toward Helicon, but I may just stick with DPP to replace Photoshop for this function and get used to its limitations and to deleting .bin files.
March 28: Things have taken a surprising turn. I decided to use Helicon as a default for the next few days, but it crashed a several times this morning. It is a Beta, version 9.0. They promised a lot of upgrades over version 8.3.11, so I threw caution to the wind and went with the Beta. I don't want to mess with downgrading to the supposedly-stable version, so I turned to DPP to do more testing. DPP version 4.19.10.0 shows a copyright date of 2024 so it is definitely not a Beta version. This image has a little bit of haloing, but compared to Photoshop's version the haloing does not have a hard edge and is thus less noticeable. And, I experimented with a tool in DPP called the Depth Compositing Editing Tool that can be used refine particular areas. Using this tool it would possible to bring the cactus flower into focus, eventually. It is a tedious process, like going back and removing dust spots in the old days or removing artifacts in Zerene images. It would take hours, but taking a few minutes to sharpen up a few areas in this image took just a few minutes.
In my history of using photography software, to me DPP has been like Lightroom, an object of disdain. (My dislike of Lightroom is another story.) But this DPP tool is useful and might be enough to swing me toward using the imperfect DPP program for this function rather than one of the other imperfect programs.





















Visiting was a mediocre Yankee team, six years removed from winning the World Series and nine years away from winning their next one. Twins pitcher Jim Kaat got the first two Yanks to fly out, but the third connected for a home run. It was my first major league hit, so to speak. Referring to the scoring instructions, next to the name "Mantle" I drew four horizontal bars (four-base hit) and a "7" (to left field) then circled all of it (run scored). The scoreboard flashed the message that it was the 528th home run of Mickey Mantle's career.