When photographing small organisms, stacking is the only way to show a reasonable level of detail. Without it, you’re not going to be worrying about slight differences in the proportion of the antenna segments, you’ll be lucky if you see the antenna at all.
I do a LOT of stacking, and I mean a lot, and I was about to write a long answer in defence of the technique. But then I thought, bracketing/stacking is not the problem here, neither is denoising, or even fiddling with white balance or cloning out disturbing elements in the background. It doesn’t matter whether you take photographs with a smartphone or a high level camera and lens. When posting on iNaturalist, what matters is that whatever you do is aimed at making the image as close as possible to the original specimen being photographed with as much detail as possible in view. And that requires care and awareness.
Now, you could make it obligatory to disclose focus stacking, but that would only make sense if you also included details of the process used… because a quick in-camera focus stack doesn’t necessarily have much in common with a carefully bracketed set of images stacked with attention in dedicated software. And it would only make sense if you also oblige observers to state the brand and model of smartphone (because nowadays every model does its own behind-the-scenes processing), or type of camera and lens, what post-processing was done with what applications and what settings… everything can modify the accurate rendering of colours, details, proportions, unless performed with awareness… there’s that word again.
At the end of the day, I believe that is the only thing that actually matters… the awareness of the observer that care and attention is necessary to render the image as close as possible to the observed reality and the awareness of the identifier that to varying degrees said image is not reality.
I fear that when we get to the level of expertise required to ID certain arthropods based on the proportion of the antenna segments (for example), if the IDer has doubts, the only valid way to try and resolve them would be to contact the observer and ask for more information on the process involved. Is that going to happen? Will there be a response? Who knows… but I really can’t see any other valid way forward.
I generally agree, but disagree that
would be ok. This would seem to go against iNat’s definition for what types of manipulation are allowed: https://www.inaturalist.org/posts/118284-new-tools-to-flag-and-assess-evidence-on-inaturalist which apply not just to the organism but also the scene: “Because images and sounds are evidence that may be used for research or conservation, they should accurately reflect the organism and the scene.” Some of the provided examples note that removing elements of the picture via photo editing tools (other than cropping) isn’t ok, and clone tools are generating parts of a scene programmatically that aren’t there in real life.
Quotation in part:
Not Acceptable
-
Removing or replacing elements from the organism or the scene
-
Use of generative fill
-
Replacing the sky
-
Cloning or stamping, except to remove sensor dust or backscatter
Sorry, perhaps I wasn’t clear in my original post… in the context of iNaturalist, I absolutely agree. I meant that to be intrinsic in…
I suppose I should have said “original scene” rather than “original specimen” 
.
Hi. Sorry for the delay (house guests have taken over my computer ‘lair’).
I primarily have used the Nikon P950 in 4K video mode to do video-frame stacking. Here’s some examples (all handheld):
In the end though, I have pretty much stopped with stacking shots for several reasons:
- for me, it seemed only practical with relatively slow, stationary, or low-movement subjects. With insects and such, that’s a very small percentage (especially in the field!)
- once I got a decent macro lens for my Sony Alpha (a Laowa 100mm 2x) I found that I could close that right up to f22 and with a judicious amount of soft flash fill-in, capture both moving and stationary things with just about the same DOF and far less fiddling, than working with stacks.
- stacking enthusiasts seem to rely heavily on captured and euthanized/anestheticized specimens, and I just didn’t want to get into that (I like to also capture natural action where possible)
Still, if you don’t have the budget for a good camera/lens macro combo, you can still ‘milk’ a lot of detail with a little stacking experimentation. I have also had success using my smartphone (Samsung Galaxy Note 8) to take short 4k videos with a clip-on ‘microscope’ lens. That got me these:
I think it as basically a given that if you see a macro photo with any depth of focus that it is made with focus stacking. Disclosing it is great but if you know much about macro photography you can consistently tell when it has been used.
Just a quick clarification… I am a great stacking enthusiast, but I have NEVER captured, killed, anaesthetised, immobilised or deliberately injured or damaged in any way any form of organism just to take an image for my own enjoyment or to satisfy my own curiosity. And I never will. OK, disclaimer done. Happy observing, photographing, stacking, IDing or whatever 
.
Agreed here, although this doesn’t help less experienced users.
Due to environmental conditions I use Olympus TG/ OM TG cameras with their inbuilt photos stacking in macro mode, where despite the above warnings about image veracity, I see very little size distortion. The TG stacking automatically provides a choice later of the first image in the stack or the stack image, to make veracity comparisons dead easy. Most of the time I take the stack image, unless the target is moving, which for inverts or plants in high wind, happens often enough.
I’ve never run across this problem, so, since I sometimes use Zerene Stacker instead of in-camera stacking, I emailed them to ask if this is an issue. I don’t think he’ll mind me quoting the detailed, and quick response:
The question is more subtle than it might seem. Please excuse an answer that may be more than you want to know!
The alignment method used in Zerene Stacker models frame-to-frame change in appearance as a combination of translation (shift in X and/or Y), rotation, and scaling. Scaling is done by a single factor that is applied equally in all directions. That single factor for scaling guarantees that there will be no change in aspect ratio for any single frame.
However, certain stacks might appear to have a change in aspect ratio, caused by measuring length and depth across frames at different depths.
A simple example is that if your subject is a triangular wedge with uniform thickness, oriented with apex toward the camera and base farther away, then with most optics the thickness of the wedge at its apex will appear to be larger than at its base that is farther away. Of course this case is “just a simple matter of perspective”, but that aspect is easily overlooked when you’re trying to take precision measurements of a 3D subject that was photographed with ordinary optics and default settings for the software. The moral is to beware scale bars in stacked photos – they’re probably valid only in one depth plane!
A more subtle example is that with some combinations of subject, scene layout, illumination, and optics, the computational alignment process can be led astray by how features change appearance as they go in and out of focus. Especially with high magnification images such as from a microscope, it’s common for this effect to result in accumulated error in shift/rotate/scale estimates. At high magnification you can probably turn off the attempted corrections for rotation and scale, but if you’re using a focus rail and not a microscope focus block, then probably you’ll have to leave X and Y shift corrections turned on in order to get a rendering with details rendered crisply. But with X and Y shift corrections turned on, you’re vulnerable to accumulating error. If it happens that say shift accumulates in X, but not in Y, and you measure the distance between points at different depths, then distances in X in the rendered image may be larger or smaller than corresponding distances in Y.
Circling back to your original question, the issues that I’ve described for Zerene Stacker also apply to Photoshop. In addition, Photoshop gives you more opportunity to mess up because it provides several different geometry models for stack alignment.
In Photoshop, when you select Edit > Auto-Align Layers, the equivalent to Zerene Stacker’s default is named “Collage” (described by tooltip as Allow image rotation, scale and translation). The equivalent to Zerene Stacker with rotation and scale not checked is Photoshop’s “Reposition” (Only allow image translation). Those two are pretty safe – basically to the same extent that Zerene Stacker is.
However, the other four options in Photoshop – notably including “Auto” – allow more complicated transformations that can change aspect ratio even within an individual image. Those are useful (required!) for aligning layers in a side-by-side panorama, but they should be avoided for focus stacks.
So, getting back to that iNaturalist user, there are at least two strong possibilities for what happened. First is that they might have innocently left Photoshop’s setting on “Auto” when doing the alignment, and something about the details of their stack led Photoshop to decide that the best transform was to alter aspect ratio even for individual frames. Second is that they might have measured distances in different depth planes, and encountered one of the problems that I describe above. No doubt there are other possibilities, but nothing likely occurs to me at this moment.
If you can point me to the particular iNaturalist post where the user mentioned this issue, perhaps I can make a better guess.
I hope this helps. Please write again if you would like to discuss further or if you can find that iNaturalist post. Thanks!
Best regards,
Rik Littlefield
Zerene Systems