Is background blurring and retouching acceptable for microscopy images?

[ps72]

In the case of a photo of a lone organism on an otherwise empty microscope “scene”, am I allowed to make adjustments to the background for the purpose of removing or reducing the visual effect of in-focus dust/dirt/scratches and out-of-focus grey blobs of dust/dirt/scratches? I have read Which image and sound editing techniques are acceptable on iNaturalist? but I am not sure whether or not background blurring and retouching is allowed for microscopy images in such cases.

Example situation: I take a small bottle of almost-clear water from a pond and bring the bottle home. At home, I use a dropper to place a few drops of the water onto a glass slide. The microscopy equipment is not of the best condition, and there may be scratches or dust on the glass slide or microscope optics. I see an interesting organism through the microscope. For example, an alga or a diatom. Other than small out-of-focus grey blobs of dirt or dust, the organism is the only object in the field of view. I take a photo.

I then crop the photo, adjust its brightness, contrast, white balance, and sharpness. These are generally acceptable photo adjustments for iNaturalist. But what if I then:

• Blur to the entire background (i.e. blur the entire photo except the organism) so that the background dust/dirt/scratches become less apparent?
• Retouch parts of the background using cloning or healing tools to remove background dust/dirt/scratches?

Would the answers be any different if the blurring or retouching removes in-focus dirt or scratches rather than out-of-focus grey blobs?

Below is an example of background blurring of out-of-focus grey blobs.

Before:

After:

Thank you for your help.

[Star3]

Would that fall under “replacing the background”?
It’s not entirely replaced, but it does seem risky for being similar.

Which image and sound editing techniques are acceptable on iNaturalist? : iNaturalist Help

Then again:

This comment from New tools to flag and assess evidence on iNaturalist · iNaturalist sounds like it may be fine.

[cthawley]

Technically, I think this would not be acceptable under the linked guidelines as: "

• Replacing the sky or background

• Cloning or stamping, except to remove sensor dust or backscatter"

are not permitted.

I don’t see why the changes you proposed are really needed to aid in identification, so it seems easy enough not to do them to me. Other users are likely to notice them and may wonder what you have removed or changed and have less faith that your photos depict reality.

That said, dealing with scratches on the optics seems at least similar in motivation to dealing with sensor dust to me (addressing imperfections in the photography system).

But I don’t see the value of bending the rules in a situation like this for something that doesn’t add value to the observation.

[tiwane]

Not too familiar with microscopy, but I agree this seems fine. Replacing the sky or removing elements of an in-situ shot seem quite different from editing the background of a microscope image. It’s already understood to not be the organism’s habitat, I imagine.

[paul_dennehy]

The only downside I can see is that the background “noise” that’s being removed might also be interfering with the appearance of the organism itself. ie if I post a ciliate with some little blobs in it, you might interpret those circles as either organelles in the organism or as an artifact of the microscope, depending on whether you can see the whole untouched image. For example, here’s a Loxodes I saw the other day:

What’s this odd pale streak through the cell, anything important?

In context, it’s obviously part of the “background dirt”:

Probably not an issue 99.9% of the time, but something to consider, especially if what’s being removed are streaks or other imperfections on the coverslip, which will always carry over into the image of the organism itself.

[AdamWargon]

I think for any observation, notes from the observer are always valuable. It doesn’t hurt to say,

“This is a drop of pond water on a microscope slide. I retouched the background, since it was full of distractions like dust and scratches. I did not alter the appearance of the organism in any way.”

That detailed explanation gives identifiers confidence in your observation, even if they notice some retouching.

Thank you for your service! We need more microscopic observations on iNaturalist! I was just reading @loarie’s post where he said that, “Birds represent about 0.6% of named species, but represent about 83% of all GBIF records since 2020.”

[annkatrinrose]

I think for any images that have been retouched to clean up dirt etc. it’s a good idea to post both the clean and the untouched versions. One clarifies which organism is the focus of the observation, the other shows what patterns in the image may be due to overlay with other stuff on the slide. Similarly for focus stacks I like to include at least one of the originals in addition to the Z-stacked image. Having a detailed description of how the picture was processed helps me remember what I did, as well as informs others that the image was modified and how.

[bioshots_jm]

I’m curious what this means for the removal of backgrounds when the background may reveal a location that you don’t want revealed (e.g. research site, homes, etc.). If the background is edited to hide things like that and the original background provided no real information about habitat of the animal and the organism itself isn’t affected by the edit, is there any issue?

[tiwane]

How are you removing it? I say drawing over it or blocking it out is one thing. Asking a model to generate a different background is something else. With the former, it’s obvious that something’s been intentionally masked and no new information is being added. With the latter, you’re asking a model to make up a realistic-looking background that may be perceived as the actual scene, which is not OK.

[cthawley]

Yes, I think scribbling over something in the background MS Paint style to “censor” it, or pasting a square on top of something or similar would be fine - it’s obvious what the general change was. Leaving a note to explain it would also be good. But using some type of “magic eraser” which will replace a person /housewith AI-generated background wouldn’t be ok in my mind.

[ltdbjd]

I think there are two different issues being mixed together here.

I agree that an iNaturalist photo should not misrepresent the organism being observed. If someone removes diagnostic structures, adds features, changes colors beyond accuracy, replaces the background in a misleading way, or otherwise changes the evidence in a way that could affect identification or the meaning of the observation, that is a problem.

But I do not think “the image must be shown exactly as found” can be taken literally. If that were the standard, cropping, zooming in, and focus stacking would all be prohibited. Even using a shallow depth of field in-camera would be questionable because it changes how much of the background is visible. Photography always involves choices about framing, focus, lighting, magnification, depth of field, and what is or is not included in the image.

For microscopy, I think the same distinction matters. A drop of pond water under a microscope often contains dirt, debris, air bubbles, algae, detritus, and other distracting material, and it’s no longer in situ. If the organism being observed remains accurately represented, and the edit is limited to making the image clearer or easier to interpret, I do not see that as the same thing as falsifying the observation.

That said, I agree with the posters who suggested transparency (e.g., AdamWargon, annkatrinrose). If the background has been blurred, retouched, or otherwise cleaned up, I think it is reasonable to mention that in the observation comments. Even better, when practical, upload both the edited and unedited versions so that identifiers can evaluate the evidence for themselves.

That is generally how I handle my own observations. I may take a wider photo to show the environment or general context, then take closer photos for identification, either by moving closer or by zooming/cropping. Those close-up images necessarily remove some of the surrounding background, but they are often much more useful for identification.

Coming full circle, perhaps the solution to ps72’s dilemma is to avoid the problem altogether. Instead of blurring the background and walking the tightrope between what is acceptable and what is not, crop the background out.

[bioshots_jm]

Ah completely agreed; I sometimes darken or blur backgrounds if they provide no information about habitat and show something I’d rather not have people seeing (through windows or showing details of a location for sensitive organisms). I don’t ever generate fake backgrounds - I wasn’t even aware people did do this other than for bird photos where they change the sky to look cooler for photography pages.

[cthawley]

I agree that cropping is often a good practice for many reasons and could be a good solution here.

I also wonder whether the “background” might also provide useful information for IDers much like habitat does in non-microscopic shots. The background could include info about other organisms present in the water, other characteristics of the water (organic debris, etc.) as aspects of the aquatic habitat. No idea if this would potentially be valuable to IDers of microscopic observations though…