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They say it's a picture of atoms, but what are the atoms: the glowing yellow balls or the entire meatball including the darker red? If it's the meatballs, then why do some have apparently two nuclei?
Here's the public press release: https://news.cornell.edu/stories/2021/05/cornell-researchers-see-atoms-record-resolution
Here's the actual scientific article: https://www.science.org/doi/10.1126/science.abg2533
These images are generated from processing many out of focus images while scanning across the area. They use the differences between the out of focus images to compute what must have caused those differences.
So this technique is pretty far from being able to capture real time events as it requires capturing hundreds of images to produce a single computed image. The paper talks about how thermal motion of the nuclei is what now dominates the limits of resolution for this method.
There are other ultrafast imaging techniques that can capture essentially real-time chemical reactions, but I believe those don't come close to this spatial resolution.
Not 100% comparable, but synchrotron XRD allows for real-imaging of solid state chemical reactions and can, in a sense, resolve the unit cell structure of the crystal. However, what you get from an XRD is nothing like this "photo-like" image, but a diffractogram. I think you could probably re-create an image like this from a 2D diffractogram though, but I'm not sure.
I could be wrong, but I think XRD requires very pure crystals of sufficiently large size. That can help you ascertain the structure and composition of something you can synthesize and crystalize, but I don't believe xrd can image specific regions of interest like single doping sites like this article talks about.
Synchrotron XRD also has a major drawback in having a very significant equipment requirement that requires being able send samples away for analysis at a dedicated facility. That puts limits on sample preparation and stability time, as well as sharing beam time with lots of other groups.
It's been a while since I've read up on synchrotron xray diffraction though, so there could be workarounds for some of those limitation or I could be misremembering details.
You're definitely correct that getting sychrotron time is hard :(
On the first part though: Yes and no. XRD will tell you about things like strain and unit cell size distribution, so in that sense, you can't resolve a single doping site. On the other hand, if you have a reaction going on, or some dopant diffusing into your sample, synchrotron XRD is powerful/fast enough that you can "film" how the crystal structure changes in real time. That "film" will be a kind of average of many sites, but can still be focused to a relatively small region (don't remember exactly how small off the top of my head, but I believe we're talking nm-scale).