Most of those images are triumphs of postprocessing, rather than particularly impressive microscopy.
Take the first one, for instance. If you visualize that in the standard way, it'll look like a bunch of light grey dots on a dark grey background. But if you take the data, convert it to a 3D surface plot, grossly exaggerate the vertical axis, choose some pretty colours and a sufficiently dramatic angle, you get something that looks cool enough to publish in Wired.
Take the first one, for instance. If you visualize that in the standard way, it'll look like a bunch of light grey dots on a dark grey background. But if you take the data, convert it to a 3D surface plot, grossly exaggerate the vertical axis, choose some pretty colours and a sufficiently dramatic angle, you get something that looks cool enough to publish in Wired.