What is a scanning probe microscope?

It's a microscope that builds images of physical things by poking them in lots of places with a probe. Instead of illuminating a specimen with photons and then collecting the ones that bounce back all at once with an image sensor, a scanning probe microscope (SPM) collects the measurements it needs in order to give you an image one by one. While this approach sounds like a step backwards (maybe a throwback to the first scientific instrument - the poking stick), it actually provides many very cool benefits. For example, your resolution is no longer limited by the diffraction limits of light so it is possible to take images of really small things, like atoms! Here are carbon atoms in graphite, as imaged by a scanning tunneling microscope (a type of SPM):

Big benefit #2 of SPMs comes from the fact that you can get really creative with the probe. The image above was generated by measuring the tunneling current between an electrically conductive tip and the sample of graphite. But a different type of microscope, the atomic force microscope, generates images by measuring how much the sample deflects the probe at each point. That is, it measures the force that the atoms exert on the probe at every point in the area of interest. Other probes are designed to measure heat, capacitance, chemical nature, or a host of other properties. This makes SPMs an extremely flexible tool for doing science on a small scale.

The last major benefit is that SPMs are not limited to just looking at very small things - they can make very small things too. To see how that can be, imagine the probe as the cutter on a CNC mill. By allowing the tip to interact with what is under it the SPM can be used to precisely modify nanostructures. For example, IBM famously used one to write their name in xenon atoms on nickel in 1990:

Why?

A great deal of cutting edge research nowadays in many fields, like microelectronics, biology, and material science to name a few, are only possible thanks to scanning probe microscopes. They, along with a handful of other instruments, are the Swiss Army knives of nanotechnology. I believe that a great number of our achievements as a species this century will trace back in part to the fantastical ability of SPMs to precisely measure and manipulate matter on the atomic scale. As a result, I believe that their commoditization would accomplish two great aims: 1) Lower the barrier of entry for development of nanotechnologies. 2) Speed our progress towards further technological revolutions.

How?

Scanning probe microscopes are generally extremely expensive instruments found at universities, only operated by crufty ex-industry engineers or twitchy, sleep-deprived PhD candidates. Making them cheap enough to show up on the desks of hackers and makers seems infeasible. But there are good reasons to think it can be done:

1. It has been done before, multiple times and by different people. But not yet in a robust, reproducible way that would have direct impact in science and engineering.
2. Lasers, optics, microprocessors, sensors, and analysis tools are all free or cheap these days. The design of Automatic Jack leans heavily on the great resources that have been brought to bear in mass-manufacturing of high technology goods.
3. Modern computer-aided rapid manufacturing makes putting the pieces together much easier and improves the reproducibility of designs.

Challenges

1. Touching individual atoms takes structures on the order of individual atoms. Whether they are physical probes or light waves, they need to be infinitesimal.
2. To get atomic-scale data from probes takes mechanisms and electronics of great finesse. Atomic force is measured in probe deflections of tens of angstroms and tunneling current is in the range of pico or nano amps.
3. A probe interacting with a single atom returning clear data above the noise is an exciting achievement, but to do useful work - imaging or manipulation -...