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kaszz writes:

Holographic microscopy has been made a reality that can create 3-D images of living cells, almost in real time, and track their reaction to various stimuli without the use of contrast dyes or fluorophores.

The resolution is less than 100 nanometers using a low-intensity laser that scans the sample, numerous images extracted by holography are captured by a digital camera, assembled by a computer and "deconvoluted" in order to eliminate noise.

As a comparison the diameter of the DNA helix is 2 nanometer and a myoglobin protein is 4.5 nanometer in diameter.

DOI: 10.1038/nphoton.2012.329 "Marker-free phase nanoscopy"

(From 2013 but still very interesting as it enables researchers to essentially "debug" cells!)

A more recent article at phys.org describes the hardware and software used to create the images:

An EPFL spin-off company, NanoLive, has developed the 3D Cell Explorer first-ever microscope that allows users to see inside living cells without any prior sample preparation, by using MRI-like technology and proprietary software that uses holographic algorithms.

The microscope is called the 3D Cell Explorer. It combines state-of-the-art hardware with cutting-edge imaging software to record stunning 3D images of entire living cells within seconds and with a higher resolution than any conventional microscope available in the market. The device works as an MRI scanner, taking photographs at different depths across the cells. The photographic "slices" are then recombined using clever holography software that digitally "stains" the cells, labeling its different parts. The result is a high-resolution 3D image of the cell that can be rotated and explored in depth.

Original Submission