A 3D Microscope for Thick Samples

Volumetric reconstructions with no moving parts

Most microscopes capture images that are only two dimensional. If your goal is to look closely at a thick sample, then typically your only choice is to just focus the microscope objective to a particular plane of interest and snap a photo. Unfortunately, the resulting image will only offer sharp information from this particular plane. Furthermore, light from above and below this plane of interest will mix into the image to reduce its contrast. To see the entire sample, you will have to refocus the microscope through many different planes and take multiple images in sequence, which can become burdensome.

Recently, we have figured out a way to capture and reconstruct an entire 3D sample without re-focusing or moving anything. Instead, we simply turn on different LEDs and capture multiple images, just like in Fourier ptychography. Then, we use a new algorithm to combine the captured data into a 3D "tomogram." The movie below demonstrates the type of volumetric data that we can capture with a thick starfish embryo sample:

Comparing our approach (the first sequence, in color) to standard microscope refocusing (the second sequence, in grayscale), you'll first notice that our technique recovers more detail (e.g., we can resolve new features). Second, you'll see that our technique offers a more accurate reflection of the actual composition of the embryo (e.g., its features appear and disappear as we scan through it, instead of simply changing from bright to dark or vice-versa).

We call our new measurement and reconstruction process "Fourier ptychographic tomography" (FPT, for short). Unlike standard tomography, FPT relies on the diffraction of light through the sample, as opposed to just its absorption. This allows FPT to measure very small changes in the index of refraction of primarily transparent samples, which are otherwise nearly impossible to capture without using interferometry (i.e., useing a phase-stable laser and a reference beam).