Design and Characterization of a Microfluidic System for Scanning Transmission Electron Microscopy

Abstract

For years it has been a goal to image biological specimens in liquid in the electron microscope, avoiding possible artifacts introduced by sample preparation procedures. Here, I present a microfluidic system that allows for the imaging of gold labels in a whole eukaryotic cell in liquid in a Scanning Transmission Electron Microscope (STEM). The system consists of two ultra-thin silicon nitride windows, supported by silicon microchips with a spacer layer between them. They are placed in a modified STEM sample holder, which seals the sample from the vacuum of the STEM, and incorporates tubing to and from the sample, which connects to a syringe pump, allowing for fluid flow. A bypass channel around the chips allows for rapid fluid exchange.

In order to optimize the process of assembling the device, I experimented with growing cells on the microchips under different conditions. Then, I calibrated an equation to model the flow through the entire system, using results obtained from fluorescence microscopy of microspheres flowing through the system. I also captured images of moving 30 and 100 nm gold nanoparticles in liquid in the STEM. I found that despite influences from Brownian motion and possible charging effects of the STEM, both the light and electron microscopy flow data match the calculated flow velocity within an order of magnitude. The difference can be explained by a change in the bypass channel depth on the scale of microns.