Virtual Microscopy – Turning Bystanders Into Players

Most researchers who use microscopes to view biological specimens are bystanders. They may initiate a reaction and witness its outcome but they can’t touch or manipulate the sample along the way. Watching from the sidelines isn’t acceptable to Richard Superfine, a physics professor at the University of North Carolina (UNC), Chapel Hill.

To transform bystanders into players, Superfine and a team of computer scientists, physicists, chemists, and biochemists at the Center for Computer Integrated Systems for Microscopy and Manipulation (CISMM), have developed a suite of imaging tools to immerse researchers in their experiments. They can visualize and manipulate living cells, molecules, and even strands of DNA with unprecedented control as well as intervene in reactions in real time.

“This system provides an intuitive connection with the sample,” says Superfine. “Researchers can get into the reaction and think more precisely about the science they’re doing rather than typing in commands. Haptics puts you in discovery mode.” Haptic feedback gives scientists a sense of touch and allows them to feel forces, vibrations, or motions within the experiment.

The heart of the system combines an optical microscope and an atomic force microscope (AFM). A virtual reality component called the nanoManipulator provides tactile feedback from the sample under study to the user. Typically, atomic force microscopes use an ultrasharp tip to probe the surface of a sample. The tip scans across the surface producing a two-dimensional (2-D) array of heights and can be pushed down on the surface enabling the AFM to both image and modify the sample. The nanoManipulator takes the 2-D array of heights and, with a graphics supercomputer, draws it as a surface in three dimensions. As users move the handheld pen of the nanoManipulator, they can feel their specimen and view it at the same time.

Russell Taylor, a research professor of computer science and physics at UNC, Chapel Hill, and co-director of CISMM, has worked on the project since his days in graduate school. Although the visual interface is compelling, Taylor notes that researchers who use the tool also like to have raw data from the experiments that they can take back to their labs for further analysis.

Feeling the Fibrin

Blood clots, a meshwork of fibrin fibers created by the body to prevent blood loss, can cause strokes and heart attacks if they form in the brain or in blood vessels around the heart. Understanding the structure and strength of these frameworks may lead to improved therapies to break up unwanted formations.

Using the haptic interface atomic force microscope at CISMM, Susan Lord, a professor in UNC’s Department of Pathology and Laboratory Medicine, and her research group have studied the mechanical properties of single fibrin fibers. From their data they have concluded that blood clots rupture not from the breakage of individual fibers, as previously assumed, but from the breakdown of branch points within the fiber network.

The virtual reality interface enabled Lord to literally become part of the experiment and experience what was occurring as different forces were applied to the fibrin fibers. “In most of what I do, I can’t see what’s going on,” Lord explains. “I just have to trust what’s happening. With the nanoManipulator you can actually see what’s going on. It gives a very different sense of what’s happening and you are able to put yourself in a different orientation,” she says. Stretching the fibers was “like taking a rubber band and stretching it sixfold. It was remarkable.”

Lord says she could have performed the experiments conventionally with atomic force microscopy. But the fibrin would not have been visible and the forces created between the microscope tip and the sample could not approximate those experienced by fibrin in the human body.

Control software for the three-dimensional force microscope shows the user a complete set of information about the smaple during the experiment.
The control software for the three-dimensional force microscope shows the user a complete set of information about the sample during the experiment. Here a magnetic bead is bound to the cell surface, and the yellow line shows the past motion of the center of the bead. The “blue shell” shows the volume that the bead has swept out during this motion, and the green mesh shows the diameter of the sphere. In the background is the immediate video image of the cell layers from the microscope.Image courtesy of Richard Superfine.

Measuring Mucus

Mucus, a gooey fluid the consistency of egg whites and only as thick as a sheet of paper, acts as the lung’s filter. To change the filter, the body creates a flow of mucus from the lung to the throat, where the mucus flows into the stomach. Cilia, the lung’s fine hairs, keep the mucus moving.

In lung diseases such as cystic fibrosis and in lungs damaged by pollutants, infections can destroy lung tissue because the organ cannot clear the contaminated mucus. Discovering how cilia move mucus through the lung could help explain why the lung fails to clear mucus and lead to more effective therapies to restore healthy function.

Superfine and his group will collaborate with 15 other investigators on the Virtual Lung Project, an effort to build a model of how the lung clears mucus. Project participants will develop models of mucus, cilia, and the chemistry of the lung’s entire clearing system. Using the atomic force microscope system and a magnetic bead technique in which beads are attached to cilia and manipulated with a magnet, Superfine will measure the stickiness of mucus and the forces exerted by cilia.

Changing the Process of Science

For the immediate future Superfine and his team will continue to refine the suite of AFM instruments and the magnetic bead technique. They will expand their studies of how cells respond to forces as both individual cells and in tissue cultures. Eventually, Superfine wants to develop a high-throughput system using the magnetic bead technique so that hundreds of experiments can be performed simultaneously. This will aid in drug discovery, especially for a class of drugs called fibrolytics, which are used to thin mucus. “We’ll be able to measure the visco-elasticity of a few microliters of samples and do it all at once,” says Superfine. Visco-elasticity refers to materials that are both viscous, like honey, and elastic or stretchy. In this way hundreds of drugs can be tested at one time. Russell Taylor comments, “We are changing the process of doing science by accelerating the discovery process.”

This work is supported in part by the National Institute of Biomedical Imaging and Bioengineering; the National Heart, Lung, and Blood Institute; and the National Center for Research Resources.


Liu W, Jawerth LM, Sparks EA, Falvo MR, Hantgan RR, Superfine R, Lord ST, Guthold M. Fibrin fibers have extraordinary extensibility and elasticity. Science 2006 Aug 4;313(5787):634. 

Technology development group within the Center for Computer Integrated Systems for Microscopy and Manipulation.

Technology development group within the Center for Computer Integrated Systems for Microscopy and Manipulation (CISMM) at the University of North Carolina, Chapel Hill. In the front row, Center Director Richard Superfine is kneeling fourth from left and co-principal investigator Russ Taylor is kneeling beside him, third from left. Image courtesy of Richard Superfine.
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