Simulated MicroscopesCISMM: Computer Integrated Systems for Microscopy and Manipulation

Collaborators: Mike Falvo, Tim O’Brien, Dorothy Erie (Department of Chemistry)

Project Director: Russell M. Taylor II Investigators: Alvin Richardson

http://www.cs.unc.edu/Research/nano/cismm/mix/

December 2003

Simulated AFM

Simulated Fluorescence Microscopy

Does the model explain this scan?

c.

a.

b.

Mike Falvo is using the simulator (a) to determine whether ridges observed in an AFM scan of cilia (b) match up with a theoretical model of cilia structure(c.)

The AFM Simulator enables the user to create and manipulate complex model specimens and view simulated surfaces for different tip settings.

Simulating AFM images assists the scientist in experiment planning and in interpreting the resulting data.

Graphics hardware acceleration enables interactive calculation of the expected image for an AFM scan*.

* Varadhan, et al.,“Fast Simulation of Atomic-Force-Microscope Imaging of Atomic and Polygonal Surfaces Using Graphics Hardware”, (SPIE 2002).

?

Model:

SimulatedScan:

Actual AFM

Scan:

Could an AFM see these configurations?

There is an ongoing collaboration with Dorothy Erie’s chemistry group to understand AFM scans of DNA wrapped around proteins. AFM simulation ruled out the possibility that certain wrappings(c) of the DNA could have been hidden by imaging or reconstruction artifacts.

a. b. c.

A simplified model of overlapping fibrin strands.

Individual fluorophores are modeled by filling the surface or volume of a model specimen with a user-settable density of points.

Create a Model

A Point Spread Function (PSF) describes how light from a single fluorophore spreads out in 3D for a given microscope configuration.

Specify Microscope PSF

Available for Download.

Microscope simulation seeks to solve the forward problem of convolving a model by a microscope’s transfer function for direct comparison with experimental results.

Recent advances in graphics hardware such as full floating-point support and user-programmable GPUs make it possible to simulate optical/confocal microscope images and at interactive rates.

Simulating fluorescence images allows a scientist to determine what a specimen would look like in a given microscope. This can aid in planning experiments and in interpreting microscope images.

The light emitted from each point is determined given the focus and PSF. The light is accumulated to create an image.

Our extensions to the Visualization Toolkit make it possible to compute the image entirely on the graphics card.

Nvidia GeForce FX 5900 Ultra

Simulation of AFM+Fluorescence for Fibrin

Experimental AFM with overlaid fluorescence image of fibrin. Adding fluorescence lets us see labeled strands beneath the reach of an AFM tip.

The simulated image shows brighter areas where the fibrin strands overlap. An AFM scan would merely hide the overlapped strand.

The user can adjust the model to fit the AFM and fluorescence experimental data while getting interactive updates.

See Mike Falvo’s poster