Topic: The Virtual Microscope: a project that provides simulated scientific instruments

[Software Santa]

The Virtual Microscope is a NASA-funded project that provides simulated scientific instrumentation for students and researchers worldwide as part of NASA's Virtual Laboratory initiative.


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The Virtual Microscope

The Virtual Microscope is a NASA-funded project that provides simulated scientific instrumentation for students and researchers worldwide as part of NASA's Virtual Laboratory initiative. This site serves as home base for the Imaging Technology Group's contributions to that project—namely virtual microscopes and the multi-dimensional, high-resolution image datasets they view. Currently we provide 90 samples totaling over 62 gigapixels of image data. The Virtual Microscope, which is available for free download supports functionality from electron, light, and scanning probe microscopes, datasets for these instruments, training materials to learn more about microscopy, and other related tools. The project is open source and the code is available on Sourceforge.

Our Virtual Instruments

Our virtual instrument code currently supports data from three different instruments in our Microscopy Suite: a Philips Environmental Scanning Electron Microscope (ESEM), a Fluorescence Light Microscope, and an Atomic Force Microscope. We have also adapted a high-resolution Digital SLR with a 5x magnifying macro lens to capture some specimens, as well as included some artistic renderings of microscopy data.

The virtual microscope aims to present the user with a method for exploring these pre-captured image data as if they were using the real instrument in real-time. To fulfill this goal, the virtual microscope provides the ability to load/unload specimens, to navigate to any point on that specimen, to change magnification, to adjust image parameters (contrast and brightness), to change focus, to analyze elemental composition, to measure features, and to render data in three dimensions. Additionally, the interface allows experts and laypeople alike to annotate specimens and/or load previously-created annotations.

Beyond the user interface, we have written a backend suite of custom software for the various tasks involved in collecting and processing the image data. This includes automated data collection of the thousands of images it takes to describe a single specimen, and routines for stitching and blending those tiled image datasets.

Microscope Training

As part of our educational mission, we have produced animations that teach the basics of electron, light, and scanning probe microscopy, videos detailing sample preparation for those instruments, videos of interviews with graduate students about their career paths in the sciences, and help videos about how to use our application. These materials animations use a multitude of media to explore various topics relevant to the theory and craft behind the images.

About the Imaging Technology Group

The Imaging Technology Group (ITG) at the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign provides state-of-the-art imaging facilities to the surrounding research community. We also develop advanced technology projects in the areas of remote (i.e. Bugscope!) and virtual instrument control, and scientific visualization.


Virtual Microscope Data:

To make these 90 samples we've processed 67,817 images totalling 62.2 gigapixels weighing in at 174GB worth of raw data.

We're adding more all the time! We try to produce one or two new samples each week, so stop by frequently or use an RSS reader to subscribe to the RSS feed advertised on this page to be notified when we add to our library.

Image data is the core component for the Virtual Microscope. On the Data page you will find links to each of the samples we have collected and constructed so far. They are arranged by source instrument.

In order to view these specimens, you will need to download the Virtual Microscope if you haven't already. Once you have installed the software this list of specimens will show up in the load screen and you can download and use them in one easy step. If you have any questions, please don't hesitate to let us know.

For an example of multiple focus levels you can try this housefly sample. Try switching illumination with the algae sample. You can change the polarization of the light source in our meteorite sample. In our sand sample you can switch imaging detectors and examine X-ray spectra from the energy dispersive spectroscopy (EDS) detector.

Where did the download links go?

In the latest versions of the Virtual Microscope software we built-in the ability to download samples directly to the right place, eliminating a lot of confusion and trouble. The initial window, the load screen, features the same list of available samples with download buttons. Once the software finishes downloading a sample it moves into the pool of samples you can use right away!

Electron Microscope (EM)

All of our VSEM samples are collected using custom software that runs a Philips XL-30 Environmental Scanning Electron Microscope (ESEM). These images are all taken in hi-vacuum mode, and generally range up to 1800x.

NASA and St. Leo Post COGS Website

NASA and Saint Leo University have posted their COGS Website to support teaching and learning with the Virtual Microscope. The site includes lesson plans by teachers who have used our software in the classroom, a discussion forum for those teachers, and more. The project is run by our collaborator, Dr. Laura Blasi, a professor of education at St. Leo. Check it out!  http://www.nasa-inspired.org/

Get your Virtual Instruments Here:  http://virtual.itg.uiuc.edu/downloads/index.shtml
Get your Datasets Here: http://virtual.itg.uiuc.edu/data