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  Exploring The Mouse Brain Library

Our lab at the University of Tennessee is home to a slide collection of the brains of genetically defined mice. With almost 3,000 slides, the collection is a unique, valuble resource for quantitative genetic studies. The Mouse Brain Library website, located at http://www.mbl.org, is an online database containing detailed information about the collection as well as high resolution images of each slide in the collection.

The iScope project takes the MBL one step further by facilitating real-time access to the the collection's original slides using light microscopes rather than pre-acquired images. Through this technology, any slide in the collection can be viewed at 40X magnification, using the MBL's images as a navigational aid. Gumbo, our free microscope control software, allows Internet users to schedule time on one of our microscopes and control it, acquiring images in real-time.

Worldwide Remote Stereology:

Quantitative genetic research techniques, such as QTL mapping, collect data with a microscopy technique known as stereology. Simply put, this process involves selecting a region of tissue to view through a light microscope and recording some numerical attribute of the region, usually the number, kind, or size of individual cells in the tissue.

Traditionally, stereology has been performed in front of a light microscope by a technician with physical access to the slide collection. With the advent of the iScope system and Aria 3-D, however, the same research can be performed from any desktop computer. The possibilities for collaboration and sharing of resources are staggering.

Workflow for Remote Stereology with the iScope

  • Register a username and password for the system. Contact Dr. Rob Williams about your interest in using the system for stereology so that we can upgrade your access privileges.
  • Using our Gumbo software, login in, schedule microscope time, and select the regions of interest that comprise your study. This may be a large number of sample sites on a single slide, or samples spread across several slides. Give the set of sample sites a name so that you can identify it later.
  • Submit the list to the iScope server. You can now exit the Gumbo program.
  • While it is not actively serving users, the iScope system will acquire image stacks at the sites you requested, emailing notification when the process is complete.
  • After acquisition is complete, start Aria 3-D, our remote stereology application. Log in to the iScope server and begin downloading the image stacks you requested. As soon as the first stack has been received, you may begin analysis, using the arrow keys to focus through the tissue while outlining cells. File transfer will continue in the background as you work on existing image stacks.
Please note that the present version of Gumbo does not include support for defining sampling regions. This feature, as well as our robotic slide handlers, should soon be available, completing the workflow.

Submit a new use:

If you have come up with a super-smart way to use the internet microscope, we'd love to hear about it. Email Michael Connolly at mtconnol@umich.edu or Senhua Yu at syu5@utmem.edu.