Automated Imaging Microscope System
Given the non-standard format, we will need a way to view individual segments on a slide. A multi-resolution display tool uses preprocessed images from the slide to create a mosaic, which shows multiple frames at the same time. By saving each frame at multiple resolutions, we do not need to decompress hundreds of JPEG images, only to throw 9999/10,000ths of the detail away.
Using this tool, we can zoom out to view the entire slide, zoom in on a specific region of a single sample, then view a specific field of vision. Figure 5 is a mosaic of one portion of one slide.
Refinements would allow integration with the counting algorithm. By drawing a border around a region of interest, counts and densities of cells in that region could be displayed.
When successive sections of the same tissue sample are placed in a known sequence, those successive sections can be merged to form a single three-dimensional image of the original tissue. Distortions in the sample are likely to cause some difficulty, but standard feature-recognition techniques should be able to compensate.
A further refinement is possible. With cells ~25 microns in size, 4 micron slices span several cells. By staining successive sections with different factors, it is possible to determine several different facts about each cell.
The Automated Imaging Microscope System (AIMS) will be used by my colleague Lee R. McCook at the University of California at Berkeley. He will use the system to compare the 3-D cellular densities in the hypothalamus of normal mice and calorically restricted mice. I have downloaded his Ph.D. proposal to the Aging Research Centre's web site at www.arclab.org/linux/leephd.html.
ARC has two research facilities in North America: the first is located in Berkeley, California and the second in Waterloo, Ontario, Canada. The near-term objectives of the Aging Research Centre are to conduct experiments that shed light on the underlying mechanisms that cause the aging process to occur and to develop tools which will help researchers better understand why humans and other organisms undergo this process. Our long-term objective is to use the information that has been accumulated on this subject and develop intervention procedures that will dramatically slow down the aging process. The aging of an organism is a very complex and multifaceted process that encompasses many disciplines in biology such as neuroendocrinology, histology, genetics, enzymology, biochemistry, molecular biology and so on. At this time, there is approximately 100GB of information in journals and books that relates to the aging process, and more and more information is being added every day to this body of knowledge. One of the tools we are developing will allow a researcher to see this massive quantity of data via a computer using graphical and interactive methods in order to represent this information in a more comprehensible and coherent manner.
The other major tool is the focus of this article: an Automated Imaging Microscope System to be used for an experiment at the University of California at Berkeley. It will be used to study the effects of calorie deprivation on neural tissue. Mice on calorie-reduced diets often live longer, and this may be based on changes in the hypothalamus.
Steven A. Garan founded the Aging Research Centre (http://www.arclab.org/) in 1994 and has been in the computer field for 22 years. Steven has worked on machines from TRS 80s to IBM 360/75 to HP3000s to Linux/Intel PCs, and has worked in Canada, UK, Italy and the USA. Of all the systems he has worked on, Linux has to be the one that is the most flexible and powerful environment he has seen thus far.
- March 2015 Issue of Linux Journal: System Administration
- High-Availability Storage with HA-LVM
- DNSMasq, the Pint-Sized Super Dæmon!
- Localhost DNS Cache
- Real-Time Rogue Wireless Access Point Detection with the Raspberry Pi
- Days Between Dates: the Counting
- You're the Boss with UBOS
- The Usability of GNOME
- Multitenant Sites
- Linux for Astronomers