Project 1: The Mouse Brain Library Project 2: Internet Microscopy (iScope) Project 3: Neurocartographer and Segmentation of the MBL Project 4: The Neurogenetics Tool Box


















Principal Investigator/Program Director Williams,Robert W.

  Aim 3: A web archive of image stacks and software for stack analysis.

We will develop an automated system to acquire large archives of through-focus image stacks. This system will ultimately free users from the microscopes, because most of the high-magnification images they want will already be archived. In combination with software we are writing, these stacks will be ideal for quantitative stereological analysis of CNS cell populations. Online microscopists will be able to obtain high-magnification images directly from the MBL. Our plan is to create a system that will allow us and other research groups to generate virtual brain tissue that can be stored digitally, transferred without loss, and analyzed both on- and off-line. We have three immediate goals:

1. To develop batch processing methods to acquire and process through-focus series. This involves the integration of databases, coordinate registration and verification, and the simultaneous computer control of a robot, a microscope, and a digital video camera. This is a challenging bioinformatic and hardware problem.

2. To exploit this batch image acquisition system to automatically acquire sets of as many as 400 stacks from each case in the MBL. We will design an interface that will allow neuroscientists to order the microscopes to image particular coordinates on particular slides at high magnification and automatically generate through-focus series. These stacks will then be added to the MBL and will be integrated into the NeuroCartographer Project. Our goal is to make it possible for a scientist to order up sets of systematic high-magnification sample sites from any slide or structure in the MBL collection.

3. To adapt existing open-code software (including the Leydon-Williams Counting Box program, MacMeasure, Wayne Rasbands Image/J, and Melburn Parks deconvolution programs) so that clients can use modern stereological methods to study through-focus series. Our stack analysis programs will be provided as open-source Java applet and compiled C programs. They will permit the simultaneous viewing and analysis of multiple stacks.


Next Topic

  Aim 4. Streaming Video.