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



























 

 

 

 

 

 

 

 

 

 

 

 

  

 

  
 

RESEARCH PLAN

  
 

Principal Investigator/Program Director Williams,Robert W.

 
 

Limitations of existing approaches

Construction of high-fidelity atlases has relied on blockface imaging (Nissanov et al. submitted). The tissue block is imaged prior to collection of each section, and this image is used to guide 3D reconstruction. There are two major difficulties with this approach. First, blockface imaging demands specialized equipment that is difficult to adapt for use with celloidin-embedded material. Second, alignment of data sets collected using different techniques (intermodal) has limited reconstruction accuracy. We propose a section-to-section alignment strategy that should permit reconstruction accuracy approaching 10 mm.

The difficulty with current alignment strategies is only partly due to the lack of appropriate algorithms. Although the task inherent to this setting is 2.5 dimensional (ordered, unaligned sections that do not necessarily constitute a complete series of sections) and most available alignment strategies are either 2D or 3D (exceptions do exist; see Kozinska et al. 1996; Kim et al. 1997;Schormann and Zilles 1998; Cohen et al. 1998; Ibrahim and Cohen 1998), we plan a

straightforward modification of existing approaches to tackle this problem. We propose to extend our 3D distance-based alignment method (Kozinska et al. 1997) ) to solve the 2.5D registration problem at a coarse level of accuracy. Intersubject registration will then be improved using implicit fiducials and splines.

The most severe limitation of available technology, however, is the present interface to the MBL. Navigation within the current system is inefficient: an investigator wishing to look at homologous planes from multiple animals must inspect the data from each animal at a moderate level of resolution, establish homology visually, select the desired section from each brain separately, and then download the high-resolution views. To estimate volumes of structures, the investigator must delineate the ROIs. If unbiased cell density is to be determined from through-focus series, the user must navigate across the slide while it is mounted on the iScope and select the field desired. The technology to be developed in this project will facilitate access to the MBL, increasing its usefulness to collaborating scientists.

 

 
   
   
   
 

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