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.


Potential pitfalls and potential solutions

Aim 1: Construction of mouse 3D brain atlases and navigation software

3D atlas reconstruction

Reconstruction using fiducials located by the correlation filter may fail. Should implicit fiducials defined using a matched filter prove insufficient for reconstruction of any given atlas, point fiducials will be obtained using bisected cells or blood vessels (the iScope will be used to acquire images of these). While this approach is straightforward and is likely to yield highly accurate reconstruction, it requires a high degree of operator interaction and thus is not as attractive as using matched filters. If this approach is required, it will add another 6 months to the atlas construction phase of the work. However, it will introduce only a moderate delay in the alignment phase of Specific Aim 2, which can commence when one atlas becomes available.

Cross-atlas alignment

Failure to achieve acceptable cross-atlas alignment as proposed will necessitate use of a larger number of fiducials. Since each brain will eventually be delineated, all VOIs can be used for this purpose.



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