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 2: Linear alignment of MBL into the standard coordinate system

2.5-dimensional alignment

The possibility exists that 2.5DBA might fail. A fallback approach to registration is the use of semiautomatic tools already in place in MacOStat. In this approach, an operator visually selects the homologous atlas plane for the first and last sections of a slab of tissue. The matching atlas planes for the intervening sections are defined by interpolation. Each experimental section is then automatically aligned to its homolog using an affine transformation.


To test the accuracy of this approach, we aligned 3 rat brains to our rat atlas. Each brain consisted of >90 coronal sections, and all the sections were matched independently to the atlas. Matching accuracy was assessed by comparing placement of sequential sections under the assumption that adjacent sections should match parallel atlas planes with a distance equal to the known intersection interval. The deviation from that expectation was defined to be the error and was measured as the maximum distance error on the outer section contour between the expected and the assigned position. That error was measured to be 212 mm. In this manual mode, alignment requires about 2 hours per brain



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