Figure 3.

Registration and quantification of histological sections. Corresponding landmarks were placed on the average RA map (A) and each of the digitized histological images (B; SMI31 shown here). Landmarks were manually placed along the white matter border and along prominent white and gray matter interfaces. A thin-plate spline deformation grid was derived and overlaid on the histological image (C; magnified view) in which each square of the grid corresponds to a single pixel on the MRI image. The histological image was segmented (D) into foreground (red) and background (black) using a threshold value derived from the pixel intensities of the surrounding spinal nerves, which are not affected in MOG-induced EAE. The area fraction of foreground staining for each square of the grid was computed to produce a quantitative histological image (E) that was registered to the MR images.