3D Reconstruction and Standardization of the Rat Vibrissal Cortex for Precise Registration of Single Neuron Morphology
Figure 3
Reconstruction of 3D barrel dimensions.
(A) Barrel contour in a single optical section overlaid on the filtered image (gray values linearly enhanced for visualization). White lines indicate border of the VR of this barrel. Dashed circles with diameters of 90 and 170 pixels (approx. 165 and 315 µm) indicate the regions used to estimate the barrel extent. (B) Histogram of background pixels inside the barrel contour in A (black) and histogram of background pixels in septum (gray), i.e. outside of the barrel contour and inside of the VR. Dashed white lines mark mean gray value. (C) Ratio of means inside/outside of the contour as a function of the contour radius. Black: circular regions in A; red: segmented contour. (D) Side view of all segmented contours. Subsequent tangential sections are aligned using blood vessels. (E) Top row: Individual optical sections from different tangential sections (marked bold in D). Red – regular segmented contours. Green – optimized minimal contours. Bottom row: Radial dependence of the ratio of means for all contours in the corresponding optical sections. The slope of the black line gives an estimate of the relative size of the true barrel extent compared to the segmented contour. At the top and bottom of the barrel it may be necessary to segment an optimized minimal contour (see Supplemental Materials).