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Volumes were calculated by multiplying the traced area on each slice by slice thickness, and then summing volumes across slices.
For quantitative analysis of Fluorojade C labeling, the peri-lesion area was traced and 400 μm grids were randomly placed throughout the traced area.
The volume of the GCL and hilus was estimated using a stereological system by summing the traced area for each section, and multiplying this by the section thickness and sampling interval.
IgA deposition areas (Area-IgA,%) were calculated by the following formula: Area − IgA % = black pixel count / whole pixel count within the traced area × 100 IgG and C3 deposition areas (Area-IgG, Area-C3, respectively) were also calculated using the same procedure.
To calculate the number density of osteocyte lacuna in each bone region the number of lacunae within each 10× confocal image were counted and divided by the traced area of bone tissue in the same image and expressed as number per mm.
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Three persons independently scored at least 200 cells for 50% or more overlap of yellow and red traced areas, each of which was defined as a colocalization.
The reference volume was obtained multiplying the sum of the traced areas of the dentate gyrus or hippocampus by the 320 µm distance between sections analyzed [35].
The reference volume of the GCL was determined by summing the traced areas of GCL in each section and multiplying the result by the distance between sampled sections (180 µm).
Large bilateral clusters traced areas of white matter extending from the medial temporal lobes to the occipital pole.
In the present study, a comparison of the original EDI-OCT images to the binary images showed that the traced areas coincided with the dark choroidal areas of the EDI-OCT image.
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